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Text Embedding Map → Taxonomic UMAP → ESM-2 Sequence Map →Aalborg East Full-Scale EBPR Activated Sludge Community
An engineered full-scale activated sludge microbial community from the Aalborg East wastewater treatment plant in Denmark carrying out enhanced biological phosphorus removal. The community was profiled with an 18.2 Gb Illumina metagenome and qFISH, revealing phosphate-removal organisms including Candidatus Accumulibacter and Tetrasphaera-related Actinobacteria, flanking substrate-providing bacteria, and metagenomic enrichment for phosphate metabolism and biofilm/floc formation functions.
Acetobacterium woodii-Clostridium drakei CO2 Electrolysis Coculture
A defined anaerobic synthetic coculture that combines a lactate-producing Acetobacterium woodii mutant with Clostridium drakei to convert CO2 and H2 into longer-chain products. A. woodii fixes CO2 with H2 and is engineered to release lactate, which C. drakei uses as an intermediate for chain elongation to caproic acid. The system is DOE-relevant because it couples microbial CO2 valorization with in situ water electrolysis or CO2/H2 gas feeding for production of value chemicals.
Acetylene-Fueled Trichloroethene Dechlorination Groundwater Enrichment
A microbial community enriched from TCE/PCE-contaminated groundwater and amended with acetylene (C2H2) as the sole electron donor and organic carbon source. The stable enrichment performs reductive dechlorination of trichloroethene (TCE) and tetrachloroethene (PCE), coupling acetylenotrophy to organohalide respiration. Metagenomic analysis of the stable community identified a novel anaerobic acetylenotroph in the phylum Actinobacteria, expanding the known diversity of this metabolism beyond previously documented Pelobacter SFB93 + Dehalococcoides mccartyi laboratory cocultures.
Achromobacter-Enterobacter SL8-SL12 Cadmium Immobilization Coculture
A defined two-member bacterial coculture assembled from the Cd-contaminated mine-area soil isolates Achromobacter sp. SL8 and Enterobacter sp. SL12 to immobilize cadmium. In 100 mg/L Cd2+ LB assays the SL8-SL12 coculture removed 80.9% of dissolved Cd after 7 days, exceeding both monocultures at the same Cd dose; Cd partitioning, microscopy, and spectroscopy associated this performance with CdS bioprecipitation, intracellular Cd accumulation, surface aggregation with possible EPS involvement, and phosphate-, amino-, and hydroxyl-bearing surface groups. In greenhouse Chinese-cabbage pots the inoculated coculture decreased bioavailable soil Cd fractions and lowered Cd in aboveground cabbage tissue under high Cd stress.
Acidic Nitrification Minimal Consortium
A minimal aerobic ammonia-oxidizing consortium from three acidic nitrification bioreactors operated between pH 2.0 and 5.0. Genome-resolved meta-omics and chemical measurements linked the pH 5.0 cultures to a novel Nitrosococcaceae ammonia-oxidizing bacterium, "Candidatus Nitrosoglobus kelleri", that reached up to 56% relative abundance and linked the strongly simplified pH 2.0 community to "Ca. Nitrosoglobus kelleri" together with Mycobacterium species.
Aerobic Denitrification Disturbance-Stable SynCom
A three-member aerobic denitrification SMC that maintains function under dibutyl phthalate and levofloxacin disturbances through division of labor.
Aerobic Denitrification Quorum-Quenching SynCom
A three-member aerobic denitrification SynCom whose quorum-quenching and AHL-mediated interactions improve nitrate removal.
Alaska Tundra Permafrost Iron-Redox Community
A northern Alaska wet sedge tundra microbial community studied across the permafrost thaw gradient, where iron-cycling Gammaproteobacteria - the heterotrophic Fe(III)-reducing Rhodoferax sp. and the chemoautotrophic Fe(II)-oxidizing Gallionella sp. - become numerically dominant during extended anaerobic thaw of transition-zone and permafrost soils. Functional gene abundance shows that Fe(III) reduction and Fe(II) oxidation increase in lockstep with benzoate degradation and pyruvate metabolism, supporting a carbon-cycling model in which acetate and benzoate are oxidized to CO2 coupled to Fe(III) reduction. Concurrent decreases in CH4-metabolism gene abundance suggest that dissimilatory Fe(III) reduction competitively suppresses acetoclastic methanogenesis under the reducing thaw conditions examined.
Alfalfa Stress-Adapted Bacterial SynCom
A defined five-member bacterial SynCom assembled from plant-associated Bacillus sp. G3, Bacillus sp. G12, Acinetobacter sp. G13, Plantibacter flavus M251, and Plantibacter flavus M259 isolates from stress-affected Canadian environments. Shipar et al. validated the members for in-vitro plant growth-promoting and abiotic-stress traits, mixed equal volumes of OD600-standardized LB cultures, and applied the mixture twice to alfalfa grown in non-sterilized field soil under well-watered, moderate-drought, and severe-drought growth-chamber regimes.
Algal-Methanotroph Biogas Valorization Coculture
A laboratory enriched haloalkaliphilic microalga-methanotroph co-culture assembled by mixing a halotolerant methanotrophic consortium with a non-axenic algal culture. Triplicate 2.1 L gas-tight glass bioreactors containing 450 mL 6% NaCl mineral salt medium were supplied with a 70:30 CH4:CO2 biogas headspace under light; after two external O2 additions, the culture maintained methane oxidation via algal O2 production and removed 92% CH4 and 89% CO2 while producing ectoine, hydroxyectoine, and carotenoids. Shotgun metagenomics identified Chlorella vulgaris and Dunaliella viridis as the dominant Chlorophyta, Methylotuvimicrobium as the dominant methanotroph, and Methylophaga plus Methylonatrum as co-dominant methylotrophs.
Altered Schaedler Flora Gnotobiotic Mouse Community
The altered Schaedler flora (ASF) is an eight-member defined murine gut bacterial community used in gnotobiotic mice. The community was developed as a standardized, culturable intestinal flora from mouse-derived bacteria and has been used for decades to study host-microbiota relationships, member stability, spatial distribution, immune effects, and genome-informed community metabolism.
AM-AB Chlorella-MLSS Wastewater Consortium
A microalga-bacteria wastewater-treatment consortium assembled by combining activated Chlorella vulgaris with separately activated mixed liquor suspended solids (MLSS) bacteria in an outdoor high-rate algal pond. Kumar et al. 2026 called this pairing an activated microalgae-activated bacteria, or AM-AB, consortium and reported rapid nitrogen, phosphate, and biological oxygen demand removal during biological wastewater treatment.
AMD Acidophile Heterotroph Network
A heterotrophic microbial network in acid mine drainage (AMD) systems dominated by Acidiphilium species and related acidophilic heterotrophs. This community plays a crucial role in coupling carbon and iron cycles in extremely acidic environments, supporting autotrophic iron oxidizers through organic matter processing and nutrient remineralization. The network thrives at pH 2-4 in AMD sites globally, where heterotrophs metabolize organic compounds produced by autotrophs or released from lysed cells, preventing organic carbon accumulation that would inhibit autotrophic iron oxidizers. Key members include Acidiphilium multivorum (facultative Fe(III) reducer and organic carbon degrader), Ferrimicrobium acidiphilum (iron-oxidizing heterotroph and dissolved organic carbon remover), Acidocella facilis (obligate aerobic heterotroph), Acidisphaera rubrifaciens (photoheterotrophic bacteriochlorophyll producer), and Acidobacterium capsulatum (chemoorganotrophic acidophile). These organisms collectively perform organic matter degradation, ferric iron reduction, biofilm formation, and nutrient cycling. The heterotroph-autotroph coupling maintains community stability by removing inhibitory organic carbon, recycling nutrients (nitrogen, phosphorus), generating ferrous iron for autotrophic energy generation, and facilitating metal tolerance through extracellular polymeric substances (EPS) production. This network represents a critical functional guild in AMD ecosystems, enabling the persistence of autotrophic iron-oxidizing communities through metabolic cooperation and resource partitioning.
AMD Nitrososphaerota Archaeal Community
A novel archaeal community from acid mine drainage environments dominated by ammonia-oxidizing archaea (AOA) of the phylum Nitrososphaerota (formerly Thaumarchaeota). This community represents a unique nitrogen-cycling system operating at extremely low pH (2.5-4.5) where archaeal nitrifiers outcompete bacterial ammonia oxidizers. The dominant members include acidophilic AOA such as Candidatus Nitrosotalea devanaterra and Nitrososphaera-like archaea that possess extraordinary substrate affinity (Km 0.6-2.8 nM for NH3) and specialized adaptations for acidophily. These archaea oxidize ammonia to nitrite through the copper-containing ammonia monooxygenase (AMO) enzyme while maintaining cytoplasmic pH homeostasis in extremely acidic environments. The community also includes supporting acidophilic archaea from Thermoplasmata (Ferroplasma, Acidiplasma) that provide ecosystem services including organic matter processing and metal tolerance. Unique features include: (1) Amt-type ammonium transporters enabling NH4+ uptake rather than NH3 diffusion, (2) urea hydrolysis pathways providing localized ammonia generation, (3) extensive cell surface glycosylation reducing proton permeability, and (4) metabolic cooperation with nitrite-oxidizing bacteria (Nitrospira, Leptospirillum) completing the nitrification pathway. This system demonstrates how archaeal nitrifiers dominate nitrogen cycling in acidic environments where bacterial counterparts cannot function, with AOA abundance 3-10 fold higher than AOB in AMD sediments. The community thrives in acid sulfate soils, acid mine drainage sediments, and acidic tailings, representing a critical component of nitrogen cycling in the 30% of Earth's soils with pH <5.5. Based on genomic data from NCBI BioProject PRJNA1261802 and related AMD archaeal community studies.
Amsterdam 10-Species Gut Invasion SynCom
A defined ten-strain human gut bacterial synthetic-community panel used to quantify soluble, environmentally mediated interactions and predict community assembly and invasion outcomes. van Leeuwen et al. generated cell-free YCFA spent media from each DSMZ strain, grew every other strain in 40% spent plus 60% fresh YCFA medium, validated generalized Lotka-Volterra predictions with two- to four-member YCFA co-cultures, and tested whether Escherichia coli DSM 18039 or Bacteroides ovatus DSM 1896 could invade predicted stable resident assemblages.
Anabaena / MGS-1 Anaerobic-Digestion Methanogen Consortium
An anaerobic-digestion microbial consortium studied as part of a bioregenerative life-support concept for Mars: cyanobacterial biomass (Anabaena sp.), which can be grown on Martian resources, is anaerobically digested to mobilize nutrients (ammonium and phosphate) for use as a crop fertilizer, with biogas as a co-product. Ramalho et al. (2025, Bioresource Technology) tested three microbial communities for their ability to digest Anabaena biomass in three matrices — a minimal medium, 200 g/L MGS-1 Mars regolith simulant, and water. In minimal medium the taxonomic (16S) analysis revealed a SYNTROPHIC community: fermentative bacteria degrade the cyanobacterial biomass and cross-feed hydrogenotrophic methanogenic archaea (interspecies H2/CO2 transfer driving methanogenesis). In the MGS-1 regolith matrix, however, the methanogens were outcompeted by sulfate-reducing bacteria, and the regolith also adsorbed organics and lowered phosphate/ammonium recovery. The Anabaena biomass here is the digestion FEEDSTOCK (substrate) rather than a live member of the digesting consortium. All communities produced ammonium and removed organic carbon, supporting the viability of a Mars-relevant bioprocess for fertilizer production. The specific dominant genera resolved by the paper's 16S analysis are reported in the full text, which is paywalled; only the functional guilds (fermentative bacteria, hydrogenotrophic methanogens, sulfate-reducing bacteria) are named in the openly available abstract and are therefore represented here as interactions/roles rather than as NCBITaxon-grounded members.
Anaerobic Indole-Degrading Sludge Consortium
A long-term acclimated anaerobic sludge consortium established to transform the nitrogen heterocycle indole under laboratory conditions. Meng et al. (2026) combined anaerobic degradation assays, metabolite profiling, metatranscriptomics, and genome-resolved metagenomics after 120 days of acclimation; the enrichment stably degraded 100 mg/L indole but did not effectively remove skatole under the same strategy. Abstract-level MAG and transcript evidence implicated Bacteroidota, Chloroflexota, Desulfobacterota, and Methanobacterium populations in a candidate division of labor linking upstream indole oxidation, anthranilate-like aromatic-CoA processing, and methanogenesis-associated carbon flow.
Anammox Bioreactor DNRA Destabilization Community
A laboratory-scale anaerobic ammonium oxidation (anammox) bioreactor community followed from inoculation through a performance destabilization event and back to robust steady-state operation, characterized by metagenomics. Metabolic analyses showed selection for nutrient-acquisition capacities in the core community. Dissimilatory nitrate reduction to ammonium (DNRA) was the primary nitrogen-removal pathway that competed with anammox, and increased replication of DNRA-capable bacteria out-competed anammox bacteria, causing the loss of nitrogen-removal capacity. The DNRA-capable bacteria were closely associated with the anammox bacterium and are considered part of the core microbial community, underscoring how bacteria that are otherwise core members can be detrimental.
Anammox Granule Metabolic Interaction Community
A laboratory-scale anammox granular-sludge bioreactor community reconstructed with genome-centric metagenomics and metatranscriptomics. Brocadia-affiliated anammox bacteria dominate nitrogen removal, while Chlorobi-affiliated and other heterotrophic bacteria recycle nitrate to nitrite, degrade EPS-derived peptides, and scavenge detrital products from anammox growth.
Angelarchaeales Thermoplasmata CuMMO Soil and Sediment Community
A soil and aquifer-sediment microbial community in which a newly defined Thermoplasmatota archaeal order, Ca. Angelarchaeales, encodes divergent copper membrane monooxygenases (CuMMOs). Twenty genomes from distinct archaeal species were recovered from grassland and hillslope soils and aquifer sediments. The CuMMO proteins resemble Nitrososphaerales (ammonia monooxygenase) enzymes more than bacterial CuMMOs and retain all functional residues required for monooxygenase activity. Angelarchaeales genomes are enriched in blue copper proteins (BCPs) including plastocyanin-like electron carriers and divergent nitrite reductase-like (nirK) 2-domain cupredoxin proteins, encode strong peptide and amino-acid uptake/degradation capacity, and share electron transport mechanisms with Nitrososphaerales. Angelarchaeales are abundant in some of the source environments.
ANME-SRB Marine Methane Seep Consortium
Natural marine methane-seep consortia in which anaerobic methanotrophic archaea (ANME) grow in syntrophic partnership with sulfate-reducing bacteria (SRB). These structured aggregates couple anaerobic oxidation of methane to sulfate reduction, limiting methane release from ocean sediments. The interaction is frequently organized as multicellular consortia containing ANME archaeal cells and bacterial sulfate reducers, with genomic evidence supporting direct interspecies electron transfer from ANME to the SRB partner.
ANME/SRB Anaerobic Methanotrophic Syntrophic Consortia
Marine syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) that couple the anaerobic oxidation of methane to sulfate reduction in marine sediments. Sediment-free enrichment cultures of three consortium types (ANME-1/Desulfofervidus, ANME-2a/Seep-SRB1, and ANME-2a+2c/Seep-SRB1+2) exhibited high dry conductance close to that of electrogenic biofilms. Cyclic voltammetry revealed redox activity and generator-collector measurements showed electron transport over micrometer-scale distances, establishing that the symbiosis uses redox conduction (consistent with multiheme cytochrome c) for direct interspecies electron transport between the archaeal and bacterial partners.
Apple Fire Blight A+N+P SynCom
A nine-member bacterial synthetic community assembled from three apple fire-blight biocontrol design groups: Streptomyces recifensis SN1E1 and Paenibacillus polymyxa AF2927 as direct anti-Erwinia amylovora strains, Labrys miyagiensis NBRC101365, Labrys okinawensis DSM18385, Novosphingobium mathurense SM117, Novosphingobium endophyticum EGI60015, and Terriglobus aquaticus 03SUJ4 as healthy apple network taxa, and Kitasatospora papulosa AF6313 plus Pseudomonas lundensis AB23 as pathway-associated strains. The full A+N+P mixture eliminated visible disease in Fuji apple fruit wounds, matched oxytetracycline at 1.67% disease severity in rose flowers, and reduced Erwinia amylovora TS3128 density in apple flower exudate during follow-up co-cultivation assays.
Arabidopsis Bacillus Biocontrol SynCom150
A 150-member bacterial synthetic community assembled from genome-sequenced isolates recovered from surface-sterilized Brassicaceae roots, nearly all Arabidopsis thaliana, and applied to Arabidopsis Col-0 plants in gamma-irradiated coconut-coir and MS-agar microcosms. The study used top-down dropout and add-in deconstruction to test SynCom subsets against the leaf pathogen Pseudomonas syringae pv. tomato DC3000, resolving Bacillus and Pseudomonadota as protective components; follow-up halo assays, Bacillus-only inocula, leaf-recovery CFU assays, and Arabidopsis RNA-seq supported a model in which diverse rhizospheric Bacillus suppress Pto without requiring host immune activation.
Arabidopsis Coumarin Root SynCom
A hydroponic 22-member Arabidopsis root-isolate SynCom used to detect strain-level rhizosphere community shifts caused by phytoalexin, flavonoid, and coumarin exudates. Under iron deficiency, F6'H1-dependent catecholic coumarins suppress the coumarin-sensitive isolate Pseudomonas sp. Root329 through a peroxide-linked mechanism that contributes to the overall wild-type-like community profile.
Arabidopsis Phyllosphere SynCom7
A seven-strain reduced-complexity Arabidopsis phyllosphere SynCom used to test host genetic effects on microbiota composition.
Asgard Archaea Wetland Soil Methanogenesis-Substrate Community
A wetland soil community in which terrestrial Asgard archaea modulate potential methanogenesis substrates. Two complete genomes were reconstructed for soil-associated Atabeyarchaeia, a newly defined Asgard lineage, alongside a complete genome for Freyarchaeia. Metatranscriptomic data show in situ expression of [NiFe]-hydrogenases, pyruvate oxidation, Wood-Ljungdahl-pathway carbon fixation, amino acid metabolism, anaerobic aldehyde oxidation, hydrogen peroxide detoxification, and carbohydrate breakdown to acetate and formate. Soil-associated Asgard archaea are predicted to act as non-methanogenic acetogens, suggesting that they modulate wetland-soil methanogenesis substrate pools (H2, acetate, formate) and shape terrestrial carbon cycling.
At-RSPHERE SynCom
A synthetic bacterial community derived from the Arabidopsis root microbiota culture collection (At-RSPHERE), representing 16 bacterial families isolated from Arabidopsis thaliana roots grown in natural soil. This community was established to study plant-microbe interactions and their effects on plant productivity and carbon cycling in the rhizosphere. The consortium members were selected to represent a broad taxonomic range covering the major bacterial phyla (Proteobacteria, Actinobacteria, and Bacteroidetes) found in the Arabidopsis root microbiome. Assembly sizes vary from 5-20 members depending on experimental design, enabling reductionist studies of root microbiota assembly and function.
Australian Lead Zinc Polymetallic Tailings Consortium
A sulfidic mine-tailings community model centered on a weathered volcanogenic massive sulfide dump in arid Western Australia and related Pb-Zn tailings acidification studies. Oxidative weathering of S- and Fe-rich waste rock disperses mobile ions including zinc, sulfur, chloride, and aluminium, while Pb-Zn tailing impoundments at progressive acidification stages contain Acidithiobacillus, Leptospirillum, and Ferroplasma acidophiles associated with iron oxidation, sulfur oxidation, carbon fixation, nitrogen fixation, and acid mine drainage generation. The curated causal graph therefore represents acidophile-driven Fe/S oxidation, Pb-Zn tailings acidification, and pH-ordered community succession as community-level processes rather than unsupported species-by-species exchanges.
Auxenochlorella-Pseudomonas Florfenicol Phycosphere Coculture
A defined freshwater green-alga and bacterium co-culture pairing axenic Auxenochlorella pyrenoidosa with Pseudomonas_sp1, a phycospheric isolate recovered after high-florfenicol and polylactic acid microplastic stress. Liu et al. isolated Pseudomonas_sp1 from the stressed phycosphere and used the isolate in short co-culture validation experiments showing promoted A. pyrenoidosa growth and Pseudomonas-associated pyridoxal production under florfenicol stress.
Avena Rhizosphere and Detritusphere Niche-Differentiated Decomposer Guilds
A rhizosphere and detritusphere microbial community of Avena fatua characterized by time-resolved metatranscriptomics across rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Transcripts were binned using a unique reference database from soil isolate genomes, single-cell amplified genomes, metagenomes, and stable-isotope-probing metagenomes. Soil habitat significantly affected both community composition and overall gene expression, but the succession of microbial functions occurred faster than compositional change. Hierarchical clustering of upregulated decomposition genes resolved four microbial guilds whose functional succession patterns suggest specialization for fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere.
Avena Rhizosphere Cross-Kingdom 13C-SIP Community
A rhizosphere community of Avena fatua traced with stable isotope probing (SIP) by growing the plant in a 13CO2 atmosphere. Paired rhizosphere and nonrhizosphere soils sampled at 6 and 9 weeks were density-fractionated and sequenced to recover 55 bacterial genomes (>=70 percent complete), complete 18S rRNA sequences of 13C-enriched microeukaryotic bacterivores and fungi, and 10 circularized bacteriophage genomes. Some phages were the most labeled entities in the rhizosphere, suggesting phage are important agents of turnover of plant-derived carbon in soil. CRISPR spacer targeting linked one phage to a Burkholderiales host predicted to be a plant pathogen and another to a Catenulispora sp. predicted to be a plant growth-promoting bacterium. Heavily 13C-labeled bacterial genes include those involved in modulating plant signaling hormones, plant pathogenicity, and defense against microeukaryote grazing.
Bacillales Lignin-Degrading LDSynCom
An engineered eleven-strain Bacillales synthetic community assembled for aerobic beechwood-lignin degradation in M9 minimal medium. Zhou et al. 2026 screened a 121-strain Bacillales collection with a bottom-up clear-halo lignin-utilization assay and a top-down M9-lignin enrichment, distilled 15 candidates with crystal-violet biofilm and methylene-blue/Azure-B dye-decolorization assays, and retained 11 strains for the lignin-degrading SynCom. The final LDSynCom formed biofilms on lignin particles, accumulated more Folin-Ciocalteu-reactive phenolics than uninoculated and 11B-dropout controls, and produced extracellular proteomes whose lignin-induced proteins included Paenibacillus sp. 11B ring-cleaving dioxygenase candidates.
Bacillus A1-A3 Naphthalene Biofilm Consortium
A defined two-isolate Bacillus consortium, Consortium 3, assembled from Bacillus paranthracis isolate A1 and Bacillus licheniformis isolate A3 after enrichment of petroleum-contaminated soil from Ras Gharib, Egypt on polycyclic aromatic hydrocarbons. The A1/A3 pair was one of four consortia built from the three strongest phenanthrene- and naphthalene-degrading isolates. Consortium 3 was induced to grow as a glass-attached biofilm, showed the highest reported synergistic interaction during planktonic naphthalene degradation, reached 94.69% naphthalene degradation as a biofilm culture, and its preformed biofilm degraded 81.47% of naphthalene in artificially contaminated soil. Phenanthrene behaved differently: individual isolates outperformed the consortia, and the authors attributed the lower consortium rates to antagonistic interactions under the more complex PAH substrate.
Bacillus and Aspergillus Lignocellulose-Degrading Co-Vermicomposting SynCom
Synthetic lignocellulose-degrading cross-kingdom microbial consortium (SynCom) composed of Bacillus licheniformis, Bacillus subtilis, Aspergillus nidulans, and Aspergillus rugulosus applied at 5% inoculation during earthworm (Eisenia fetida) co-vermicomposting of high-lignin green waste and cattle manure. The SynCom stimulates lignocellulolytic enzyme and urease activities, enriches carbohydrate esterases, glycosyltransferases, and nitrification gene hao, reduces the C/N ratio, and increases humic substance and nitrate nitrogen content.
Bacillus and Pseudomonas Antagonistic Synthetic Community T7 Against Chili Root Rot
Synthetic bacterial community (T7 SynCom) constructed from core antagonistic rhizosphere biomarker isolates of Bacillus and Pseudomonas depleted during prolonged continuous cropping of chili pepper (Capsicum annuum). T7 SynCom directly antagonizes the root rot pathogen Fusarium solani, reduces chili root rot incidence, and induces systemic plant resistance by activating MAPK, ethylene, jasmonic acid, and salicylic acid immune signaling pathways.
Bacillus G12-Y4-X25 Tobacco Biocontrol SynCom
A three-member Bacillus synthetic microbial community assembled from Bacillus amyloliquefaciens G12, Bacillus pumilus Y4, and Bacillus velezensis X25 to combine complementary antagonistic activities against Fusarium oxysporum and Phytophthora nicotianae, the causal agents of tobacco Fusarium root rot and black shank. G12 was isolated from the tobacco rhizosphere and the Y4 and X25 endophytes from tobacco tissues in Luoyang, China. The strains showed only mild mutual inhibition in pairwise plate confrontations, the 1:1:1 SynCom produced more indole-3-acetic acid than any single strain, and glasshouse and two-site field assays linked the consortium to reduced soil-borne disease, improved tobacco root traits, and higher middle-leaf-based estimated yield.
Bacillus siamensis-vallismortis HT Masson Pine SynCom
A two-strain HT synthetic plant growth-promoting rhizobacterial community assembled from Trichoderma koningiopsis-conditioned Pinus massoniana rhizosphere isolates. The community combines Bacillus siamensis RW5 and Bacillus vallismortis RW8 and was tested against Fusarium oxysporum damping-off in Masson pine seedlings. Relative to the pathogen challenge control, HT reduced disease incidence by 36.67%, increased seedling height by 9.44%, enhanced protective enzyme activity, alleviated membrane damage, and activated the resistance genes PR1, FLS2, and CAT1.
Bacillus-Bradyrhizobium Straw Humification SynCom
A two-member Bacillus siamensis and Bradyrhizobium japonicum SynCom that promotes maize straw humification and soil organic carbon.
Bacillus-Pseudomonas Galveston PET Consortium
A naturally occurring five-member bacterial consortium isolated from petroleum-polluted coastal soil in Galveston Bay, Texas, and examined for polyethylene terephthalate (PET) biodegradation in carbon-free basal medium with PET granules or MHET. The consortium contains Bacillus thuringiensis 9.1, Bacillus cereus 13.1, and Pseudomonas species strains 9.2, 10, and 13.2. Integrated comparative genomics, secreted-proteome profiling, HPLC, and LC-MS analyses support a distributed PET-degradation model in which Bacillus strains contribute more strongly to extracellular hydrolysis, polymer-surface association, and persistence, while Pseudomonas strains contribute more strongly to aromatic transport, redox balancing, and downstream assimilation of PET-derived intermediates.
Bacillus-Saccharomyces Daqu Spatial-Cooperation SynCom
A Bacillus-Saccharomyces synthetic consortium used as a representative Daqu solid-state fermentation model for starch-mediated spatial cooperation. Temporal transcriptomics connected Bacillus-dominated starch hydrolysis with Saccharomyces-driven ethanol production across fermentation stages, fluorescently labeled synthetic consortia showed that starch availability governed colony expansion and spatial cooperation, and an engineered consortium carrying an IPTG-inducible alpha-amylase expression system was applied in Daqu fermentation to improve starch conversion efficiency and flavor compound formation.
Bacteroides-Desulfovibrio Carrageenan H2S Coculture
A defined in vitro two-species human-gut bacterial coculture in which Bacteroides thetaiotaomicron degrades carrageenan, releases inorganic sulfate, and fuels dissimilatory sulfate reduction and hydrogen sulfide production by Desulfovibrio desulfuricans.
Bacteroides-Eubacterium Gnotobiotic Gut Model
A defined two-member gnotobiotic mouse gut model pairing the human gut Bacteroidetes member Bacteroides thetaiotaomicron VPI-5482 with the human gut Firmicutes member Eubacterium rectale ATCC 33656. The model was used to examine niche specialization and metabolic interaction between dominant human gut phyla under controlled host and diet conditions. B. thetaiotaomicron expands polysaccharide utilization and host mucin glycan foraging in the presence of E. rectale, while E. rectale shifts away from glycan-degrading enzymes toward amino acid and sugar transport, glycolytic support, and butyrate generation from acetate.
Bacteroides-Methanobrevibacter Gnotobiotic Mouse Mutualism
A defined host-associated gnotobiotic mouse community used to test archaeal-bacterial mutualism in the gut. Germ-free mice were colonized with Bacteroides thetaiotaomicron with or without Methanobrevibacter smithii or Desulfovibrio piger, revealing a specific interaction in which M. smithii redirects B. thetaiotaomicron toward dietary fructan fermentation to acetate while using B. thetaiotaomicron formate for methanogenesis.
Baia de Todos os Santos Mangrove Alkane-Degrading Consortium
A petroleum-contaminated mangrove bacterial consortium from Baia de Todos os Santos, Brazil, reported as a 36-organism consortium and represented by nine selected Bacillus, Brevibacillus, Pseudomonas, and Stenotrophomonas isolates. de Santana Nazare et al. sequenced and compared the nine isolates, grew them in Bushnell-Haas broth with paraffinic crude oil, and found that the complete consortium was required for statistically significant intermediate n-alkane degradation while Pseudomonas/Stenotrophomonas and Bacillus members occupied rapid and delayed alkane-degradation roles.
Baijiu Pit Mud Hexanoic Acid SynCom G4
An ethanol-fed, hexanoic-acid-producing synthetic community constructed from Chinese baijiu fermentation pit mud using a top-down strategy. The G4 SynCom was dominated by Clostridium sensu stricto 12, described as primarily Clostridium kluyveri with an 86% value, with Clostridium sensu stricto 18 and Pseudoclavibacter also reported among dominant prokaryotes. Functional predictions and fermentation profiling suggested a potential association between G4 hexanoic acid production and reverse beta-oxidation; under optimized pH 7.9, 37.6 C, 8.2% inoculum, and 77% loading-volume conditions, SynCom G4 reached 4.69 g/L hexanoic acid.
Banana Fusarium Wilt Biocontrol SynCom1.2
A three-member banana rhizosphere SynCom designed for biological control of Fusarium oxysporum f. sp. cubense tropical race 4.
Barley DT Rhizosphere SynCom
A defined sixteen-strain drought-tolerant bacterial synthetic community assembled from barley-rhizosphere isolates collected at the Global Change Experimental Facility in Bad Lauchstadt. Rigerte et al. selected isolates with overlapping 16S rDNA sequences to drought- or future-climate-associated amplicon sequence variants, cultured the barley isolate set on YME agar, combined equal proportions of the sixteen single-strain suspensions, and applied the Barley DT-SynCom to barley seedlings before Blumeria graminis f. sp. hordei challenge and pre-challenge rhizosphere multi-omics assays.
Bayan Obo REE Tailings Consortium
An acid-producing bacterial consortium engineered to extract rare earth elements (REE) from tailings at the Bayan Obo mine in Inner Mongolia, China, the world's largest rare earth deposit. This functional bacterial consortium achieves exceptional REE recovery rates of 82-83% for the five main light rare earth elements (La, Ce, Pr, Nd, Sm) after 18 days of bioleaching using one-step or two-step processes. The tailings are iron extraction residues from medium-poor oxidized ores containing bastnaesite (REE(CO₃)F) and monazite as primary REE minerals. The consortium employs acid-producing bacteria including actinomycetes (Streptomyces sp.), autotrophic acidophiles (Acidithiobacillus ferrooxidans), and heterotrophic acidophiles (Acidiphilium cryptum) that work synergistically to mobilize REE through acidolysis and organic acid complexation. Key mechanisms include production of organic acids (citric, oxalic, lactic, pyruvic), siderophores, and complexing ligands that solubilize REE from carbonate-fluoride minerals. The two-step process (sequential inoculation with heterotrophs followed by autotrophs) achieves 83.51% recovery versus 82.78% for one-step (simultaneous inoculation), demonstrating synergistic enhancement through pH control and organic acid accumulation. This system represents a critical sustainable biotechnology for recovering strategic REE materials essential for clean energy technologies, permanent magnets, and electronics while remediating millions of tons of existing Bayan Obo tailings.
Bifidobacterium breve-Trichomonas vaginalis Vaginal Co-culture
A defined two-member co-culture of the vaginal commensal Bifidobacterium breve with the sexually transmitted protozoan parasite Trichomonas vaginalis, assayed against HeLa epithelial cells. The result runs counter to the expectation that a beneficial commensal antagonises the parasite: over 4 h the protozoan proliferated 1.2-fold more while bacterial abundance fell 27%, microscopy showed direct physical association between the two organisms, and transcriptomics of T. vaginalis showed upregulation of fatty acid metabolism and DNA replication genes together with virulence-associated genes including adhesins, corroborated by metabolomic changes in long-chain fatty acids. B. breve conferred no protection on host epithelial cells, and the effects on the parasite were transient. The record captures a commensal-parasite association in which the commensal is depleted while the parasite is enhanced.
Bifidobacterium longum DSM20219 and Bacillus subtilis SOM8 Alginate Biofilm Probiotic Co-Culture
Engineered probiotic co-culture of oxygen-sensitive anaerobic Bifidobacterium longum DSM20219 and biofilm-forming Bacillus subtilis SOM8 co-encapsulated in sodium alginate hydrogel beads. Bacillus subtilis SOM8 promotes interspecies cell aggregation, extracellular polymeric matrix development, and biofilm formation within the alginate matrix, enhancing B. longum DSM20219 survival by ~3-log CFU/g (>7-log CFU/g) in simulated gastric and intestinal fluids and maintaining >6-log CFU/g over 28 days of aerobic storage.
Bifidobacterium-Faecalibacterium 2′-FL/FOS Butyrate Coculture
Defined two-strain anaerobic gut coculture containing Bifidobacterium bifidum JCM1254 and Faecalibacterium prausnitzii A2-165 (JCM31915). The strains were grown in 48-well batch cultures of sugar- and volatile-fatty-acid-free YCFA broth supplied with 0.5% total carbohydrate as 2′-fucosyllactose, fructooligosaccharides, or mixtures of the two. Monocultures showed B. bifidum responding to 2′-FL-rich substrates and F. prausnitzii growing in FOS-containing conditions; in the two-member coculture, total OD600 and lactate/acetate accumulation increased under 2′-FL-rich conditions, but butyrate peaked specifically at 10% 2′-FL plus 90% FOS, indicating ratio-dependent substrate complementarity and metabolite-mediated interaction.
Bifidobacterium-Ruminococcus Infant HMO Cross-Feeding Coculture
An infant gut microbiome cross-feeding system reconstructed from individualized cultivations with three infant fecal inocula and supplemented with the human milk oligosaccharide 2'-fucosyllactose (2'FL). Bifidobacterium breve typically cannot metabolize 2'FL on its own, but extracellular fucosidases encoded by coexisting Ruminococcus gnavus release lactose from 2'FL and unlock extensive B. breve growth. Targeted cocultures and supplementation of R. gnavus into an infant microbiome showed that R. gnavus promotes B. breve growth through HMO breakdown, demonstrating that infant HMO utilization depends on synergistic interactions among coexisting species.
BioAsteroid ISS Chondrite Biomining Consortium
The BioAsteroid experiment tested microbial biomining of asteroidal (L-chondrite) material under microgravity aboard the International Space Station (ISS). Two heterotrophic microorganisms — the bacterium Sphingomonas desiccabilis CP1D and the fungus Penicillium simplicissimum DSM 1078 — were flown both as single strains and as an artificial two-member consortium on crushed Northwest Africa (NWA) 869 L-chondrite meteorite fragments, in a 50% v/v R2A medium, inside BioMining Reactors housed in KUBIK incubators. The study measured leaching of 44 elements (including the platinum-group elements ruthenium, palladium and platinum, and other elements of industrial interest) from the meteorite and compared microbial versus abiotic (non-biological) leaching under microgravity and terrestrial gravity. Penicillium simplicissimum was the most effective bioleaching organism in microgravity, enhancing release of palladium, platinum and other elements relative to non-biological controls, while Sphingomonas desiccabilis formed a contiguous biofilm on the rock surface but performed similarly or worse than the abiotic control for most platinum-group elements. In the consortium, the fungus alone outperformed the mixture for palladium, suggesting an antagonistic effect of the bacterium. Metabolomic analysis showed distinct, microgravity-dependent changes in microbial metabolism, particularly for P. simplicissimum, with increased production of carboxylic acids and other molecules of potential biomining or pharmaceutical interest. The work demonstrates proof of principle for microbe-driven transformation of asteroidal material for in situ resource utilization in space.
BioModels MODEL1806250003 Spittlebug Sulcia-Sodalis Symbiosis
BioModels record MODEL1806250003 is a multi-compartment metabolic model of the spittlebug Philaenus spumarius and its bacterial endosymbionts Sulcia and Sodalis.
BioModels MODEL1806250004 Sharpshooter Sulcia-Baumannia Symbiosis
BioModels record MODEL1806250004 is a multi-compartment metabolic model of the sharpshooter Graphocephala coccinea and its bacterial endosymbionts Sulcia and Baumannia.
BioModels MODEL1806250005 Cicada Sulcia-Hodgkinia Symbiosis
BioModels record MODEL1806250005 is a multi-compartment metabolic model of the cicada Neotibicen canicularis and its bacterial endosymbionts Sulcia and Hodgkinia.
BioModels MODEL2204300001 Kefir Community Model
BioModels record MODEL2204300001 is a genome-scale model from the Blasche et al. kefir study and is described as a model of a microbial species participating in a kefir community.
BioModels MODEL2209060002 D pigrum - S aureus Community
BioModels record MODEL2209060002 is a community GEM combining Dolosigranulum pigrum and Staphylococcus aureus to emulate interactions in a human nasal-like environment.
BioModels MODEL2310020001 Mouse Metaorganism Model
BioModels record MODEL2310020001 contains an integrated metabolic metaorganism model of aging mice that connects a merged mouse gut microbiome metabolic model to colon, liver, and brain host-tissue models through gut lumen and bloodstream exchange compartments.
BioModels MODEL2405300001 Infant Gut HMO SynCom
BioModels record MODEL2405300001 contains genome-scale metabolic models used to study a synthetic human infant gut microbial community in the context of human milk oligosaccharides.
BioModels MODEL2407300002 Sponge Holobiont Network
BioModels record MODEL2407300002 provides simulations and model assets for an eight-species sponge microbiome network, modeling interactions among symbiont clades in a Stylissa holobiont.
BioRock ISS Basalt Biomining Consortium
A defined three-species bacterial panel flown as the ESA BioRock experiment on board the International Space Station to test microbial bioleaching of economically important elements from basaltic rock under microgravity, simulated Mars gravity, and simulated Earth gravity (with ground 1 x g controls). Sphingomonas desiccabilis CP1D (DSM 16792), Bacillus subtilis NCIB 3610 (DSM 10), and Cupriavidus metallidurans CH34 (DSM 2839) were each cultivated on slides of olivine basalt (collected near Gufunes, Reykjavik, Iceland; chosen as an analogue of Moon/Mars surface material) inside a purposely designed miniature biomining reactor housed in the KUBIK incubator. Sphingomonas desiccabilis enhanced mean leached concentrations of rare earth elements (the lanthanides plus yttrium) relative to non-biological controls in all gravity regimes, while Bacillus subtilis reduced REE bioleaching efficacy and Cupriavidus metallidurans showed no difference, demonstrating the microbial specificity of the process as on Earth. A companion analysis showed that Sphingomonas desiccabilis and Bacillus subtilis both enhanced vanadium leaching by 184.92 to 283.22% relative to sterile controls, and a third study found no significant differences in final bacterial cell concentrations between gravity regimes. Gravity level had no significant effect on mean leaching in any case, establishing the principle of biomining and associated bioindustrial processes on Solar System bodies with non-1 x g gravity.
Black Soldier Fly Larvae Gut SynCom (Bacillus + Lactobacillus + Issatchenkia)
A tripartite synthetic microbial community (SynCom) engineered from the core gut microbiota of black soldier fly larvae (BSFL) to enhance protein bioconversion from organic wastes. The SynCom combines the bacteria Bacillus and Lactobacillus with the yeast Issatchenkia and was assembled and tested in germ-free (gnotobiotic) larval hosts using multi-omics. Bacillus provides direct proteolytic activity, whereas Lactobacillus and Issatchenkia are associated with improved protein-conversion performance and amino-acid metabolic responses. The tripartite SynCom showed the highest protein conversion performance and distinct spatiotemporal distribution along the gut pH gradient, increasing final larval protein content by 63%.
Black-Soil Glucose-Activated Herbicide-Mixture Degrading Synthetic Community
Simplified four-isolate bacterial synthetic community (SynCom) constructed from keystone taxa—Burkholderia-Caballeronia-Paraburkholderia complex, Rhodanobacter, and Achromobacter—identified in a natural microbial consortium enriched from herbicide-stressed agricultural black soil in Northeast China. Activated by glucose supplementation that fuels glycolytic and TCA cycle energy supply and environmental acidification, the SynCom co-metabolically degrades a recalcitrant mixture of nicosulfuron (97.27%), mesotrione (68.00%), and atrazine (22.91%) via enriched catabolic genes including atzF (allophanate hydrolase) and gst (glutathione S-transferase).
Bosea-Pseudomonas Dimethachlon-Degradation Consortium
A defined two-strain consortium reconstructed from the dimethachlon-enriched community JHJ-2. Bosea sp. S6 transforms dimethachlon into the toxic intermediate 3,5-dichloroaniline, and Pseudomonas sp. KH-1 consumes that intermediate, completing a sequential degradation and detoxification handoff.
Bothnian Bay GAC-Dependent CIET-SAO Consortium
A coastal-sediment-derived, granular-activated-carbon-dependent enrichment consortium serially transferred for about a decade from Bothnian Bay sediments. In anaerobic, acetate-fed cultures amended with granular activated carbon (GAC), the consortium couples syntrophic acetate oxidation to methane formation by moving electrons from the dominant electrogenic syntroph Candidatus Geosyntrophus acetoxidans through the GAC matrix to a Methanosarcina-related electrotrophic methanogen. Long-read metagenomics recovered 24 MAGs from the GAC-propagated enrichment, including MAGs for the core acetate-oxidizing and methanogenic partners plus GAC-enriched Lentimicrobium, Sedimentibacter, and Desulforhopalus lineages.
Brachypodium Young Root Rhizosphere EcoFAB Community
A young Brachypodium distachyon primary-root rhizosphere community analyzed at two spatially distinct zones (root tip and root base) using EcoFABs fabricated ecosystems and conventional pot and tube containers with natural soil. 16S rRNA gene analysis shows a strong rhizosphere effect with significant enrichment of OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria, while community composition did not differ between root tips and root base or across growth containers. Bulk metagenomic functional analysis revealed enrichment of metabolic-pathway and root-colonization genes in root tips, whereas nutrient-limitation and environmental-stress genes were enriched in bulk soil, indicating root-driven gradients in labile carbon and nutrient availability.
Brocadia Low-Nitrogen Anammox Consortium
An operated anammox biofilter community subjected to sustained low-substrate nitrogen stress, where metagenomics, metatranscriptomics, co-occurrence networks, and SMETANA supported functional succession from Ca. Kuenenia toward a multispecies, transcriptionally active Ca. Brocadia assemblage with lower modeled resource overlap and complementary auxotrophies.
Buchnera-Serratia Cinara cedri Endosymbiont Consortium
A natural co-obligate aphid endosymbiont consortium in the cedar aphid Cinara cedri, composed of Buchnera aphidicola BCc and Serratia symbiotica SCc. Genome-based metabolic inference shows that Buchnera BCc has lost some ancestral nutritional functions, while Serratia SCc retains or takes over functions needed by the host-associated consortium, including shared tryptophan biosynthesis and broader metabolic complementation.
Burkholderia-Pseudomonas YB2 PET Degradation Consortium
A defined two-strain synthetic consortium, YB2, constructed from Burkholderia cepacia ZY1 and Pseudomonas harudinis G1B at an optimized 4:5 inoculation ratio to improve polyethylene terephthalate (PET) depolymerization and downstream PET-hydrolysis-product conversion. At pH 7.0 and 30 °C, YB2 reached 4.30% +/- 0.11% PET film mass loss after 3 days, outperformed the individual strains, released BHET, MHET, TPA, and ethylene glycol, and converted 96.4% of BHET plus 97.3% of MHET within 2 days.
Butyrivibrio fibrisolvens + Selenomonas ruminantium + Ruminococcus albus Lignocellulolytic Rumen Consortium
A synthetic lignocellulolytic bacterial consortium designed from six bovine rumen microbial strains to enhance lignocellulose degradation for biofuel and enzyme production. Genome-scale community metabolic models were used with flux-based parameters (pairwise metabolic assistance, PMA; growth support index, PGSI) to predict compatible, mutualistic pairs, which were validated in experimentally grown cocultures. The strongest pairwise enzymatic synergism was observed for Butyrivibrio fibrisolvens with Selenomonas ruminantium (a 41% increase in endoglucanase activity), and a three-membered community of B. fibrisolvens, S. ruminantium, and Ruminococcus albus showed synergistic activity across all lignocellulosic substrates, indicating strong metabolic interplay among compatible species.
Cable Bacteria beneath Photosynthetic Biofilm Sediment Community
A coastal sediment community in which long filamentous Desulfobulbaceae cable bacteria connect sulfide-rich deeper sediment to oxygen supplied near the sediment-water interface by an oxygenic photosynthetic biofilm. The system links sulfur oxidation, oxygen production, sulfide availability, and centimeter-scale long-distance electron transfer.
Calcium-Tomato Bacterial Wilt SynCom
A four-member tomato-root SynCom assembled from calcium-enriched antagonists to suppress Ralstonia solanacearum bacterial wilt. Bi et al. isolated Dyella japonica, Rhodanobacter glycinis, Paenibacillus polymyxa, and Pseudomonas aeruginosa from tomato roots after calcium chloride amendment, selected them because they antagonized R. solanacearum, were promoted by calcium or calcium-induced root metabolites, and encoded plant-growth-promoting traits, and mixed OD600-normalized LB-grown suspensions 1:1:1:1. In 96-well root-exudate co-culture assays, the SynCom plus exudates from 20 mM calcium-treated tomato seedlings reduced R. solanacearum density; in greenhouse soil, the SynCom combined with a reduced 100 mg Ca kg-1 soil dose dropped bacterial wilt incidence from 74.07% to 0%.
Caldibacillus-Clostridium Aerotolerant Cellulose Coculture
A designed two-member thermophilic coculture for aerotolerant cellulose conversion. The community pairs the cellulolytic strict anaerobe Clostridium thermocellum with the noncellulolytic facultative anaerobe Caldibacillus debilis GB1. C. debilis GB1 provides respiratory protection under oxidative conditions, enabling synergistic cellulose utilization and ethanogenic biofuel production under an aerobic atmosphere.
Caldicellulosiruptor Two-Species Hydrogen Coculture
A de novo constructed, continuous-flow, hydrogen-producing coculture pairing Caldicellulosiruptor saccharolyticus DSM 8903 with the strain reported as Caldicellulosiruptor kristjanssonii DSM 12137. The system was designed to test whether two extreme thermophilic sugar-fermenting Caldicellulosiruptor strains could stably coexist while converting glucose and xylose, major lignocellulosic hydrolysate sugars, to hydrogen-rich fermentation products.
California Grassland Precipitation Legacy Soil Community
A semiarid California Mediterranean-climate grassland soil microbial community studied under two field-imposed precipitation regimes (100 percent versus 50 percent of mean annual precipitation) and assayed during the first autumn rewet. Quantitative H2-18O stable-isotope-probing, 16S rRNA amplicon sequencing, metagenomics, and metatranscriptomics revealed that reduced winter precipitation imposed a lasting legacy on community turnover: microbial growth declined by about one order of magnitude and mortality by about two orders of magnitude relative to ambient plots, lowering community growth efficiency (new biomass growth divided by respiration). Soil organic carbon shifted from microbial-necromass-derived lipid-, amino-sugar-, and protein-like compounds toward more oxidized lignin- and tannin-like plant detritus compounds. Meta-omics linked high-CGE communities to N-rich necromass consumption with elevated amino acid and peptidoglycan biosynthesis and aromatic compound degradation, while low-CGE communities had elevated carbohydrate metabolism and lipid turnover consistent with plant-detritus processing and membrane maintenance.
Candida parapsilosis Hospitalized Infant Gut Microbiome Community
An in situ infant gut microbiome study of Candida parapsilosis colonization in hospitalized infants, combining metagenomics, metatranscriptomics, and metaproteomics. Infant-06 fecal samples recovered C. parapsilosis alongside Enterococcus faecalis, Lactobacillus gasseri, and Staphylococcus epidermidis; the time series placed Candida in an early low-complexity gut community, followed its replacement or outnumbering largely by E. faecalis, and linked Candida-positive samples to shifts in Enterococcus ribosomal and mannitol phosphotransferase-system transcript features.
Caragana korshinskii Cross-Kingdom Forage Bio-Valorization SynCom
A defined three-member, two-kingdom synthetic microbial community assembled to break the lignocellulose barrier of Caragana korshinskii, a shrub legume used as an arid-region feed resource. Lactobacillus plantarum supplies rapid acidification, Bacillus subtilis supplies fibrolytic enzyme secretion, and Aspergillus niger supplies what the source calls oxidative delignification potential. Against the control, the SynCom treatment reached higher in vitro dry matter digestibility (49.68%) and neutral detergent fibre digestibility (25.65%), shifted the silage microbiome so that Lactobacillus exceeded 95% of it, suppressed the spoilage genera Staphylococcus and Weissella by competitive exclusion, and upregulated predicted pyruvate metabolism and amino-acid biosynthesis. CURATION SCOPE. Only the abstract of the source is available: the paper is gold open access at the publisher but has no PMC deposit, Europe PMC serves no full text, and the publisher blocks programmatic retrieval, so references_cache/PMID_42432469.md is content_type abstract_only. Strain designations, inoculation rates, ensiling vessel, temperature, moisture and duration, control-arm values, pH and organic-acid data, sequencing methods and any sequence accessions are all unavailable and are therefore absent here because they were not readable, not because the study did not report them. Re-check with the Europe PMC search for EXT_ID:42432469 and curate the rest once a pmcid appears.
Caragana-Wheat Drought SynCom15
A fifteen-member bacterial synthetic community constructed from drought-responsive core microbes of the desert shrub Caragana korshinskii and tested as a cross-host wheat drought-tolerance inoculant. Hao et al. combined four functional strains with eleven core microbial strains, assayed the full SynCom15 in potted plant experiments, and linked SynCom inoculation to wheat growth under drought, Pseudomonas-associated biofilm and quorum-sensing functions, and later streamlining into a biofilm-forming SynCom5.
Cellulomonas-Rhodobacter Cellulose Photohydrogen Coculture
A defined anaerobic cellulose-to-hydrogen coculture pairing cellulolytic Cellulomonas sp. strain ATCC 21399 with the purple nonsulfur phototroph Rhodopseudomonas capsulata, now classified as Rhodobacter capsulatus. The Cellulomonas partner ferments cellulose to organic acids, while R. capsulata grows photoheterotrophically on those products and evolves molecular hydrogen through nitrogenase. The system is DOE-relevant as an early model for lignocellulosic biohydrogen production by division of labor between cellulose fermentation and phototrophic hydrogen evolution.
Cellulose-to-Methane Combinatorial SynCom Panel
A bounded anaerobic synthetic-community panel assembled from the cellulolytic bacterium Ruminiclostridium cellulolyticum H10, the hydrogenotrophic methanogen Methanospirillum hungatei JF-1, the acetoclastic methanogen Methanosaeta concilii GP6, and the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. The experiment co-cultured all cellulose-fed bi-, tri-, and quad-species combinations containing R. cellulolyticum, plus the R. cellulolyticum monoculture, and used proteogenomics, stoichiometric flux modeling, and SMETANA to resolve context-dependent cross-feeding, competition, and methanogenic carbon flow.
Cellulose-to-Methane Quad-Culture SynCom
A four-species anaerobic synthetic community coupling cellulose degradation, sulfate reduction, and methanogenesis.
CeMbio Caenorhabditis elegans Microbiome
CeMbio is a defined, ecologically informed twelve-strain bacterial community representing the natural Caenorhabditis elegans microbiome. The v1.0 community includes Enterobacter hormaechei CEent1, Lelliottia amnigena JUb66, Acinetobacter guillouiae MYb10, Sphingomonas molluscorum JUb134, Stenotrophomonas indicatrix JUb19, Pseudomonas lurida MYb11, Pseudomonas berkeleyensis MSPm1, Comamonas piscis BIGb0172, Pantoea nemavictus BIGb0393, Ochrobactrum vermis MYb71, Sphingobacterium multivorum BIGb0170, and Chryseobacterium scophthalmum JUb44. The resource pairs a genetically tractable host with cultured, genome-sequenced, CGC-distributed commensal isolates that colonize the worm gut as a community, alter nematode developmental timing, and support follow-up behavioral and metabolic studies with the same reference composition.
Cheese Rind In Situ-In Vitro Model Community
A tractable fermented-food surface biofilm system based on cheese rind microbial communities. Wolfe and colleagues surveyed 137 rind communities across 10 countries, isolated representatives of the dominant bacterial and fungal genera, and reconstructed simplified cheese-curd-agar communities in vitro to test how moisture, washing, pH, and bacterial-fungal interactions shape reproducible community assembly and succession.
Chicken BL6 Anti-Salmonella SynCom
A defined six-strain synthetic consortium, BL6, assembled from Wenchang and Danzhou chicken gut isolates with in vitro anti-Salmonella activity. The consortium contains Bacillus velezensis CMLH125, Ligilactobacillus salivarius CMLH112, novel Bacillus sp. CMLH124, Lactobacillus johnsonii CMLH106, Lactobacillus crispatus CMLH109, and Lactobacillus gallinarum CMLH110. The strains were normalized after 72 h of cultivation, combined in equal proportions, washed, and resuspended in PBS with 20% glycerol for oral gavage of 1-day-old chicks before Salmonella Typhimurium challenge. In the chick model, BL6 mitigated Salmonella-associated intestinal injury, helped maintain barrier and liver function, reduced systemic inflammatory responses, and favored sustained Lactobacillus enrichment in the ileal microbiota.
Chinese Distillers Grains Dual Fungal Lignin Consortium
A two-member fungal solid-state fermentation system consisting of Phanerochaete chrysosporium and Pleurotus eryngii that was constructed to convert the recalcitrant lignin fraction of Chinese Distillers' grains. Chen et al. 2026 measured 58.66% lignin degradation in Chinese Distillers' grains, day-10 peaks in laccase and manganese peroxidase activity, a day-15 peak in lignin peroxidase activity, and transcriptomic/metabolomic evidence that P. chrysosporium was most active in early oxidative lignin cleavage while P. eryngii became dominant during later aromatic catabolism.
Chlamydomonas-Bacterial Hydrogen Production Consortium
A synthetic algae-bacteria consortium for sustainable hydrogen production, composed of the green alga Chlamydomonas reinhardtii and three bacterial species: Microbacterium forte sp. nov., Bacillus cereus, and Stenotrophomonas goyi sp. nov. This mutualistic association produces up to 313 mL H2/L over 17 days in high-cell density cultures. M. forte is the primary bacterial species responsible for improving algal hydrogen production, while the complete bacterial community enhances and sustains photobiological H2 generation through metabolic cooperation.
Chlamydomonas-Methylobacterium Mutualistic Consortium
A two-member mutualistic consortium consisting of the green alga Chlamydomonas reinhardtii and the methylotrophic bacterium Methylobacterium aquaticum, isolated from a freshwater environment. This natural association demonstrates reciprocal metabolic exchange under nitrogen stress conditions, mediated by indole-3-acetic acid (IAA) signaling. The alga provides photosynthetically fixed carbon and oxygen, while Methylobacterium modulates IAA levels through both production and degradation, influencing algal physiology and stress responses. This system serves as a model for understanding algae-bacteria interactions in freshwater ecosystems and potential applications in sustainable algal biotechnology under nutrient limitation.
Chlorella fusca CHK0059 Keystone-Taxa Antifungal SynCom
A four-isolate bacterial synthetic community selected from Chlorella-associated plant microbiome networks: Pseudomonas 8C3D12, Pseudoduganella rivuli FT92W (KACC 21474), Pseudomonas 6C7F4 and Brevibacterium renqingii REN4 (KCTC 49366). The two Pseudomonas isolates share a genus-level taxonomy entry here; three bacterial taxonomy entries do not mean three isolates. Table 1 distinguishes the network label Duganella from the inoculated Pseudoduganella strain. Treat8 combines all four bacteria with Fusarium challenge; Treat9 also contains C. fusca CHK0059. Host disease-index responses depend on treatment, host and time, without demonstrated universal superiority to single isolates or formal synergy. Separate in-vitro strawberry rhizosphere microbiome-fraction assays show compositional responses to live/killed Chlorella, methanol extract and mannitol. Algal mannitol secretion, strain-specific recruitment and the mechanism mediating plant protection remain unresolved. The 2025 precursor names Rhizomicrobium rather than Brevibacterium as its third correlated genus; the two studies do not establish identical keystone sets.
Chlorella vulgaris Whey Co-culture
A defined microalgal co-culture pairing the Chlorella vulgaris culture abbreviated CVB with Chlorella vulgaris CCAP 211/19 in casein whey-based media for dairy-whey valorization. Kelarijani et al. 2026 reported that the Chlorella vulgaris co-culture exhibited synergistic growth relative to single cultures and to a four-species algal mix in the casein whey panel.
Chlorella-Azospirillum Synthetic Mutualism
A defined algal-bacterial synthetic mutualism pairing the freshwater green microalga Chlorella sorokiniana UTEX 2714 with the plant-growth-promoting bacterium Azospirillum brasilense Cd. The pair has been studied in co-immobilized alginate bead systems and related culture formats to test how nutrient availability shapes mutualistic population growth, tryptophan, thiamine, and indole-3-acetic acid exchange, starch accumulation, and algal-bacterial aggregation. The system is relevant to environmental biotechnology, microalgal biomass production, and algal-bacterial interaction design.
Chlorella-Ecoli Mixotrophic Biofuel Precursor Coculture
A defined algal-bacterial coculture in which Chlorella minutissima was grown with Escherichia coli in airlift reactors under mixotrophic glucose, glycerol, and acetate conditions. The coculture produced more algal biomass, consumed more carbon substrate, and increased lipid and starch productivity relative to axenic algal cultures. This system is relevant to DOE-aligned algal biofuel biotechnology because it tests whether bacterial contamination or partnership can improve production of algal biofuel precursors rather than suppressing algal biomass.
Chlorella-Rhizobium Bioflocculation
A co-culture system pairing the microalgae Chlorella vulgaris with the bioflocculant-producing bacterium Rhizobium radiobacter F2 for enhanced algal harvesting in wastewater treatment applications. The bacterium produces extracellular polysaccharide bioflocculants that induce aggregation and flocculation of algal cells, enabling efficient biomass recovery for biofuel production. This bioflocculation approach avoids the negative effects of traditional chemical flocculants and provides a cost-effective, environmentally friendly method for microalgae harvesting, with flocculation efficiency improving from 0.2% (axenic algae) to >90% with bacterial co-culture.
Chlorochromatium aggregatum Phototrophic Consortium
A structured freshwater phototrophic bacterial consortium in which one central motile heterotrophic beta-proteobacterium, Candidatus Symbiobacter mobilis, is surrounded by approximately 15 green sulfur bacterial Chlorobium chlorochromatii epibionts. Genome analyses support a highly specialized symbiosis involving metabolite exchange, central-bacterium sensing and motility toward light and sulfide, cell-cell adhesion, and possible quinone-mediated electron exchange.
Choysum SynLAV DEHP-Degrading Rhizobacterial SynCom
A five-member synthetic rhizobacterial community assembled from the low-accumulation choysum rhizosphere isolates Flavobacterium sp. L11, Pseudomonas sp. L29, Sphingomonas sp. L75, Rhodococcus sp. L44, and Gordonia sp. L115. The isolates were selected as non-antagonistic, DEHP-degrading representative strains, mixed at equal ratios after OD600 0.5 normalization, and tested in choysum pots containing 100 mg/kg DEHP-contaminated soil.
Chromium Sulfur Oxidation Enrichment
An enrichment consortium in which microbial chromate reduction is coupled to anaerobic oxidation of inorganic electron donors. A 60-day cultivation study showed that sludge enrichments supplied with elemental sulfur, S(0), or zerovalent iron, Fe(0), as sole electron donors biologically reduced Cr(VI), deposited Cr(III) as the main reduction product, and achieved high chromate removal in both independent donor systems. High-throughput 16S rRNA sequencing linked this transformation to a consortium-level division of labor in which S(0)- or Fe(0)-oxidizing bacteria such as Thiobacillus or Ferrovibrio generated volatile fatty acids that chromate-reducing bacteria such as Geobacter or Desulfovibrio could further use to reduce chromate.
CICC Three-Strain Probiotic M-MV Luteolin Consortium
Defined anaerobic co-culture of Bifidobacterium longum CICC25033, Clostridium butyricum CICC23847, and Limosilactobacillus reuteri CICC6131 used to produce mixed-species probiotic membrane vesicles (M-MVs). Hou et al. grew the strains singly, pairwise, and as a 1:1:1 three-strain combination in MRS broth, observed higher viable counts in co-culture and with cell-free supernatants from partner strains, isolated M-MVs from the supernatant of the co-culture, found a distinct M-MV proteomic profile with antioxidant activity, and loaded luteolin into the resulting M-MVs for in-vitro and DSS-induced mouse-colitis assays.
Cinnamate β-Oxidation Consortium
A syntrophic 3-member anaerobic consortium for degradation of cinnamate via β-oxidation to benzoate, consisting of Papillibacter cinnamivorans, Syntrophus sp., and Methanobacterium formicicum. P. cinnamivorans performs β-oxidation of cinnamate to benzoate, followed by syntrophic benzoate degradation by Syntrophus sp. to acetate, H2, and CO2, with the methanogen consuming H2 to produce methane. This stepwise aromatic compound degradation pathway is important for anaerobic bioremediation.
Clostridial isoDCA Mini Consortium
A two-member engineered Clostridia consortium pairing Peptacetobacter hiranonis with Ruminococcus gnavus VPI C7-9 WT so the community converts host-derived taurocholic acid through cholic acid and deoxycholic acid to isodeoxycholic acid. Ionescu et al. also built a matched P. hiranonis plus R. gnavus KO consortium with rumgna_00694 disrupted as an isoDCA-negative control, enabling in vitro bile-acid conversion assays and antibiotic-treated mouse engraftment experiments that isolate the host effects of isoDCA.
Clostridium acetobutylicum and Clostridium ljungdahlii Carbon-Negative Isopropanol Syntrophic Coculture
High-cell-density syntrophic bacterial coculture pairing genetically engineered Clostridium acetobutylicum (CACas9 delta-hbd-p95ace02_atoB, lacking 4-C metabolism and overexpressing an acetone-formation pathway) with the acetogen and ketoreductase partner Clostridium ljungdahlii in a 3.6-L perfusion bioreactor. C. acetobutylicum ferments glucose to acetone, CO2, and H2; C. ljungdahlii consumes dissolved H2—relieving the thermodynamic bottleneck of NADH-driven H2 evolution in C. acetobutylicum—and reduces cross-fed acetone to isopropanol at supratheoretical yields in continuous carbon-negative glucose fermentation.
Clostridium acetobutylicum-Clostridium ljungdahlii Syntrophic Fusion Coculture
A defined two-member anaerobic coculture of the solventogen Clostridium acetobutylicum ATCC 824 and the acetogen Clostridium ljungdahlii DSM 13528. CO2 and H2 produced by C. acetobutylicum feed C. ljungdahlii, and the pairing also produces interspecies cell fusion with large-scale exchange of protein, RNA, and DNA between the two organisms. RNA sequencing of the coculture against the two monocultures, and of membrane-separated against unseparated cocultures in a transwell system, separates the effect of soluble signals from the effect of direct cell-to-cell contact. The transcriptional program shows differential regulation of the C. ljungdahlii Wood-Ljungdahl pathway and of the motility machinery, and of amino-acid biosynthesis and degradation; arginine and histidine made by C. acetobutylicum are proposed to be metabolized by C. ljungdahlii for extra ATP and carbon. The authors read the pairing as mutualistic rather than the commensalism previously assumed. This record is scoped to the WILD-TYPE pairing. The same laboratory has since reported much higher isopropanol and butanol titers from the same species pair using genetically modified C. acetobutylicum; those are properties of the engineered pairing and are deliberately not curated here.
Clostridium autoethanogenum-Clostridium kluyveri Syngas Coculture
A defined anaerobic synthetic coculture combining the acetogenic syngas fermenter Clostridium autoethanogenum with the chain-elongating bacterium Clostridium kluyveri. C. autoethanogenum converts carbon monoxide or syngas into acetate and ethanol, while C. kluyveri consumes these products for chain elongation, producing C4 and C6 fatty acids and higher alcohols. The system is relevant to DOE carbon utilization and renewable fuels because it couples gas fermentation with microbial upgrading of CO/syngas-derived intermediates in one growth vessel.
Clostridium carboxidivorans-Clostridium kluyveri CO Chain-Elongation Coculture
A defined anaerobic synthetic coculture pairing the autotrophic solventogenic acetogen Clostridium carboxidivorans with the chain-elongating bacterium Clostridium kluyveri. In CO/CO2-fed stirred-tank bioreactors, C. kluyveri elongates C2 products to organic acids, and C. carboxidivorans reduces those acids to longer-chain alcohols such as butanol and hexanol. The system is DOE-relevant because it couples waste-gas/syngas fermentation, carbon utilization, and production of liquid fuels and platform chemicals.
Clostridium cellulolyticum-Geobacter sulfurreducens Cellulose MFC Coculture
A defined binary microbial fuel cell coculture pairing the cellulolytic fermenter Clostridium cellulolyticum with the electrochemically active bacterium Geobacter sulfurreducens. The community couples cellulose hydrolysis and fermentation to anode respiration: C. cellulolyticum metabolizes cellulose, while G. sulfurreducens uses fermentation products to transfer electrons to the anode. The same exact two-species composition was reported in an initial cellulose-to-electricity study and a follow-up cellulose-fed microbial biofilm ecology study. The system is relevant to DOE bioenergy because it converts cellulosic biomass into electricity in a controlled bioelectrochemical reactor.
Clostridium cellulovorans-Beijerinckii AECC ABE Coculture
A defined anaerobic artificial symbiosis pairing the cellulolytic, butyrate-producing mesophile Clostridium cellulovorans 743B with the non-cellulolytic solventogenic bacterium Clostridium beijerinckii NCIMB 8052. The coculture was designed for consolidated bioprocessing of alkali extracted deshelled corn cobs, where C. cellulovorans saccharifies lignocellulose and produces butyric acid, and C. beijerinckii converts the released soluble sugars and butyric acid into acetone-butanol-ethanol solvents. The system is DOE-relevant as a lignocellulosic biomass-to-biofuel community model using an agricultural residue feedstock.
Clostridium cellulovorans-Methanosarcina barkeri Cellulose Methane Coculture
A defined anaerobic cellulose-to-methane coculture combining the cellulolytic fermenter Clostridium cellulovorans 743B with the metabolically versatile methanogen Methanosarcina barkeri Fusaro. C. cellulovorans degrades cellulose and produces methanogenesis precursors including hydrogen, formate, and acetate, while M. barkeri consumes those products for methanogenesis. The system is relevant to DOE bioenergy because it is an experimentally tractable model for renewable methane production from cellulosic biomass and for engineering anaerobic biomethanation consortia.
Clostridium cellulovorans-Rhodopseudomonas palustris Cellulose Biohydrogen Coculture
A defined two-member cellulose-to-biohydrogen coculture combining the cellulolytic dark-fermentative bacterium Clostridium cellulovorans 743B with the purple nonsulfur photosynthetic bacterium Rhodopseudomonas palustris CGA009. The coculture links cellulose degradation, volatile-fatty-acid exchange, pH stabilization, and photofermentative hydrogen production. It is DOE-relevant as a genetically tractable model for lignocellulosic bioenergy, integrated dark/photo fermentation, and mechanistic design of biohydrogen consortia.
Clostridium ljungdahlii-Clostridium kluyveri Syngas Alcohol Coculture
A defined anaerobic synthetic coculture that combines the acetogenic syngas fermenter Clostridium ljungdahlii with the chain-elongating bacterium Clostridium kluyveri in a continuously fed syngas bioprocess with in-line product extraction. C. ljungdahlii converts syngas into ethanol and acetate, while C. kluyveri uses ethanol for reverse-beta-oxidation chain elongation to butyrate and caproate. The same community also produced longer-chain alcohols including butanol, hexanol, and traces of octanol within a narrow pH range. The system is relevant to DOE carbon utilization and renewable fuels because it converts C1 gases into C4-C8 fuels and chemicals through microbial cross-feeding.
Clostridium phytofermentans-E. coli Cellobiose Biofilm Consortium
A rationally designed two-member artificial consortium composed of Clostridium phytofermentans ISDg, currently represented in NCBI Taxonomy as Lachnoclostridium phytofermentans ISDg, and Escherichia coli K-12 MG1655. The community was built to improve conversion of cellulose-derived sugars into ethanol, biomass, and other bioproduct-relevant outputs through division of labor between a cellulolytic obligate anaerobe and a facultative anaerobe. It is DOE-relevant because it models consolidated lignocellulosic bioprocessing, cellobiose conversion, biofilm oxygen partitioning, and cross-feeding mechanisms that can improve cellulosic fuel and chemical production.
Clostridium Thermocellum-Saccharoperbutylacetonicum Cellulosic Butanol Coculture
A staged two-member coculture for producing n-butanol from crystalline cellulose. The cellulolytic thermophile Clostridium thermocellum, represented in NCBI Taxonomy as Acetivibrio thermocellus ATCC 27405, first hydrolyzes Avicel cellulose. The butanol-producing Clostridium saccharoperbutylacetonicum strain N1-4 is then added for solvent production. The system is DOE-relevant because it couples consolidated cellulose deconstruction to cellulosic butanol production, a liquid biofuel and bioproduct target.
Clostridium-Caldicellulosiruptor Minimal Medium Coculture
A thermophilic, anaerobic, two-member laboratory coculture pairing Clostridium thermocellum ATCC 27405 with Caldicellulosiruptor bescii DSM 6725. The system was used to test whether low-ionic-strength defined medium with reduced nitrogen, sulfur, phosphate, and vitamin supplements could maintain both cellulolytic bacterial populations during conversion of cellulosic substrates relevant to consolidated bioprocessing.
Clostridium-E. coli-Nitratidesulfovibrio Minority-Mediator Consortium
A defined anaerobic three-strain consortium containing Clostridium acetobutylicum ATCC 824, Escherichia coli DH10B, and Nitratidesulfovibrio vulgaris Hildenborough NCIMB 8303. In glucose-yeast extract medium, the minority N. vulgaris population persists as a physical and metabolic mediator, reduces E. coli-associated inhibition of C. acetobutylicum growth, and can exchange cytoplasmic material with both other members.
Clostridium-Saccharomyces Cellulose Ethanol Coculture
A synthetic two-member cellulose-to-ethanol coculture pairing the cellulolytic mesophile Clostridium phytofermentans ISDg, currently represented in NCBI Taxonomy as Lachnoclostridium phytofermentans ISDg, with the engineered cellodextrin-fermenting yeast Saccharomyces cerevisiae cdt-1. The consortium is maintained by controlled oxygen delivery: the yeast removes inhibitory oxygen and receives soluble sugars released during C. phytofermentans cellulose hydrolysis. With added endoglucanase, the coculture produced approximately 22 g/L ethanol from 100 g/L alpha-cellulose. This system is relevant to DOE lignocellulosic biofuel and consolidated bioprocessing goals.
Clostridium-Thermoanaerobacter Cellulosic Bioethanol Coculture
A thermophilic, anaerobic, two-member laboratory coculture for consolidated cellulosic bioethanol production. The cellulolytic Clostridium thermocellum LQRI member hydrolyzes and ferments cellulose, while the non-cellulolytic Thermoanaerobacter pseudethanolicus strain X514 partner improves ethanol production from cellulose-derived fermentation intermediates. The system is DOE-relevant because it uses a defined coculture to increase ethanolic fermentation of recalcitrant cellulosic material under batch and cyclic fed-batch bioprocess conditions.
Clostridium-Thermoanaerobacterium JN4-GD17 Cellulosic Biofuel Coculture
A thermophilic two-member cellulosic biofuel coculture composed of Clostridium thermocellum JN4 and Thermoanaerobacterium thermosaccharolyticum GD17. The system improves overall cellulosic biofuel production efficiency relative to C. thermocellum alone, but later mechanistic work indicates that GD17 also competitively hampers C. thermocellum JN4 growth while using glucose and cellobiose released during cellulose degradation.
Coastal Forested Wetland Seawater-Ion Microcosm Community
A restored coastal forested freshwater wetland soil community from the Timberlake Observatory for Wetland Restoration in North Carolina, curated around a manipulative laboratory microcosm experiment that disentangled sulfate from other seawater ions. Intact wetland soil cores received deionized water, artificial seawater, artificial seawater without sulfate, or sulfate alone, followed by DNA sequencing, biogeochemical measurements, and greenhouse gas flux measurements. The experiment found that artificial seawater altered microbial richness, composition, functional genes, and emissions of carbon dioxide, methane, and nitrous oxide whether sulfate was present or absent, whereas sulfate alone did not alter emissions or enrich sulfate-reducing bacteria or sulfur cycling genes. The record is DOE-relevant because authors were affiliated with the DOE Joint Genome Institute and Lawrence Berkeley National Laboratory, and sequencing followed DOE JGI methods.
Cold-Seep ANME-2b and Seep-SRB1g Carbon Monoxide-Oxidizing Syntrophic Consortium
Syntrophic consortium of anaerobic methane-oxidizing archaea (ANME-2b, family Candidatus Methanocomedenaceae / Candidatus Methanomarinus) and sulfate-reducing bacteria (Seep-SRB1g, phylum Thermodesulfobacteriota) from deep-sea methane seep sediments on the Costa Rica margin capable of oxidizing carbon monoxide (CO) in the absence of methane. CO oxidation is coupled syntrophically to dissimilatory sulfate reduction and, under sulfate-free conditions, to CO2 (bicarbonate) reduction to methane by ANME-2b to support cellular maintenance.
Community G GenX Biodegradation Consortium
A Prospector nanowell-derived bacterial consortium from cotton detritusphere enrichments that was re-tested for hexafluoropropylene oxide dimer acid (GenX) degradation. Community G underwent rapid taxonomic restructuring in sterile agricultural-soil microcosms amended with GenX: Salmonella enterica, Pseudomonas tolaasii, Stenotrophomonas sp. LM091, and Stenotrophomonas sp. MYb57 expanded by day 3, while Stenotrophomonas cyclobalanopsidis and Pseudomonas arcuscaelestis declined or disappeared. Active Community G removed 80.6% of GenX in the 3-day soil microcosm and reached 69.6% defluorination.
Coniochaeta-Sphingobacterium-Citrobacter Wheat Straw Consortium
A three-member bacterial-fungal synthetic consortium cultivated on wheat straw to study division of labor during lignocellulose degradation. The community combines the fungus Coniochaeta sp. 2T2.1 with the bacterium originally reported as Sphingobacterium multivorum w15 and later proposed as Sphingobacterium paramultivorum w15, plus Citrobacter freundii so4. The system is relevant to DOE bioenergy because it links a Joint Genome Institute fungal genome resource to transcriptomic and metatranscriptomic evidence for cellulose, xylan, hemicellulose, lignin-modification, detoxification, and vitamin B2-associated functions in a model lignocellulose-degrading consortium.
Copper Biomining Heap Leach Consortium
An industrial microbial consortium used for commercial copper bioleaching from low-grade sulfide ores in heap leach operations. This acidophilic community oxidizes ferrous iron and reduced sulfur compounds, generating ferric iron (Fe³⁺) and sulfuric acid that solubilize copper from chalcopyrite (CuFeS₂) and other copper sulfide minerals. The consortium demonstrates temporal succession over the 200-300 day leaching cycle, with Acidithiobacillus ferrooxidans dominating early stages (pH >2, low Fe, ~10⁷ copies/ml at 200 days), followed by Leptospirillum ferriphilum and Ferroplasma acidiphilum in aged heaps (pH 1.67-1.83, high Fe³⁺ ~1.9 g/L, ~10⁵ copies/ml at >250 days). Acidithiobacillus thiooxidans maintains constant sulfur oxidation activity (10⁵ copies/ml) throughout the cycle. Sulfobacillus species contribute at low abundance (10³-10⁴ copies/ml) with increased activity in older heaps. The community operates at pH 1.5-2.5, temperatures 20-60°C depending on thermophilic strains, and produces the Fe³⁺ oxidant critical for copper dissolution (reaching 1.86-1.9 g/L Fe³⁺). This biohydrometallurgical process extracts copper from ores uneconomical for conventional smelting, with industrial operations achieving commercial-scale metal recovery through percolation of acidic leach solutions through heaps of crushed ore.
Cordyceps-Malbranchea Antimicrobial Coculture
A defined two-fungus coculture pairing Cordyceps militaris ZYb8 with Malbranchea ostraviensis SS1 for natural-product discovery. Yang et al. 2026 used LC-MS/MS molecular networking and compound isolation to show that the coculture produced eight previously undescribed aromatic compounds, including eutypoid G-K, gotjawalides A-B, and ocauxarthrol B, along with eleven known natural products; antibacterial assays on the isolated products found weak to moderate selective activity against Gram-positive and Gram-negative bacterial test strains.
Corynebacterium glutamicum + Shewanella oneidensis Succinic-acid Co-culture
Engineered two-member co-culture pairing the succinic-acid producer Corynebacterium glutamicum (including an ldhA-deleted, lactate-deficient strain K1) with the electroactive bacterium Shewanella oneidensis to enhance anaerobic succinic acid biosynthesis through interspecies interactions. Co-cultivation raised succinic acid yield markedly over monoculture without altering glucose consumption, and supplementation with riboflavin (the most effective of five screened redox-active additives) further improved production. Transcriptomics showed co-culture reprogrammed C. glutamicum metabolism, reinforcing its electron transport system and redistributing carbon flux toward the reductive TCA pathway.
Coscinodiscus Synthetic Community
A synthetic marine phytoplankton community consisting of the large centric diatom Coscinodiscus radiatus and four phylogenetically distinct bacterial isolates from different marine bacterial lineages. This model system was established to examine species-specific diatom-bacteria interactions and community dynamics. The bacteria include two Roseobacteraceae members (Mameliella CS4 and Roseovarius Rose1), a gammaproteobacterium (Marinobacter CS1), and a Flavobacterium (Croceibacter Crocei1). The consortium demonstrates context-dependent bacterial effects on diatom growth that vary with algal fitness state, growth phase, and community composition, with no universal algicidal or growth-promoting bacteria observed. This system is relevant to understanding carbon cycling and primary production in marine ecosystems.
CRC Fusobacterium Control SynCom
A bottom-up designed seven-species synthetic microbial community for ecological control of Fusobacterium nucleatum-associated colorectal cancer models.
Crucian Carp Gut Disease-resistance SynCom
A simplified synthetic microbial community of three gut genera (Cetobacterium, Paraclostridium, and Pseudomonas) assembled from the intestinal microbiota of crucian carp (Carassius auratus). These genera were enriched in fish that displayed mild symptoms after Aeromonas hydrophila infection, and fecal microbiota transplantation from mild-symptom fish conferred enhanced resistance to the pathogen. The reconstituted SynCom significantly reduced A. hydrophila abundance by activating intestinal immune responses and reinforcing the gut barrier, supporting microbiome-based disease prevention in aquaculture.
Crystal Geyser CO2-Rich Aquifer Autotrophic CPR Lysolipid Community
A deep CO2-rich subsurface aquifer community below the Colorado Plateau, sampled from groundwater brought to the surface by eruptions of Crystal Geyser. Coupled lipidomic and metagenomic analyses show that bacterial and archaeal CO2 fixation in the deep subsurface provides the organic carbon pool, supporting an autotrophy-based deep biosphere. Candidate Phyla Radiation (CPR) bacterial putative symbionts lack complete lipid biosynthesis pathways but still possess regular lipid membranes, which may originate from other community members; these other members also adapt to high in situ pressure by increasing fatty acid unsaturation. An unusually high abundance of lysolipids attributed to CPR bacteria may represent an adaptation to membrane curvature stress induced by their small cell sizes.
Cucumber Low-Phosphorus Cross-Kingdom Bacterial-Fungal Biocontrol Synthetic Community
Cross-kingdom synthetic microbial community (13 bacterial and 6 fungal strains) assembled from signature taxa enriched in the low-phosphorus rhizosphere of cucumber (Cucumis sativus): bacterial genera Bacillus, Cupriavidus, Sphingopyxis, and Devosia together with fungal genera Aspergillus and Amesomyces (reported as Amesia). Recruited and sustained by low-phosphorus distinguished rhizosphere metabolites (succinic acid, azelaic acid, threonic acid, and methionine), the cross-kingdom SynCom engages in mutualistic biofilm and hyphal facilitation and reduces Fusarium oxysporum f. sp. cucumerinum abundance by 85-99%, suppressing cucumber Fusarium wilt even under high-phosphorus conditions.
Cultivated Meat Contaminant SynCom
A six-isolate synthetic microbial community assembled from microbial contaminants that originated in the cultivated-meat cell-culture environment. Whole-genome functional mapping suggested potential metabolic complementarity and ecological robustness among the contaminants, and the SynCom was used as a severe cell-cultured-meat contamination model for antimicrobial-peptide intervention tests. In a screen of 11 antimicrobial peptides and proteins, the synthetic peptide 1018-k6 was the most effective agent, with a 37.5 μg/mL minimum inhibitory concentration against the SynCom and complete microbial inhibition across a 14-day production-cycle assay challenged with 10^6 CFU/mL bacteria.
Cyantraniliprole Fahmy Consortium T4
A defined six-member bacterial consortium, designated T4 or Fahmy-consortia, that was previously characterized for pesticide bioremediation and was re-evaluated as a cyantraniliprole-removal benchmark in simulated contaminated water. The consortium contains Bacillus subtilis subsp. subtilis AZFS3, Bacillus pumilus AZFS5, Bacillus mojavensis AZFS15, Bacillus paramycoides AZFS18, Pseudomonas aeruginosa KZFS4, and Alcaligenes aquatilis KZFS11. In 20-day, 30 C simulated-water microcosms seeded with standardized bacterial inocula, T4 achieved the highest tested cyantraniliprole removal: HPLC measured 98.27% removal from the 57.79 mg/L zero-day residue and a 1.00 mg/L residue after 20 days in the nominal 60 mg/L treatment.
Cyprus Copper Sulphide Bioleaching Consortium
An acidophilic copper bioleaching consortium established from a copper bioleaching column in Cyprus on chalcopyrite (CuFeS2) and sub-cultured to chalcocite (Cu2S) to test how mineral type and surface chemistry shape community composition. Genome-resolved metagenomics after 4 and 8 weeks of cultivation identified dominant members including Acidithiobacillus species and strains, a Rhodospirilales, Leptospirillum ferrodiazotrophum, and Thermoplasmatales archaea, with abundance trends linked to mineralogy and to surface-attached versus planktonic lifestyles. Many bacteria carried plasmids encoding metal resistance, sulphur metabolism, and CRISPR-Cas loci, with evidence of intra-plasmid competition via CRISPR spacers on an Acidithiobacillus plasmid targeting plasmid-borne conjugal transfer genes.
Dairy Wastewater Algal-Cyanobacterial Cultivation Panel
A bounded non-sterile laboratory panel that compared mono-, co-, and sequential cultures of the screened phototrophs Chlorella sorokiniana, Euglena gracilis, Synechocystis sp., and Desertifilum tharense during dairy-wastewater treatment. The 12-day experiment grew four monocultures, four 1:1 dry-weight co-cultures, and four sequential cyanobacterium/microalga cultures in 50% diluted raw dairy wastewater in 500 mL bottles with 250 mL working volume. Samples were fractionated into phycosphere-attached and free-living bacteria for V3-V4 16S rRNA MiSeq profiling, with raw sequence data deposited under NCBI BioProject PRJNA1265442. This is a panel record: the four named taxa were assayed across the treatment bottles rather than all co-occurring in every bottle, and indigenous dairy-wastewater bacteria were intentionally retained by non-sterile sample handling.
DCPP DBS4-DCP-4-DCP-11d Degradation SynCom
A metabolic-model-selected three-strain synthetic community composed of Sphingopyxis sp. DBS4, Sphingopyxis sp. DCP-4, and Achromobacter sp. DCP-11d. Lin et al. built genome-scale metabolic models from five DCPP-enrichment isolates, simulated 15 DBS4-containing two- to five-strain combinations, selected DBS4&DCP-4&DCP-11d as the optimal three-member DCPP degrader, and experimentally verified its DCPP removal and predicted metabolite exchange in mineral medium and DCPP-contaminated soil.
Deep-Sea Whale-Fall Vallitalea and Trichloromonas Chitin-Degrading Electrogenic Consortium
Anaerobic deep-sea whale-fall sediment microbial consortium and reconstituted defined co-culture enriched in potentiostatically controlled bioelectrochemical reactors poised at +0.22 V vs. SHE mimicking iron-reducing conditions. Primary chitin-degrading Vallitalea sp. hydrolyzes insoluble crystalline chitin and ferments oligomers to soluble intermediates (N-acetylglucosamine, glucose, acetate) that are cross-fed to iron-reducing, electrogenic Trichloromonas sp. performing extracellular electron transfer (EET) to electrodes or iron oxides.
Deepwater Horizon Deep-Sea Oil Plume Succession
A natural, perturbed deep-sea hydrocarbon-plume microbial community that developed during the 2010 Deepwater Horizon blowout in the Gulf of Mexico. The plume selected indigenous hydrocarbon-degrading Gammaproteobacteria, with early enrichment of Oceanospirillales-like petroleum degraders followed by Colwellia, Cycloclasticus, methylotrophic bacteria, and other taxa with non-redundant hydrocarbon degradation capacities.
Defined Multispecies Enamel Caries Model
A defined four-member oral biofilm model for in vitro enamel caries development, composed of Lactobacillus casei, Streptococcus mutans, Streptococcus salivarius, and Streptococcus sanguinis on salivary-pellicle-coated enamel slabs. The system was used to quantify how sucrose, fluoride, and calcium shift biofilm growth and enamel demineralization.
Defined Three-Strain Organic-Nitrogen Nitrifying Community
A simplified synthetic nitrifying microbial community pairing Bacillus badius NBRC 15713 with Nitrosomonas europaea NBRC 14298 and Nitrobacter winogradskyi NBRC 14297 for sequential ammonification and nitrification under organic nitrogen conditions. The co-culture achieved complete ammonification and nitrification under selected organic nitrogen conditions, accumulated approximately 56 mg-N/L nitrate-nitrogen with no residual nitrite-nitrogen, and yielded RT-qPCR profiles linking N. europaea and N. winogradskyi abundance changes to inorganic nitrogen concentrations during cultivation.
Dehalococcoides mccartyi CWV2 Dechlorinating Consortium
A native groundwater microbial consortium enriched in Dehalococcoides mccartyi (Dhc) strain CWV2, a strain capable of completely dechlorinating vinyl chloride (VC) to non-toxic ethene. The consortium remediates trichloroethene (TCE)-contaminated groundwater; amendment with biochar (BC600) derived from Zizania latifolia husks enhances microbial colonization and activity, accelerating TCE degradation and reducing VC accumulation. Community analysis indicates biochar promotes syntrophic hydrogen producers and electroactive bacteria that supply reducing equivalents and ensure long-term dechlorination stability.
Dehalococcoides-Desulfovibrio Lactate-Fed TCE Dechlorination Coculture
A defined anaerobic syntrophic coculture pairing Dehalococcoides mccartyi strain 195 with Desulfovibrio vulgaris Hildenborough. In this laboratory model for chlorinated-solvent groundwater bioremediation, D. vulgaris Hildenborough ferments lactate and supplies hydrogen and acetate that support strain 195 growth and reductive dechlorination. The system is DOE-relevant because it resolves metabolite exchange and stress responses that affect organohalide-respiring communities used for in situ trichloroethene bioremediation.
Dehalococcoides-Desulfovibrio-Pelosinus Corrinoid Triculture
A defined anaerobic three-member dechlorinating consortium containing Dehalococcoides mccartyi strain 195, Desulfovibrio vulgaris Hildenborough, and Pelosinus fermentans R7. In cobalamin-free, TCE- and lactate-amended medium supplemented with the lower ligand DMB, DvH supplies hydrogen while PfR7 supplies corrinoids that Dhc195 salvages and remodels into cobalamin. The triculture is relevant to DOE subsurface bioremediation because it identifies separable hydrogen-transfer and corrinoid-transfer mechanisms that support organohalide respiration in chlorinated-solvent dechlorinating communities.
Dehalococcoides-Methanosarcina DMB-Guided Cobalamin Coculture
A defined two-member chlorinated-ethene bioremediation coculture pairing Dehalococcoides mccartyi strain BAV1 with Methanosarcina barkeri strain Fusaro. D. mccartyi BAV1 is corrinoid auxotrophic and requires a cobalamin-type cofactor for organohalide respiration. M. barkeri Fusaro produces extracellular factor III, which did not by itself support Dehalococcoides reductive dechlorination activity, but addition of 5,6-dimethylbenzimidazole enabled guided biosynthesis of cobalamin that supported Dehalococcoides activity and growth. The system is relevant to DOE chlorinated-solvent groundwater bioremediation because it resolves a cofactor-mediated interaction controlling reductive dechlorination.
Dehalococcoides-Pelobacter Acetylene TCE Coculture
A defined anaerobic laboratory coculture in which the acetylene-fermenting bacterium historically reported as Pelobacter strain SFB93 is paired with Dehalococcoides mccartyi strain 195 to sustain reductive dechlorination of trichloroethene when acetylene is provided as electron donor and carbon source. The system is relevant to chlorinated-solvent groundwater bioremediation because acetylene can be generated during abiotic TCE degradation and can inhibit dechlorination at high concentrations.
Dehalococcoides-Syntrophomonas TCE Dechlorination Coculture
A defined two-member anaerobic syntrophic coculture in which Dehalococcoides mccartyi strain 195 reductively dechlorinates trichloroethene while Syntrophomonas wolfei ferments butyrate or crotonate-derived carbon to provide hydrogen and acetate. The system is relevant to chlorinated-solvent groundwater bioremediation because it models interspecies hydrogen transfer and metabolite exchange that support TCE dechlorination by Dehalococcoides-containing communities.
Delftia acidovorans YP-3 and Klebsiella oxytoca DX-3 Light-Driven Hydrogen-Producing Denitrifying Co-Culture
Catalyst-free, light-driven defined bacterial co-culture pairing the light-responsive electroactive bio-photosensitizer bacterium Delftia acidovorans YP-3 with hydrogen-producing and nitrate-reducing Klebsiella oxytoca DX-3 for simultaneous wastewater nitrogen removal and biohydrogen recovery. Through direct contact and soluble redox-active mediators that lower electron-transfer resistance and stimulate NADH metabolism, the YP-3/DX-3 co-culture generates 345.52 mL/L H2 in 48 h and achieves 90.25% nitrate removal with minimal nitrite accumulation in synthetic swine wastewater.
Delta nrfA Shewanella-Anammox Nitrite Coupled Consortium
Engineered anaerobic batch-culture consortium pairing activated anammox sludge from a full-scale municipal wastewater process with an nrfA-deficient Shewanella oneidensis MR-1 mutant. The Delta nrfA strain was inoculated into nitrate- and ammonium-containing mixed medium with sludge from an up-flow anaerobic sludge blanket reactor; blocking the terminal nitrite-to-ammonium DNRA step favored nitrite accumulation, enriched Candidatus Brocadia anammox bacteria, and made the 5:1 anammox-sludge-to-mutant culture the fastest and highest total-nitrogen removal treatment at 97%.
Desert-Derived Tomato Salt Stress SynCom5
A five-member desert-root bacterial SynCom that protects tomato plants from high salt stress in non-sterile soil.
Desulfovibrio-Methanococcus Syntrophic Consortium
A syntrophic, obligate two-member anaerobic consortium consisting of Desulfovibrio vulgaris Hildenborough, which oxidizes lactate to acetate, H2, and CO2 in the absence of sulfate, and Methanococcus maripaludis S2, a hydrogenotrophic methanogen. D. vulgaris can reduce sulfate when available, but in sulfate-free environments it must grow syntrophically by coupling lactate oxidation to interspecies hydrogen transfer. M. maripaludis consumes the H2 and CO2 produced by D. vulgaris to produce methane, maintaining the low H2 partial pressure thermodynamically required for continued lactate oxidation. This syntrophic relationship is fundamental to understanding microbial metabolism in sulfate-depleted anaerobic environments and represents a classic model system for studying syntrophic electron transfer mechanisms.
Desulfovibrio-Methanosarcina Lactate Syntrophy
A classic anaerobic two-member syntrophic coculture in which Desulfovibrio desulfuricans degrades lactate in the absence of added sulfate and Methanosarcina barkeri consumes fermentation products for methanogenesis. Lactate is first degraded to acetate and methane; later acetate is converted to methane and carbon dioxide, illustrating how hydrogen and substrate dynamics regulate coupled lactate oxidation and methanogenesis.
Diclofenac Activated Sludge Microbial Consortium
A laboratory microbial consortium enriched from activated sludge sampled at the San Jerónimo WWTP in Seville, Spain, by diclofenac selection and a glucose-supplemented MSM subculture. The MC degraded all 10 mg/L diclofenac in a glucose-amended mineral-salts flask assay within 5 days, producing extracellular 4'-hydroxy-diclofenac, 5-hydroxy-diclofenac, and putative nitro-DCF. 16S and ITS metabarcoding at the beginning and after 28 days showed a shift from Burkholderia-, Klebsiella-, Ochrobactrum-, Chthoniobacter-, and Malassezia-rich starting profiles to final bacterial and fungal profiles dominated by Burkholderia and Talaromyces, respectively.
DIET-based Simplified Lignocellulose-to-Methane Consortia (DIETsimp)
Two simplified methanogenic consortia (DIETsimp) constructed by top-down selection from cow manure combined with paddy soil or marine sediment inocula for high-efficiency conversion of lignocellulose to methane via direct interspecies electron transfer (DIET). Metagenomic analysis identified Methanosarcina mazei, capable of accepting electrons via DIET, as the dominant archaeon, and the electroactive bacteria Sphaerochaeta globosa and Clostridium aceticum as the dominant bacteria. The proposed DIET-based methanogenic pathway has S. globosa and C. aceticum metabolizing intermediates (xylose, glucose, pyruvate, acetate) and transferring electrons to M. mazei for reduction of CO2 to methane. Both consortia shortened methanogenesis periods and increased methane production rates relative to conventional anaerobic digestion.
Dolichospermum FBCC-A233 Xenic Phycosphere Community
A unialgal xenic freshwater cyanobacterial culture centered on Dolichospermum flosaquae FBCC-A233 and two co-maintained alphaproteobacterial associates assigned to Sphingorhabdus sp. and Brevundimonas sp. Kim et al. reconstructed complete circular genomes from the FBCC-A233 culture, resolved the associated bacterial genomes at genus level, and predicted an asymmetric cofactor economy in which D. flosaquae FBCC-A233 encoded BioU-mediated de novo biotin and extensive anaerobic corrinoid biosynthesis potential while the associated bacteria lacked complete de novo biotin and cobamide biosynthetic pathways.
Drosophila Five-Species Gnotobiotic Gut Microbiota
A defined five-species Drosophila melanogaster gut microbiota assembled from fly-gut isolates of Acetobacter pomorum, Acetobacter tropicalis, Lactobacillus brevis, Lactobacillus fructivorans, and Lactobacillus plantarum. The community was used to colonize axenic Drosophila and test how Acetobacter-Lactobacillus interactions shape host development, glucose, triglyceride allocation, and host-genotype-dependent microbiota effects.
Drought-Induced Rhizosphere Iron-Enriched Actinobacteria Community
A root-associated rhizosphere microbial community in which drought stress drives reproducible enrichment of bacterial lineages whose iron transport and metabolism functionalities are overrepresented. Genome-resolved metagenomics and comparative genomics show carbohydrate and secondary- metabolite transport functions also dominate drought-enriched taxa. Time- series root RNA-Seq data show that root iron homeostasis is impacted by drought, and loss of a plant phytosiderophore iron transporter increases Actinobacteria abundance. Exogenous iron application disrupts the drought- induced Actinobacteria enrichment and removes their host phenotype improvement, implicating iron metabolism as a microbiome-drought axis.
Dual Bacillus coagulans + Pseudomonas putida Lactic-acid Co-culture
Engineered artificial microbial consortium for L-lactic acid (LA) fermentation directly from undetoxified lignocellulosic (corncob) hydrolysates. A dual Bacillus coagulans (Heyndrickxia coagulans) system pairs a phenolic acid decarboxylase (PAD)-overexpressing biodetoxifying strain, DSM1-25280, with a high-yield LA producer, CC17B-1, and reaches 124.72 g/L LA from undetoxified hydrolysate via a sequential-inoculation division of labor. Multidimensional analysis supports a niche-succession model transitioning from biodetoxification-mediated commensalism to competitive exclusion. A sugar-metabolism-deficient engineered Pseudomonas putida KT2440 ZL added as a heterologous aromatic scavenger reinforces the system, raising the LA titer to 146.00 g/L at 98.9% yield.
DVM Tri-culture
A three-member synthetic consortium consisting of Desulfovibrio vulgaris (Dv), Methanococcus maripaludis (Mm), and Methanosarcina barkeri (Mb) that converts lactate to methane under varying sulfate conditions. D. vulgaris oxidizes lactate to acetate, CO2, and H2. Both methanogens (Mm and Mb) can consume the H2 produced by Dv, with Mm being a hydrogenotrophic methanogen and Mb capable of using both H2-CO2 and acetate for methanogenesis. The community demonstrates differential responses to geochemical gradients, particularly sulfate availability. In the absence of sulfate, all three species co-exist and methane production increases by almost 100% compared to Dv-Mm co-cultures. However, increasing sulfate levels shift community dynamics as Dv preferentially uses sulfate as an electron acceptor, creating competitive situations for both methanogens. This system provides insights into how geochemical gradients (particularly sulfate) regulate microbial interactions and methane production in anaerobic environments.
E-waste Bioleaching Consortium
An engineered acidophilic iron-oxidizing culture adapted for recovering valuable base metals from spent printed circuit boards (PCBs). This culture was dominated by Leptospirillum ferriphilum with Sulfobacillus benefaciens as an additional FeOB member. The community operates at extremely low pH and moderate temperature in PCB-enriched leachates, oxidizing ferrous iron to generate ferric iron (Fe³⁺) that dissolves base metals from PCB components. PCB leachates are toxic to the consortium, delaying the onset of exponential iron oxidation, but successive subculturing adapts the consortium to PCB toxicity and reduces that delay by up to 2.6-fold. This biotechnological approach offers an environmentally friendly alternative to pyrometallurgical e-waste processing by using an acidophilic community to regenerate the ferric iron lixiviant needed for metal recovery.
E. coli GL10-XL12 D-Lactate Mixed-Sugar SynCom
A defined same-species Escherichia coli synthetic consortium in which two BL21 (DE3)-derived knockout strains partition glucose and xylose fermentation for optically pure D-lactate production. GL10 was engineered as the glucose-specialized strain, XL12 was engineered with glk and ptsI deletions to redirect it away from glucose toward xylose, and a 1:1 GL10:XL12 coculture in M9 medium containing 5 g/L glucose plus 5 g/L xylose produced 3.76 g/L D-lactate after 36 h. Agitation and inoculation-ratio perturbations identified a higher 4.53 g/L D-lactate titer at a 1:5 GL10:XL12 ratio, and the same consortium was also tested on detoxified corn straw hydrolysate supplemented into M9 medium.
E. coli K-12 MG1655 Arg-Met Cross-Feeding Coculture
A defined two-member synthetic Escherichia coli K-12 MG1655 coculture built from complementary double-mutant amino-acid auxotrophs. The ΔargA-ΔmetJ mutant requires arginine and overproduces methionine, while the ΔmetA-ΔargR mutant requires methionine and overproduces arginine, producing an obligate Arg/Met mutualism that the study used to test how metabolic cross-feeding changes single-cell fluorescence noise under liquid, strain-ratio, and spatial heterogeneity perturbations.
Early Dental Biofilm Five-Species Model
A defined five-member oral biofilm model representing early acidogenic stages of the caries process. The community combines Streptococcus oralis, Streptococcus sanguinis, Streptococcus mitis, Streptococcus downei, and Actinomyces naeslundii in flow-channel biofilms to reproduce the composition, architecture, and microscale pH heterogeneity of early dental plaque.
East River Floodplain Core Microbiome
A natural floodplain-soil microbial community from the DOE-supported East River watershed in Colorado. Metagenomic and metatranscriptomic sampling across upper, middle, and lower East River meander-bound floodplains reconstructed 248 representative subspecies-level genomes and identified a core floodplain microbiome. The core community is enriched in aerobic respiration, aerobic carbon monoxide oxidation, thiosulfate oxidation, nitrification, methanol and formate oxidation, and carbon fixation capacities that vary with soil organic carbon and floodplain position.
East River Hillslope Riparian Transect Microbial Community
A natural, depth-resolved microbial community from a hillslope-to-riparian transect in the DOE-supported East River watershed near Crested Butte, Colorado. Metagenomic and geochemical analyses showed that distance from the East River, proximity to the groundwater table, and underlying weathered shale strongly structure microbial community composition and metabolic potential. Riparian-zone communities are compositionally distinct from hillslope communities and are functionally differentiated by capacities for carbon fixation, nitrogen fixation, sulfate reduction, Candidate Phyla Radiation bacteria in saturated sediments, and selenium reduction at depth.
EcoFAB 2.0 Root Microbiome Ring Trial SynCom17
A 17-member synthetic bacterial community (SynCom17) used in a standardized inter-laboratory ring trial across five international laboratories (LBNL, UNC Chapel Hill, Max Planck Cologne, Forschungszentrum Julich, U Melbourne) to study root microbiome recruitment and exudate composition of the model grass Brachypodium distachyon in EcoFAB 2.0 fabricated ecosystem devices. All 17 members were originally isolated from switchgrass rhizosphere soil and span four bacterial phyla (Actinomycetota, Bacillota, Bacteroidota, Pseudomonadota). In the full SynCom17, Paraburkholderia sp. OAS925 reproducibly dominates root colonization (~98% relative abundance) across all five labs, uniquely possessing a Type 3 Secretion System (T3SS), high motility, and acid resistance. Removing Paraburkholderia (SynCom16) yields a more variable community dominated by Rhodococcus sp. OAS809 (~68%), Mycobacterium sp. OAE908 (~14%), and Methylobacterium sp. OAE515 (~15%). The study demonstrated that EcoFAB 2.0 with standardized protocols achieves reproducible plant phenotype, exudate, and community structure data across continents, providing benchmark datasets for plant-microbiome research.
Electrostimulated Mixotrophic VFA-producing Enrichment Consortium
A specialized mixotrophic microbial consortium enriched in a continuous electrostimulated bioreactor operated at a constant potential of 300 mV for CO2 conversion into volatile fatty acids. Decreasing hydraulic retention time (HRT) selected for a spatially organized community in which Enterococcus and Clostridium dominated the planktonic phase while Desulfovibrio and Enterococcus were enriched in the electrode biofilm. This syntrophic organization enhanced biomass-specific inorganic carbon removal and redirected carbon flux toward acetate, a key product of acetogenic pathways, with electrode-associated taxa contributing reducing equivalents that supported autotrophic CO2/HCO3- fixation.
Electrostimulated Toluene Methanogenic Microbiota
An anaerobic methanogenic toluene-degrading microbiota whose syntrophic hydrocarbon conversion was stimulated at 800 mV. Wu et al. (2024) compared electro-stimulated and non-electro-stimulated methanogenic microbiota with bamA amplification and metagenomic sequencing, and inferred a shift from a Syntrophobacteraceae MAG116-centered, acetoclastic methanogen-associated network toward anode-recruited Desulfoprunum MAG10, hydrogen-producing Aminidesulfovibrio MAG60, and cathode-recruited hydrogenotrophic Methanobacterium MAG74 interactions that boosted methane production from toluene.
Emiliania huxleyi-Phaeobacter inhibens Dynamic Interaction
A defined marine algal-bacterial co-culture model between the coccolithophore Emiliania huxleyi CCMP3266 and the Roseobacter-group bacterium Phaeobacter inhibens DSM 17395. The interaction is dynamic: attached bacteria initially promote algal growth but later kill aging algal hosts. Evidence supports algal nutrient provisioning to the heterotrophic bacterium, bacterial attachment to naked algal cells, and indole-3-acetic acid production stimulated by algal-exuded tryptophan.
Engineered Gut Amino Acid Cross-Feeding Consortium
A four-species engineered mammalian-gut consortium in which Escherichia coli, Salmonella enterica serovar Typhimurium, Bacteroides thetaiotaomicron, and Bacteroides fragilis were modified to create amino acid auxotrophies and amino acid overproduction. The design converts a consortium otherwise shaped by antagonistic interactions into one with engineered beneficial cross-feeding, increasing population evenness in anaerobic in vitro culture and in low-protein-diet gnotobiotic mice.
ENIGMA Denitrifying SynCom
A two-member denitrifying synthetic community from the ENIGMA program, composed of Rhodanobacter thiooxydans FW510-R12 and Acidovorax sp. GW101-3H11 isolated from a heavily nitrate-contaminated superfund site. The consortium exhibits pathway-partitioned denitrification via nitrite and nitric oxide exchange, with cooperativity that can be disrupted under high nitrate conditions leading to nitrite accumulation and nitrous oxide off-gassing.
Ensifer YF2 + Sphingobacterium Y2 Polyethylene-degrading Consortium
Synthetic two-strain consortium for polyethylene (PE) biodegradation, constructed after screening Ensifer sp. YF2, Sphingobacterium sp. Y2, and Chryseobacterium sp. MF1 isolates from plastic-contaminated agricultural soils. The dual-strain consortium of YF2 and Y2 degraded PE more efficiently than individual strains or the full three-strain combination, using PE as the sole carbon source and inducing oxidative modifications and physical erosion of the polymer. Genomic analysis showed a complementary enzymatic division of labor - YF2 (oxidases LadA, AlkB, CYP450) performs backbone cleavage as the primary degrader, while Y2 (esterases and lipases) carries out intermediate metabolism through cross-feeding.
Episymbiotic CPR Bacteria and DPANN Archaea Groundwater Community
A groundwater microbial community framework combining genome-resolved metagenomics from one agricultural and seven pristine groundwater sites, yielding 746 Candidate Phyla Radiation (CPR) bacterial and DPANN archaeal genomes. Pristine sites, which serve as local sources of drinking water, contained up to 31 percent CPR bacteria and 4 percent DPANN archaea. Little species-level overlap of metagenome-assembled genomes was observed across the sites, indicating that CPR and DPANN communities are differentiated according to physicochemical conditions and host populations. Cryogenic transmission electron microscopy and genomic analysis identified CPR and DPANN lineages that reproducibly attach to host cells, with attachment apparently stimulating CPR bacterial growth.
Escherichia coli + Bifidobacterium bifidum Infant-gut Mutualistic Co-culture
Two-member infant-gut co-culture of Escherichia coli and Bifidobacterium bifidum. In healthy, term-born, breastfed infants these genera co-exist despite differing ecological strategies and share evolutionary adaptations for lactose acquisition. In vitro co-culture demonstrates a mutualistic cross-feeding interaction in which E. coli supplies cysteine to its auxotrophic partner B. bifidum, facilitating cooperative degradation of 2'-fucosyllactose (the predominant human milk oligosaccharide), and the liberated monosaccharides in turn sustain E. coli growth, potentially helping regulate E. coli abundance in the infant gut.
Eucalyptus Nursery Five-Strain Bacterial Inoculant Consortium
A five-strain synthetic consortium of Eucalyptus-derived bacteria — Bacillus subtilis, Paraburkholderia caribensis, Methylobacterium tardum, and two strains representing putative novel species in Paenibacillus and Mesorhizobium — assembled from isolates of Eucalyptus rhizosphere and roots and selected for complementary functional traits in nitrogen cycling and rhizosphere colonisation. Applied to three Eucalyptus clones in a large tree-nursery field experiment and assessed after 13 weeks, the inoculant did not change bacterial richness or diversity but did alter root microbial community structure; two genotypes showed improved seedling quality and one showed mortality fall from 21.8% to 6.7%. The record captures a case where a defined inoculant reshapes community composition and host outcome without shifting diversity metrics, and where the response is genotype-dependent rather than uniform.
Euglena-Chlorella Microalgal Biorefinery Coculture
A defined coculture of Euglena gracilis and Chlorella pyrenoidosa optimized for biomass, lipid, and alpha-tocopherol production. The two phototrophs show complementary light-harvesting, carbon-fixation, electron-transport, and metabolite-secretion functions.
Ferroplasma-Leptospirillum Iron-Cycling Syntrophy
A synergistic two-member consortium consisting of the cell wall-lacking archaeon Ferroplasma acidiphilum and the iron-oxidizing bacterium Leptospirillum ferriphilum, found in extremely acidic, metal-rich environments including acid mine drainage and biomining operations. The partnership is centered on reciprocal soluble-metabolite effects: F. acidiphilum can use organic matter secreted by L. ferriphilum for growth, keeping low organic compound concentrations that would otherwise inhibit L. ferriphilum, and filtered medium from either partner favors growth of the other organism. This archaeal-bacterial partnership thrives at extremely low pH and represents a model system for studying cross-domain syntrophy in biomining acidophiles.
Five-member bacterial-fungal composting SynCom for lignocellulose degradation
A rationally designed five-member bacterial-fungal synthetic microbial community (SynCom) used to bioaugment the co-composting of cattle manure and mulberry branches. Inoculation acts as an ecological engineer that elevates pile temperatures, shortens the maturation period by roughly 7 days, and enhances degradation of lignin, cellulose, and hemicellulose while boosting humus content. Metagenomics shows the SynCom restructures the native microbiome, enriching key lignocellulose-degrading functional genera such as Thermobifida and Actinomadura and increasing the abundance of carbohydrate-active enzymes (cellulases, hemicellulases, and lignin-modifying auxiliary-activity enzymes).
Fomitopsis-E. coli Nutritional-Stress Coculture
A defined two-member fungal-bacterial coculture pairing the brown-rot basidiomycete Fomitopsis betulina CIRM-BRFM 860 with Escherichia coli ATCC 25922 to probe bacterial competition as a trigger for fungal nutritional stress and secondary metabolism. Albert et al. 2026 tested the pair in malt extract agar confrontations, where F. betulina inhibited distant E. coli growth, and in malt extract broth, where E. coli addition after 3 days of fungal growth depleted glucose within 1 day, reduced fungal dry biomass, and shifted F. betulina transcription toward carbon acquisition, transport, stress adaptation, and multiple biosynthetic gene clusters.
FOS Lactobacillus-Minimal Core Gut-Liver SynCom
A defined seven-strain in vitro human-gut model assembled by supplementing a four-strain minimal core with a probiotic Lactobacillus formulation and culturing the resulting whole community in modified MRS medium with 2% fructooligosaccharides. The probiotic arm contained Lactiplantibacillus plantarum PBS067, Lactobacillus acidophilus PBS066, and Limosilactobacillus reuteri PBS072, while the minimal core contained Bacteroides cellulosilyticus CL02T12C19, Clostridium symbiosum WAL-14673, Flavonifractor plautii 1_3_50AFAA, and Escherichia coli ATCC 25922. Finazzi et al. quantified strain dynamics by RT-qPCR, assayed Lactobacillus FOS-utilization genes, profiled SCFAs and organic acids by GC-MS, and tested culture-derived metabolites on palmitate-induced steatotic HepG2 cells.
Four-Species Aerobic Lung Microbiome Model
A simplified artificial lung microbiome model assembled as an aerobic four-species co-culture of Pseudomonas koreensis, Rothia aeria, Neisseria cinerea, and Streptococcus downei. The model was maintained for 10 days at 34°C in brain heart infusion medium and validated with qPCR, viability PCR, conventional microbiology, and metaproteomics to provide a controlled platform for lung microbiome interaction and pulmonary-drug studies.
Four-Species Pathogen Community Under DMS3vir Phage Predation
An artificial four-species bacterial community — Pseudomonas aeruginosa PA14, Acinetobacter baumannii, Staphylococcus aureus, and Burkholderia cenocepacia — propagated for 10 days in lysogeny broth with and without the lytic phage DMS3vir, which infects P. aeruginosa through its Type IV pilus. Without phage, P. aeruginosa outcompetes the other three species. Adding DMS3vir drives P. aeruginosa nearly extinct and releases A. baumannii into dominance, while maintaining community diversity. The experiment is fully factorial over all 1-, 2-, 3-, and 4-species combinations and over two P. aeruginosa clones (wild type and an isogenic CRISPR-KO), which lets the record separate the community consequences of phage predation from the consequences of which resistance mechanism evolves: the two resistance routes gave largely indistinguishable community dynamics, and surface-based resistance classified by the authors as Type IV pilus mutation became dominant even where CRISPR-Cas was functional. That classification is phenotype-based; the receptor mutants were not sequenced in this study. This is a one-phage-on-many-bacteria (1-N) system in the sense of doi:10.1146/annurev-virology-100424-123645 — a single phage population against a bacterial community — and the record exists to carry the community-level consequences of phage predation rather than the phage-host pair itself. The tested pairwise-fitted generalized Lotka-Volterra models failed to predict the larger community. This supports a context-dependence interpretation without establishing a general impossibility of prediction from pairwise information. Adding three-species data improved quantitative prediction without phage; with phage, quantitative failure remained despite a qualitative competitive-release prediction.
Fucoidan Seven-Degrader Combinatorial SynCom
A defined seven-member marine bacterial SynCom assembled from the fucoidan degraders F12, F40, F56, F94, V25, V69, and V4 to quantify complementary fucose- and rare-sugar-monomer degradation of Fucus vesiculosus fucoidan. Sichert et al. constructed all 127 possible non-empty combinations of these degraders at equal OD600 in MBL medium with 0.2% fucoidan, measured total and monomer-specific degradation by liquid chromatography mass spectrometry, and resolved a functionally synergistic community landscape in which specialized degrader combinations reached up to 97.1% total degradation.
Garlic Rhizosphere Pseudomonas SynCom6
A six-strain Pseudomonas SynCom selected from garlic rhizosphere microbiome data for plant growth promotion.
GENIA Nine-Member Multi-Pollutant Bioremediation SynCom
A nine-member bacterial synthetic community selected by the GENIA genome-informed machine-learning framework for simultaneous degradation of lignin, atrazine, and perfluoroalkyl substances. The SynCom combines Atlantibacter hermannii, Bacillus cabrialesii, Bacillus licheniformis, Bacillus pseudomycoides, Micrococcus luteus, Paenibacillus polymyxa, Pantoea dispersa, Pseudomonas fulva, and Pseudomonas pergaminensis isolates from xenobiotic-enriched cotton detritusphere material. In controlled M9 minimal-medium flask assays, the assembled consortium removed more PFOS, atrazine, and lignin than any single member and retained all nine strains during full-length 16S rRNA tracking.
Geobacter-Clostridium Interspecies Electron Transfer Coculture
A two-member consortium consisting of Geobacter sulfurreducens and Clostridium pasteurianum in which interspecies electron transfer modulates glycerol fermentation. G. sulfurreducens acts as an exoelectrogen and grows using C. pasteurianum as its sole electron acceptor; the resulting electron uptake induces a metabolic shift in C. pasteurianum's glycerol fermentation pathway, redirecting carbon flux away from ethanol and butanol production toward increased 1,3-propanediol (PDO) and butyrate production (+37% and +38% respectively). The shift is driven by a strikingly small electron uptake - under 0.6% of the electrons consumed by C. pasteurianum - and the relationship between G. sulfurreducens growth and the metabolite shift is non-linear. MECHANISM CONTESTED - do not read this record as establishing contact-dependent DIET. The discovery study (PMID:28287150) did not demonstrate physical contact, conductive pili, or nanowires in this coculture; its own discussion reports heterogeneous nanowire-rich and nanowire-poor cells and proposes growth on conductive materials as a future way to "ensure electrical connections", i.e. connection was not established. The same group's mechanistic follow-up (PMID:34939136) concluded the interaction is MEDIATED, proposing a diffusible cobamide acting on glycerol dehydratase, with a transmembrane flavin-bound polyferredoxin / cytochrome b5-rubredoxin electron-entry route offered only as a putative reinforcement. Both mechanisms remain putative; see discussion kg-geobacter-clostridium-contact-dependence-contested.
Geobacter-Methanosaeta DIET Community
A syntrophic two-member consortium consisting of Geobacter metallireducens and Methanosaeta harundinacea that performs direct interspecies electron transfer (DIET) during ethanol oxidation. G. metallireducens oxidizes ethanol and transfers electrons directly to M. harundinacea via electrically conductive pili and aggregates, bypassing the need for diffusible electron carriers like H2 or formate. M. harundinacea uses these electrons to reduce CO2 to methane. This coculture forms conductive aggregates and achieves stoichiometric conversion of ethanol to methane via DIET. Unlike hydrogen-mediated syntrophy, DIET relies on biological electrical connections between cells, with conductive aggregates serving as conduits for long-range electron transfer. M. harundinacea is an obligate acetoclastic methanogen that can also accept electrons via DIET for CO2 reduction, making it unique among acetoclastic methanogens in supporting direct electron transfer mechanisms.
Geobacter-Methanosarcina DIET Community
A syntrophic two-member consortium consisting of Geobacter metallireducens and Methanosarcina barkeri that performs direct interspecies electron transfer (DIET) during ethanol oxidation. G. metallireducens oxidizes ethanol and transfers electrons directly to M. barkeri via electrically conductive pili (e-pili), bypassing the need for diffusible electron carriers like H2 or formate. M. barkeri uses these electrons to reduce CO2 to methane. This coculture forms aggregates and achieves stoichiometric conversion of ethanol to methane via DIET. Unlike hydrogen-mediated syntrophy, DIET relies on biological electrical connections between cells, with pili serving as conduits for long-range electron transfer. M. barkeri is unique as a methanogen capable of using either H2 or electrons from DIET for CO2 reduction, making it a model organism for studying electrical connections in microbial communities.
Geobacter-Pseudomonas Formate-Fumarate Electroactive Coculture
A defined electroactive syntrophic coculture pairing Geobacter sulfurreducens with Pseudomonas aeruginosa in a restricted formate-fumarate medium. The community was used to study interspecies electron transfer and adaptive shifts from syntrophy toward competition. Early coculture growth depends on cooperative metabolism and direct interspecies electron transfer associated with Geobacter cytochromes, while adapted cocultures show increased Geobacter dominance and hydrogen/formate-linked electron-transfer features. The system is relevant to DOE biogeochemistry and bioelectrochemical applications because Geobacter-Pseudomonas interactions connect extracellular electron transfer, metal cycling, and microbial community modeling.
Ginseng CL95 Rusty Root Rot Biocontrol SynCom
A five-member synthetic bacterial community built from ginseng-associated biocontrol strains to suppress Ilyonectria robusta rusty root rot while promoting Panax ginseng growth. Tian et al. screened 98 consortia built from ten isolates and identified CL95, a 1:1 mixture of Bacillus velezensis NJ13, Bacillus velezensis NT35, Bacillus amyloliquefaciens FG14, Pseudomonas chlororaphis TU26, and Pseudomonas thivervalensis JI6, as the most effective field treatment, with 66.67% rusty-root-rot control efficacy.
GLBRC Exometabolite Transwell SynCom System
A synthetic community assay system for probing chemically mediated microbial interactions through shared exometabolites.
GLBRC Populus Variovorax SynCom28
A defined, genome-resolved 28-strain synthetic community of Variovorax isolates from Populus deltoides and Populus trichocarpa roots. The community was used to identify strain-level partitioning between rhizosphere and endosphere compartments and genomic traits associated with endosphere specialization.
GLBRC Ultra-Filtered Milk Permeate Fermentation Community
A fermentative microbial community maintained in a 282-day continuous bioreactor experiment fed ultra-filtered milk permeate (UFMP), a low-value dairy coproduct. Originally inoculated from an acid-phase digester at the Nine Springs Wastewater Treatment Plant (Madison, WI). Metagenome-assembled genomes (MAGs) revealed functional partitioning between phyla: Actinobacteriota members (Olsenella, Bifidobacterium, Pauljensenia) degrade lactose via the Leloir pathway and bifid shunt, producing acetic, lactic, and succinic acids. Firmicutes members (Clostridium, Agathobacter) perform chain elongation via reverse beta-oxidation, converting lactic acid, ethanol, or lactose into butyric, hexanoic, and octanoic acids. This cross-feeding between Actinobacteriota (acid producers) and Firmicutes (chain elongators) forms the core metabolic network enabling conversion of dairy waste into renewable chemicals via the carboxylate platform.
Glutamicibacter S11 Aquaculture Nitrogen Removal SynCom
A two-strain synthetic Glutamicibacter consortium, S11, composed of Glutamicibacter arilaitensis NFB2-4 and Glutamicibacter nicotianae CYN-C5. Su et al. isolated both heterotrophic nitrification-aerobic denitrification strains from cattle manure and aquaculture sediments, combined them as consortium S11, and reported synergistic ammonium- and nitrite-nitrogen removal in aquaculture wastewater assays, a hydrophilic sponge recirculating system, and an industrial-scale recirculating aquaculture trial.
Grassland Soil Wet-Up Virus-Host Community
A grassland soil virus-host community whose dynamics were measured following rewetting of a seasonally dry California Mediterranean-climate soil. Dry soil holds a diverse but low-biomass reservoir of virions, of which only a subset thrives following wet-up. Quantitative isotope tracing, time-resolved metagenomics, and viromics show viral richness declines by 50 percent within 24 hours post wet-up while viral biomass increases four-fold within one week. Lytic, not lysogenic, cycles dominate the response. Viruses drive a measurable and continuous rate of cell lysis, accounting for up to 46 percent of microbial death one week after wet-up, contributing to microbial biomass turnover and the widely reported post-wet-up CO2 efflux.
Groundwater Elusimicrobia Diverse Metabolisms Community
A genomic survey of 94 draft-quality, non-redundant Elusimicrobia genomes (30 newly reconstructed) from diverse animal-associated and natural environments. Genomes group into 12 clades, 10 previously lacking reference genomes. Groundwater-associated Elusimicrobia are predicted to be capable of heterotrophic or autotrophic lifestyles, oxygen- or nitrate/nitrite-dependent respiration, degradation of a variety of organic compounds, and Rhodobacter nitrogen fixation (Rnf) complex-dependent acetogenesis using hydrogen and carbon dioxide. Two groundwater-associated clades often encode a new nitrogenase paralog co-occurring with an extensive suite of radical S-Adenosylmethionine (SAM) proteins. Similar genomic loci occur in Gracilibacteria and Myxococcales genomes and are predicted to reduce a tetrapyrrole, possibly to form a novel cofactor. The animal-associated clades nest within free-living clades, supporting an evolutionary trajectory from free-living to animal-associated lifestyles via genome reduction.
Gulf of Mexico Oil-Degrading Consortium
A marine bacterial consortium from the Gulf of Mexico designed for bioremediation of oil-contaminated seawater. The consortium consists of four bacteria: Pseudomonas sp., Halopseudomonas aestusnigri GOM5, Paenarthrobacter sp. GOM3, and Alcanivorax sp. Together, they achieve 62% oil removal over 75 days, degrading both n-alkanes and 12 polyaromatic hydrocarbons (PAHs) including fluorene, dibenzothiophene, phenanthrenes, and pyrene. The consortium exhibits stable population dynamics with distributed metabolic loads across members.
Halobacillus Multi-Strain Halophilic PGPR Consortium for Black Gram Salinity Tolerance
Compatible three-strain halophilic plant growth-promoting bacterial (HPGPB) consortium comprising Halobacillus marinus MKM3, Halobacillus halophilus MKM4, and Halobacillus halophilus MKM11 applied to black gram (Vigna mungo L. varieties VBN8 and VBN11) under 50 and 100 mM NaCl stress. The consortium improves ionic balance, reduces Na+ accumulation and lipid peroxidation, enhances antioxidant enzyme activities, and increases grain yield by up to 38% under saline greenhouse conditions.
HAMBI Carbon-Gradient 16-species SynCom
A 16-species HAMBI synthetic bacterial community serially transferred for 16 days in a fully factorial panel of 96 glucose/R2A resource environments spanning eight total-carbon concentrations and 12 levels of R2A-derived carbon. The experiment tested how total carbon availability and resource complexity structure community-state shifts, with Aeromonas caviae, Pseudomonas chlororaphis, and Citrobacter koseri dominating low-, intermediate-, and high-carbon states.
Hanford 300 Area Unconfined Aquifer Community
A natural, contaminant-impacted groundwater microbial community from the Hanford Site 300 Area Integrated Field Research Challenge site in eastern Washington. 16S rRNA gene pyrosequencing of groundwater bacteria and archaea across three well clusters and multiple depths showed strong temporal and spatial community dynamics linked to Columbia River water intrusion, depth, nitrate, uranium, and redox conditions. The community includes Proteobacteria, Bacteroidetes, Actinobacteria, Acidobacteria, OP3, low-abundance archaea, and functional guilds such as putative methane oxidizers, sulfur oxidizers, ammonia-oxidizing archaea, and metal reducers.
hCom2 Complex Gut Microbiome
A complex defined human gut microbiome assembled from hCom1 and iteratively augmented after fecal challenge to improve stability and colonization resistance in gnotobiotic mice.
Hexamine Formaldehyde Consortium C6
Consortium C6 is a six-member hexamine- and formaldehyde-removing bacterial formulation assembled from environmental isolates in AS broth containing hexamine. The consortium combines two Brevundimonas diminuta isolates, two Brucella pseudintermedia isolates, Ochrobactrum sp. SRCHD06, and Micrococcus luteus SRCHD02 in a 1:1:1:1:1:1 design. C6 outperformed smaller tested combinations in suspended culture, formed a strong biofilm, and retained hexamine, formaldehyde, and chemical-oxygen-demand removal after low-dose cobalt-60 gamma irradiation, especially in the polypropylene-Raschig-ring biofilm format.
High-Ammonia Biogas 0B Butyrate-Oxidizing Enrichment
A thermophilic, high-ammonia syntrophic butyrate-oxidizing enrichment culture maintained in yeast-extract-free 0B medium after derivation from a propionate-fed biogas reactor community. The enrichment was inoculated from a laboratory bioreactor that originated from large-scale food- and slaughterhouse-waste digestate, then followed as a single long-running, butyrate-fed anaerobic culture at 51 C for 972 days. Amplicon and metagenomic analyses recovered MAG1, a putative novel ammonia-tolerant syntrophic butyrate oxidizer proposed as Candidatus Syntrophothermus ammoniitolerans, together with a putative syntrophic acetate-oxidizing MAG related to Candidatus Thermosyntrophaceticus schinkii and hydrogenotrophic Methanoculleus and Methanothermobacter MAGs that likely close the network by consuming formate or H2 and producing methane.
High-Solids Switchgrass Methanogenic Microbiome
A thermophilic, anaerobic, semi-continuously fed methanogenic enrichment microbiome cultivated on mid-season switchgrass at high solids loadings. The community maintained fractional carbohydrate solubilization as solids loading increased from 30 to 150 g/L, with methane and carbon dioxide as the main steady-state products. Metaproteomics identified bacterial carbohydrate-active enzyme strategies and archaeal methanogenesis functions relevant to DOE bioenergy efforts to understand robust lignocellulose deconstruction under industrially relevant process conditions.
Honeybee Core-20 Defined Microbiota
A stably transmitted 20-strain synthetic gut microbiota from honeybee intestine that primes host immunity and reduces Hafnia alvei prevalence.
Horonobe and Mizunami Underground Research Laboratory Subsurface Microbiome
A multi-year, depth-resolved groundwater microbiome study of the Horonobe (sedimentary rock) and Mizunami (granitic rock) Underground Research Laboratories in Japan, sampling defined intervals between 140 and 400 m below the surface over four years. Draft genomes were reconstructed for more than 90 percent of all detected organisms. The Horonobe and Mizunami microbiomes are dissimilar at the community level, but hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds, and sulfate reduction are well represented in both, while methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL. High fluid flow zones and tunnel proximity select for candidate phyla radiation bacteria in the Mizunami URL. Approximately one third of genomically defined organisms have near-identical genotypes at multiple depths within Horonobe, and closely-related species recur in three other USA subsurface environments, constraining expectations of global subsurface biodiversity.
Hualgayoc Acidic Sulfate-Reducing AMD Consortium
An engineered acidophilic sulfate-reducing bacterial enrichment derived from acidic sediments of the abandoned BSA-100 mining tunnel in Hualgayoc, Cajamarca, Peru, and assayed for bioremediation of synthetic acid mine drainage at pH 2.9. The glycerol-fed, sulfate-amended enrichment raised the synthetic AMD pH to 6.1 and removed 100% of Zn2+, more than 99% of Fe2+, and more than 94% of Al3+ after 160-200 days. Genome-resolved metagenomics recovered two high-quality dominant sulfate-reducing MAGs, Desulfosporosinus sp. MAG003 and Acididesulfobacillus sp. MAG013, whose inferred carbon metabolisms suggest a cooperative route in which Desulfosporosinus starts sulfate reduction on glycerol at pH around 3.0 and Acididesulfobacillus continues sulfate reduction on acetate once the culture rises to pH around 4.0.
Human Gut Four-Member Proteome-Complementarity Consortium
A defined four-member consortium of metabolically distinct human gut anaerobes — Eubacterium hallii, Roseburia intestinalis, Marvinbryantia formatexigens and Faecalibacterium prausnitzii — assembled in all pairwise combinations and as the full community, on distinct carbon sources, and profiled by species-resolved proteomics. The finding is regulatory rather than compositional: bacteria modulate protein abundance in response to specific partners, and those partner-specific shifts reduce functional overlap between members and are frequently associated with increased community productivity. Biotic interactions, not the carbon source, dominated proteomic variation. The record captures a community whose members divide labour by changing what they express in each other's presence, so metabolic complementarity is an outcome of regulation rather than a fixed property of the members.
Hyperaccumulator-Derived Endophytic SynCom-NS for Brassica juncea Cadmium Phytoextraction
Four-strain core endophytic synthetic bacterial community (SynCom-NS)—composed of Pseudomonas izuensis SaPI1, Leifsonia shinshuensis SaLS1, Brucella anthropi (Ochrobactrum anthropi) SaOA1, and Novosphingobium lindaniclasticum SaNL1 originally isolated from the hyperaccumulator Sedum alfredii—applied to the high-biomass crop Brassica juncea under cadmium stress. SynCom-NS increases soil Cd bioavailability, upregulates root HMA4 metal transporter expression and glutathione-mediated antioxidant defenses, increases plant fresh weight by 82%, and amplifies shoot Cd accumulation 4.07-fold.
Iberian Pit Lake Stratified Community
A permanently stratified (meromictic) acidic pit lake community from the Iberian Pyrite Belt in southwestern Spain/Portugal, distinguished by dramatic vertical metabolic zonation and subsurface anaerobic processes in an extreme acid mine drainage environment. The pit lake ecosystem exhibits three distinct layers: an upper oxic mixolimnion (pH 2.2-3.1, 0-3m depth), a chemocline transition zone (11m), and an anoxic monimolimnion (pH 3.0-4.5, 35m depth). The upper layer is dominated by acidophilic green algae (Coccomyxa onubensis) and heterotrophic bacteria (Acidiphilium), while the chemocline hosts intense sulfate reduction and iron cycling by specialized Proteobacteria (Desulfomonile, Candidatus Acidulodesulfobacterium). The deep anoxic layer harbors archaeal heterotrophs (Thermoplasmatales, 46% of sequences) that scavenge organic carbon and perform sulfide oxidation using trace oxygen, along with iron-reducing bacteria (Geobacter) and subsurface methanogens (Methanobrevibacter, Methanospirillum). The permanent stratification creates steep geochemical gradients with iron concentrations increasing from 2 mM Fe³⁺ in surface waters to 113 mM Fe²⁺ at depth, sulfate ranging from 26-126 mM, and oxygen transitioning from oxic to completely anoxic conditions. This system represents a natural laboratory for studying coupled aerobic-anaerobic metabolism, metal cycling, biosulfidogenesis, and subsurface methanogenesis under polyextreme conditions (acidity, metals, anoxia). The Iberian Pyrite Belt pit lakes demonstrate how microbial stratification can support complex biogeochemical cycling and potential natural attenuation of toxic metals through sulfide precipitation.
Industrial Bioleaching Reactor Consortium
An industrial-scale moderately thermophilic acidophilic microbial consortium operating in continuous and batch bioreactors for metal extraction from sulfide ores and concentrates. This consortium represents a unique system with complete genomic characterization of six key organisms: Acidiplasma sp., Acidithiobacillus caldus, Cuniculiplasma divulgatum, Ferroplasma acidiphilum, Ferroplasma sp., and Thermoplasmatales archaeon. The community operates at moderate thermophilic temperatures (40-50°C) and extremely low pH (1.5-2.0), oxidizing ferrous iron and reduced sulfur compounds to generate ferric iron (Fe³⁺) and sulfuric acid for dissolving chalcopyrite (CuFeS₂) and other metal sulfides. Comparative analysis across reactor modes reveals distinct population dynamics, with Acidithiobacillus caldus predominating early, Sulfobacillus acidophilus predominating in the middle stage, and Ferroplasma thermophilum accounting for the greatest proportion in the final stage. The adapted consortium achieves exceptional copper extraction of 60.4% from 20% pulp density chalcopyrite concentrate in 25 days. Operating under controlled carbon sources (CO₂, molasses) and temperature gradients (40-50°C), this system demonstrates how operational parameters shape microbial community structure and metal recovery efficiency. The availability of six complete reference genomes (PRJNA976529) enables genomic-level investigation of biooxidation mechanisms, making this the most comprehensively characterized industrial bioleaching consortium for biotechnological applications in extractive metallurgy.
Industrial Milk-Line Four-Species Model Biofilm
A laboratory four-species bacterial biofilm model derived from an industrial milk pasteurization-line biofilm. The community contains Rhodocyclus sp., Pseudomonas fluorescens, Kocuria varians, and Bacillus cereus, forms reproducible biofilms, and was used to resolve dynamic positive and negative interspecies interactions, including a Bacillus cereus thiocillin I-mediated negative interaction that shapes species distribution and robustness.
Infant Gut DNA Phageome Succession Community
A longitudinal infant gut DNA bacteriophage community reconstructed from 819 fecal metagenomes from 28 full-term and 24 preterm infants and their mothers across the first 3 years of life, using a large phage sequence database and strain-resolved analyses. Early-life phageome richness increases over time and reaches adult-like complexity by age 3. Approximately 9 percent of early phage colonizers persist for 3 years and are predominantly maternally transmitted phages infecting Bacteroides, with higher persistence in full-term infants. Phages with stop-codon reassignment are more likely to persist than non-recoded phages, and in-frame reassigned stop codons increase over the 3-year window. Maternal seeding, stop-codon reassignment, host CRISPR-Cas locus prevalence, and phage diversity together drive stable viral colonization.
Infant Gut Strain Persistence and Maternal Seeding Community
A longitudinal infant gut bacterial community studied at strain resolution over the first year of life across 13 full-term and 9 preterm infants and 17 mother-infant pairs. Infants' initially distinct microbiomes converge by age 1 year. Approximately 11 percent of early colonizers, primarily Bacteroides and Bifidobacterium, persist through the first year and are more prevalent in full-term than in preterm infants. Maternal gut strains are significantly more likely to persist in the infant gut than other strains. Enrichment in genes for surface adhesion, iron acquisition, and carbohydrate degradation may explain why some strains persist through the first year of life.
Infant-gut Prebiotic-response SynCom
A defined synthetic microbial community (SynCom) modeling the early-life (infant) gut, studied alongside donor-derived infant faecal fermentations to dissect how prebiotic substrates reshape microbial and metabolic responses. Human milk oligosaccharides (HMOs) and galacto-oligosaccharides (GOS) robustly promote bifidobacterial expansion, while Bacteroides/Phocaeicola species are modulated in a feeding-mode- and substrate-dependent manner. The SynCom reveals extensive cross-feeding networks and substrate-dependent interaction rewiring, with Phocaeicola vulgatus acting as a context-dependent ecological hub that disproportionately shapes succinate and propionate production and alters Escherichia coli metabolic activity. Competitive outcomes are driven not only by acidification but by the chemical identity of fermentation products, with lactate exerting species-specific inhibition independent of bulk pH.
Ion-Adsorption REE Indigenous Community
A highly diverse indigenous microbial community in ion-adsorption rare earth element (REE) deposits in weathering profiles of South China, demonstrating remarkable selectivity for heavy rare earth elements (HREE) through bacterial teichoic acid binding. This natural community comprises over 700 genera spanning bacterial (84.2% dominated by Proteobacteria 46.9%, Acidobacteria 14.6%, Actinobacteria 9.0%, Firmicutes 6.3%) and fungal (Ascomycota 47.8%, Basidiomycota 40.4%) lineages distributed through weathering profiles up to 40 meters depth. The community exhibits unique HREE vs LREE fractionation capability, with Gram-positive bacteria (Bacillus, Micrococcus) preferentially adsorbing HREE (82-85% efficiency) compared to LREE (70-78%), driven by teichoic acids in cell walls that provide selective phosphate binding sites for heavier lanthanides. Removal of teichoic acids reduces REE adsorption from 65.5% to 17.8%, confirming their critical role. The community accelerates REE mineralization in supergene weathering environments through bioweathering of granite, dissolution of REE-bearing minerals, and biosorption-mediated HREE enrichment. Ion-adsorption deposits represent the world's main source of strategically critical HREE (Dy, Y, Tb, Eu) used in permanent magnets and phosphors, with over 40 deposit sites in South China. The indigenous microbial community functions across pH gradients (4.3-7.0), exhibits oligotrophic K-strategist adaptations (Acidobacteria), and demonstrates co-localization of ytterbium with phosphate-rich cell walls. This natural HREE fractionation system offers a sustainable model for selective REE recovery and explains the geological genesis of commercially valuable HREE-enriched clay deposits.
Jala Maize PGPB SynCom
Synthetic microbial communities assembled from plant growth-promoting bacteria of the Jala maize landrace to improve Zea mays growth and yield.
Jeff Dangl's SynComm 35
A 35-member synthetic community (SynComm 35) composed of genome-sequenced bacterial strains representing typical taxonomic diversity of Arabidopsis root commensals. This community was designed to interrogate plant immune responses, particularly pattern-triggered immunity (PTI/MTI). Of the 35 members, 10 are robust suppressors of MAMP-triggered immunity (flg22 response), 13 are partial suppressors, and 11 are non-suppressors. The community includes 32 strains isolated from Brassicaceae roots (mainly Arabidopsis), 2 strains from unplanted soil, and E. coli DH5α as a control. SynComm 35 collectively suppresses specific transcriptional sectors of plant immunity, particularly WRKY transcription factors, receptor-like kinases, and secondary metabolite biosynthesis genes, while suppressors achieve enhanced colonization capacity.
Jiangshui LAB Directed Fermentation SynCom
A three-strain lactic-acid-bacterial synthetic community combining Jiangshui isolates Y-5-3, Y-6-2, and HN for standardized traditional Chinese Jiangshui fermentation. The strains were selected from Gansu-province Jiangshui samples, assembled across 20 empirical ratios, and optimized to a Y-5-3:Y-6-2:HN ratio of 2:3:1. The optimized SynCom improved sensory score, increased total phenols and flavonoids relative to natural Jiangshui, reduced off-odors, and improved fermentation stability.
KB-1 Chlorinated Ethene Dechlorinating Consortium
KB-1 is a natural anaerobic bioaugmentation consortium used for reductive dechlorination of chlorinated ethenes in contaminated groundwater. The culture contains Dehalococcoides-related organohalide-respiring bacteria that convert tetrachloroethene and trichloroethene through chlorinated intermediates to ethene. Nondechlorinating acetogens, including Acetobacterium and Sporomusa, support the community by providing cobamide-related cofactors needed by Dehalococcoides.
KBase Models for Zahmeeth Original PLOS
Public KBase narrative centered on metabolic model editing, merged community modeling, and flux analyses for the Zahmeeth Original PLOS model set.
KBase ORT Workflow Community Model
Public KBase ORT workflow narrative that includes genome annotation, metabolic model reconstruction and gapfilling, merged community model generation, and flux balance analysis.
KBase Synthetic Bacterial Community in R2A Medium
Public KBase narrative for community modeling and flux balance analysis of a synthetic bacterial community in R2A medium. The workflow applies gapfilling, merged community model construction, and FBA for a Populus-associated SynCom context.
Kefir Flavor Lentilactobacillus-Kluyveromyces Coculture
A defined cross-kingdom coculture of milk-kefir isolates Lentilactobacillus kefiri SLAM023B and Kluyveromyces marxianus SLAM005Y. One study reports complementary flavor-metabolism roles and enhanced ester synthesis during milk kefir fermentation; a second publication evaluates the same exact pair as a combined probiotic preparation in animal host models.
Klebsiella-Arthrobacter KZ Phenanthrene-Cadmium SynCom
A defined two-isolate bacterial consortium, KZ, assembled from Klebsiella sp. CW-D3T and Arthrobacter sp. SZ-3 to degrade phenanthrene under 25 mg/L Cd2+ stress. KZ outperformed the two monocultures by 1.2-1.9-fold for phenanthrene degradation and mineralization under cadmium stress. The division of labor inferred from biomass-normalized enzyme assays assigned stronger upstream 2H1N conversion to SZ-3 and more than 80% of downstream mineralization to CW-D3T, while metagenomics associated cadmium tolerance with CW-D3T efflux-pump/antioxidant genes and the SZ-3 oxidative-stress response.
Komagataella-E. coli Co-inducible Biosynthesis Coculture
A defined two-member engineered yeast-bacterium consortium pairing Komagataella phaffii with Escherichia coli for co-inducible relayed biosynthesis of natural products. Low-level glucose-responsive and blue-light-responsive transcriptional systems were rebuilt separately for the two hosts so a single signal could co-induce compound synthesis in coculture. After pathway redirection, genome mining, and rewiring of acyl-donor degradation targets, the living consortium produced the reporter molecule simvastatin from a simple carbon source and also supported inducible biosynthesis of (2S)-naringenin.
Kombucha KMC-IMBG1 Fermentation Community
A Ukrainian kombucha microbial community variant, KMC-IMBG1, profiled by culture-dependent isolation and 16S/ITS metabarcoding across sweetened black-tea and honey/cabbage-brine microenvironments. The core community contains cellulose-forming acetobacteria, especially Komagataeibacter and Gluconobacter, together with dominant yeasts such as Pichia and Brettanomyces/Dekkera; growth conditions alter the accessory community and yeast composition.
Lac Pavin Permanently Stratified Lake Community
A depth-stratified microbial community in Lac Pavin, a deep, permanently stratified lake in central France. Genome-resolved analyses across the oxygen gradient reveal enrichment of distinct C1 and CO2 fixation pathways in the oxic lake interface and the anoxic zone and sediments, with oxygen shaping non-CPR bacterial and archaeal metabolic strategies. RuBisCO genes are detected throughout the water column and sediments, including form II/III and form III-related enzymes encoded by Candidate Phyla Radiation (CPR) bacteria in the water column and DPANN archaea in the sediments. Methane oxidation and its byproducts are largely spatially separated from methane production, which is mediated by diverse sediment methanogens that vary on the centimeter scale.
Lake Washington Methane-Oxygen Methylotroph Community
A methane-consuming freshwater lake sediment community from Lake Washington, Seattle, represented by methane-fed sediment microcosms and follow-up community modeling studies. Methane addition selects both bona fide methane-oxidizing Methylococcaceae and non-methanotrophic methylotrophic Methylophilaceae, supporting a guild-based community rather than a single-organism methane oxidation model. Oxygen tension structures specific partnerships: Methylosarcina and Methylophilus dominate higher-oxygen microcosms, whereas Methylobacter and Methylotenera dominate lower-oxygen microcosms. The system is DOE-relevant because it links methane mitigation, freshwater sediment carbon cycling, methylotroph ecology, and genome-scale modeling of methane-cycling communities.
LBNL Brachypodium Drought SynCom15
A stable 15-member Brachypodium rhizosphere SynCom constructed with network and cultivation-guided methods to promote drought resilience.
LBNL Human Gut Interaction SynCom
A diverse synthetic human gut microbiome community used with model-guided time-series experiments to infer pairwise ecological interactions and metabolic drivers of coexistence.
LBNL Switchgrass Soil SynCom16
A 16-member synthetic soil community from switchgrass-associated soil, optimized for reproducible in vitro and EcoFAB plant-microbe experiments.
Legume-Rhizobia Mars Simulant Symbiosis
A model legume-rhizobia nitrogen-fixing symbiosis tested for its ability to establish on Mars soil simulants. The community pairs the model legume Medicago truncatula with two of its symbiotic rhizobial partners, Sinorhizobium meliloti and Sinorhizobium medicae. Plants were grown on different grades of the Mojave Mars Simulant (MMS-1: Coarse, Fine, Unsorted, Superfine) and the MMS-2 simulant. Root nodules developed on M. truncatula roots grown on the Mars simulants comparably to plants grown on sand, and nifH (a reporter gene for nitrogen fixation) expression was detected inside the nodules, demonstrating that the simulants can support the legume-rhizobia symbiosis. Total plant mass was higher on MMS-2 than on MMS-1 and its grain-size variants, indicating that simulant chemical composition matters more than grain size; MMS-2 Superfine was recommended for future studies. The system is a model for beneficial plant-microbe associations enabling sustainable, nitrogen-fixing agriculture on Mars, exploiting the nitrogen present in the martian atmosphere.
Leptolyngbya-Pseudomonas Mangrove Growth-Promotion Coculture
A defined mangrove cyanobacterium-bacterium coculture pairing Leptolyngbya lignicola with the associated bacterium Pseudomonas monteilii, both isolated from mangrove waters of Bhitarkanika, Odisha, India. Dash et al. used axenic L. lignicola comparisons, morphology, biochemical assays, scanning electron microscopy, pigment and biomass measurements, and metabolite profiling to show a close physical association, a faster and higher co-culture biomass peak, and Pseudomonas-linked production of indole-3-acetic acid, indole-3-butyric acid, vitamin B12, and siderophores.
Lotus Lj-SC3 Synthetic Community
A 16-member synthetic community (Lj-SC3) derived from Lotus japonicus roots and nodules, designed to study host preference and community assembly dynamics in legume-microbe interactions. The community represents bacterial families from the Lj-SPHERE culture collection, including nitrogen-fixing symbionts from Rhizobiaceae and Phyllobacteriaceae families, as well as commensal bacteria from Burkholderiaceae, Oxalobacteriaceae, Pseudomonadaceae, and Microbacteriaceae. This community exhibits host preference when co-inoculated with Arabidopsis-derived strains, preferentially colonizing Lotus roots in a community context. The SC3 community enables investigation of nitrogen fixation, nodulation, priority effects during microbiota assembly, and bacterial invasiveness in the rhizosphere.
Lunar and Martian Simulant PGPB Lettuce SynCom
A defined four-strain plant growth-promoting bacterial (PGPB) consortium designed for space-agriculture (In-Situ Resource Utilization) research, composed of Azotobacter chroococcum 76A, Priestia megaterium EL5, Methylobacterium populi VP2, and Kosakonia pseudosacchari TL13. The strains belong to the microbial collection of the Department of Agricultural Sciences of the University of Naples Federico II and were selected for complementary plant growth-promoting traits (nitrogen fixation, phosphate solubilization, phytohormone biosynthesis) and for mutual non-antagonism in dual-culture assays. In a greenhouse pot experiment, the consortium was combined with green compost derived from plant residues (pH 8.25, low C/N ratio) to improve lettuce (Lactuca sativa cv. Grand Rapids) growth on commercial Lunar (LHS-1) and Martian (MMS-1) regolith simulants with zero external chemical input aside from the compost. Compost amendment increased lettuce biomass and nutrient bioavailability, and PGPB inoculation enhanced leaf biomass and mineral nutritional content while significantly increasing the copy number of functional marker genes for nitrogen fixation (nifH), alkaline phosphatase (phoD), and phytase (BPP) in non-amended substrates. The system is a Bioregenerative Life Support System model relevant to regolith-agriculture and long-term space missions.
Lunar Regolith Simulant Phosphorus-Solubilizing Bacteria for Nicotiana benthamiana
A defined set of phosphorus-solubilizing bacteria (PSBs) assembled to improve the fertility of lunar regolith simulant for in-situ resource utilization (ISRU) agriculture in bioregenerative life support systems. Five commonly used microbial-fertilizer strains were tested on a CAS-1 lunar soil simulant: Bacillus mucilaginosus (AS1.232), Bacillus megaterium (AS1.217), Bacillus subtilis (CMCC 63501), Bacillus licheniformis (ATCC 11946), and Pseudomonas fluorescens (ATCC 13525). In a 21-day bio-improving experiment followed by a 24-day Nicotiana benthamiana cultivation experiment, three of the strains - Bacillus mucilaginosus, Bacillus megaterium, and Pseudomonas fluorescens - tolerated the lunar regolith simulant conditions and dissociated insoluble inorganic phosphorus from the simulant. The mechanism is chemolithoheterotrophic organic-acid production: the bacteria synthesize organic acids (e.g. oxalic, citric, tartaric acids) from carbon sources in the medium, lowering the pH and chelating metal ions in insoluble phosphates such as Ca3(PO4)2, FePO4, and AlPO4, thereby releasing available phosphate. PSB treatment raised the available phosphorus content of the simulant and promoted Nicotiana benthamiana growth, with the largest improvement when the simulant was pre-cultured with PSBs 18 days before sowing. The work establishes a microbiological route to convert lunar regolith into a plant-cultivation substrate for future lunar bases.
Lupinus SC-7 Rhizosphere SynCom
A defined twelve-strain bacterial synthetic community, SC-7, assembled from representative Bradyrhizobium, Micromonospora, Caulobacter, Kribbella, Pseudomonas, Pseudoxanthomonas, Rhizobium, Sphingopyxis, Stenotrophomonas, Streptomyces, and Variovorax isolates from the wild Lupinus angustifolius microbiome. The study selected these strains from core-hub-associated, peripheral, and satellite genera in a lupin root co-occurrence network, mixed them at equal optical density for gnotobiotic FlowPot and non-sterile soil inoculation, and found that increasing SynCom complexity reshaped root-associated microbiota while SC-7 gave the strongest lupin growth and transcriptional response among the tested SynComs.
m-CAFEs Brachypodium Reduced Complexity Consortia
A systematic framework for assembling rhizosphere-derived Reduced Complexity Consortia (RCC) from Brachypodium distachyon roots grown in field soil from Angelo Coast Range Reserve, California. Enriched co-localized microbes with carbon substrates mimicking root exudates, generating 768 enrichments. Transferred every 3 or 7 days for 10 generations to develop fast and slow-growing reduced complexity communities. Keystone taxa identified within these networks belong to genera with plant growth-promoting traits. Tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks.
Magnetite Sulfate-Stress Anaerobic Microbiome
A H2/CO2-fed methanogenic mixed culture, inoculated from mesophilic anaerobic-digester sludge and cultivated in anoxic serum bottles, that was perturbed with sulfate and magnetite to test how a conductive Fe(II)/Fe(III) oxide reshapes sulfate-stressed anaerobic digestion. Vayena et al. (2026) compared a sulfate-free control with 0.6 and 1.2 g/L sulfate, with and without 10 g/L magnetite. At the moderate sulfate dose, magnetite increased methane production by 19% while retaining sulfate reduction and supporting a genome-resolved cooperative network among Methanoculleus methanogens, putative sulfate-reducing bacteria, Limnochordia homoacetogens, and Dethiobacteria syntrophic acetate oxidizers. Community genome-scale metabolic models for representative MAGs supported acetate, amino-acid, and carboxylate exchange among these guilds, but the paper explicitly leaves direct DIET validation for future experiments.
Maize Benzoxazinoid-Metabolizing SynComs
Two maize root bacterial SynComs sharing six common strains and differing in a seventh benzoxazinoid-metabolizing member.
Maize Drought Response SynCom
A plant-beneficial bacterial SynCom that modulates physiology and drought response of commercial maize hybrids.
Maize Root Simplified Bacterial Community
A representative 7-member bacterial community from maize rhizosphere, developed through selective iterations to model root-associated microbiome function. The community consists of Enterobacter cloacae AA4, Stenotrophomonas maltophilia AA1, Ochrobactrum pituitosum AA2, Herbaspirillum frisingense, Pseudomonas putida, Curtobacterium pusillum, and Chryseobacterium indologenes. This simplified community reproducibly assembles on root surfaces and provides biocontrol against Fusarium verticillioides, a phytopathogenic fungus. E. cloacae AA4 plays a keystone role, as its removal causes dramatic community composition changes.
Maize SC2 Root-Rot Biocontrol SynCom
A three-member maize-root synthetic microbial community refined from the C7 corn root consortium to improve Pythium torulosum biocontrol while preserving plant growth promotion. Kaki et al. selected SC2 as S4, S1, and S5: Enterobacter cloacae S4, Stenotrophomonas maltophilia S1, and Chryseobacterium indologenes S5. Plate assays showed P. torulosum inhibition comparable to C7, growth-chamber pot assays showed stronger maize protection and growth than C7 under P. torulosum challenge, and metabolite assays showed that SC2 had the highest measured indole-3-acetic acid production among C7, SC1, SC2, and SC3 together with significant siderophore activity on CAS agar.
MAMC-M48 Lignocellulose-Degrading Consortium
A minimal active microbial consortium (MAMC-M48) for lignocellulose degradation, optimized through reductive screening from 18 candidate strains. The 5-member consortium consists of Stenotrophomonas maltophilia JN40, Paenibacillus sp. PALXIL05, Microbacterium sp. UYFA68, Chryseobacterium taiwanense DUCC3723, and Brevundimonas sp. R3. Enriched from soil bacteria on sugarcane waste, this synthetic community achieves 50.6% degradation of all lignocellulose fractions, reaching 96.5% of the degradation rate observed with the full 18-species pool, demonstrating high efficiency with minimal complexity.
Mangrove Benzene MFC Bioanode Consortium
An engineered electrogenic bioanode enrichment derived from mangrove sediment collected in Vitoria, Espirito Santo, Brazil and acclimated in dual-chamber microbial fuel cells first on 1000.0 mg L-1 sodium acetate and then on increasing benzene concentrations up to 330.0 mg L-1. In the benzene-fed biofilm, Bacillus and Arcobacter became the two dominant 16S rRNA genus-level assignments, while Pelobacter and Pseudomonas remained lower-abundance detected genera. The acclimated MFC removed 98.7 +/- 2.4% benzene over 96 h while generating voltage on the bioanode.
Mars Meteorite EETA79001 Microbial Growth Panel
A defined four-member panel of microorganisms tested for their ability to grow on actual martian regolith, supplied as sawdust of the Mars meteorite EETA79001, rather than on a terrestrial simulant. The panel comprises the bacterium Escherichia coli B, the two cyanobacteria Eucapsis sp. and Chroococcidiopsis sp. strain Chr20-20201027-1, and the cold-adapted bacterium Planococcus halocryophilus. Each organism was cultivated separately on EETA79001 sawdust for up to 23 days under terrestrial conditions across regolith:water ratios from 4:1 to 1:10; the study demonstrates that real martian regolith can support microbial growth and does not contain bactericidal agents. The panel is an astrobiology / In-Situ Resource Utilization model relevant to putative martian life and to bio-sustainable human habitats on Mars. Members were assayed individually, so the record captures a shared capacity to grow on martian regolith rather than measured interspecies interactions.
Mars Regolith Cyanobacteria/Microalga Biofertilizer Panel
A defined four-member panel of photosynthetic microorganisms evaluated for their ability to grow using only martian resources (water and Mars Global Simulant MGS-1 regolith extract) under an Earth-like atmosphere, as candidates to support Mars colonization through oxygen and biomass production. The panel comprises three cyanobacteria — Anabaena cylindrica, Nostoc muscorum (NCBI Taxonomy: Desmonostoc muscorum), and Arthrospira platensis (NCBI Taxonomy: Limnospira platensis) — and the green microalga Chlorella vulgaris. Each species was grown separately in a martian regolith extract culture medium and monitored for 25 days by optical density and fluorometric parameters; Nostoc muscorum grew best, while Arthrospira platensis and Chlorella vulgaris did not thrive on the regolith extract. End-of-life biomass was then tested as a biofertilizing agent for the macrophyte Lemna minor, stimulating plant biomass to levels comparable to standard synthetic medium. The panel is an In-Situ Resource Utilization model for bioregenerative life support on Mars. Members were assayed individually, so the record captures a shared capacity to grow on martian regolith resources rather than measured interspecies interactions.
Medicago Nodule Biofertilizer SynCom
A four-strain nodule synthetic bacterial community with Ensifer and Pseudomonas members for Medicago sativa biofertilization under abiotic stress.
Mediterranean AM Fungal Six-Species SynCom
A six-species arbuscular mycorrhizal fungal synthetic community assembled from southern-Spain isolates and followed for three years in soil mesocosms designed to mimic a semi-arid Mediterranean ecosystem. The mesocosms used Retama sphaerocarpa, Lavandula latifolia, Thymus mastichina, and Rosmarinus officinalis as monoculture or pairwise plant covers while tracking AM fungal root colonization by nested PCR-TTGE of SSU rDNA and rhizosphere spore morphotypes every three months. The abstract reports species-specific establishment, persistence, and sporulation trajectories, with Septoglomus constrictum showing the most consistent persistence and sporulation under the semi-arid Mediterranean conditions.
Mediterranean Grassland qSIP Rainfall-Gradient Community
An active soil microbial community in three Mediterranean-climate grassland soils sampled across a rainfall gradient and assayed with genome-resolved quantitative stable isotope probing (qSIP) following an H2-18O labeling experiment to identify actively growing organisms and link growth and motility traits to historical precipitation. qSIP-informed genome-resolved metagenomics resolves the active subset of community members, with higher year-round precipitation correlating with higher activity and growth rates of flagellar motile microorganisms.
Meghalaya Bacillus Consortia-A22ED9
Consortia-A22ED9 is a defined two-member Bacillus consortium assembled from SK22 and KHED9, two native isolates recovered from active rat-hole coal-mine sites in Meghalaya, India. The consortium was selected after compatibility screening for growth stimulation and then assayed in pH 5.0 LB medium for in vitro removal of iron, cadmium, and chromium across sublethal metal concentrations.
Mercury SFA East Fork Poplar Creek Sediment Community
A sediment microbial community from East Fork Poplar Creek (EFPC) in Oak Ridge, Tennessee, contaminated with mercury from historical weapons production at the Y-12 National Security Complex. Twenty-eight metagenome-assembled genomes were reconstructed from two sediment core sections at 0-3 cm and 9-12 cm depth, and most encoded putative heavy-metal resistance or ATPase efflux functions.
Mesorhizobium TaiHu-Synechococcus PCC 7002 Vitamin B12 Synthetic Consortium
A synthetic consortium built by co-culturing the marine cyanobacterium Synechococcus sp. PCC 7002 (Syn7002) — a model strain that lacks the gene cluster for vitamin B12 biosynthesis and therefore depends on other microbes for it — with a bloom-forming Microcystis community from Lake Taihu, then purifying the result. Metagenomics showed the early community consisted mainly of Syn7002, Mesorhizobium sp. TaiHu (MesTH) and Pseudomonas sp. TaiHu (PseTH); PseTH declined once the community stabilised, leaving the cyanobacterium and MesTH as the persistent pair. Electron microscopy found rod-shaped bacteria clustered around Syn7002 cells. Metatranscriptomics showed vitamin B12 biosynthesis and transport genes significantly upregulated in MesTH, and B12-positive control experiments supported complementarity between the two strains, so the community is a worked example of a vitamin auxotrophy being satisfied by a partner rather than by the medium.
Methane Oxidation-Cr(VI) Reduction SynCom
A methane-oxidizing synthetic microbial community coupling Cr(VI) reduction to division of labor and extracellular electron transfer.
Methane-Fed MFC Electrogenesis and Nitrogen-Fixation Consortium
A methane-fed, nitrogen-limited microbial fuel-cell enrichment that couples anaerobic methane oxidation, extracellular electron transfer, current generation, and biological nitrogen fixation through a reported division of labor. The six genera recorded here are the functional groups named by the source, not a claim that the enrichment contains only six taxa.
Methylacidiphilum-Galdieria Thermoacidophilic Methane Coculture
A defined thermoacidophilic methanotroph-microalga coculture pairing Methylacidiphilum sp. RTK17.1 with Galdieria sp. RTK37.1 for methane and carbon dioxide valorisation. In methane-fed photobioreactor studies, the methanotroph benefits from oxygen supplied by the extremophilic microalga under low-oxygen conditions, enhancing growth and methane oxidation. Follow-up work showed that this interaction is density-dependent: low initial Methylacidiphilum:Galdieria ratios improve net carbon fixation, whereas elevated methanotroph abundance can impose oxygen competition, causing chlorosis and reduced carbon assimilation.
Methylocaldum-Cupriavidus Methane Acetate Cross-Feeding Coculture
A defined artificial aerobic coculture pairing the marine methanotroph Methylocaldum marinum S8 with the non-methylotrophic acetate-utilizing bacterium Cupriavidus necator NBRC 102504. The coculture was used to test whether methane-derived metabolites excreted by M. marinum S8 can support a partner that is not a methylotroph. The system is DOE-relevant because it links methane oxidation to acetate-mediated growth of a bioproduction-relevant heterotroph, providing a model for methane-to-bioproduct community design.
Methylocaldum-Methyloceanibacter Methane Cross-Feeding Coculture
A defined aerobic methane-fed laboratory coculture pairing the marine methanotroph Methylocaldum marinum S8 with the facultative methylotroph Methyloceanibacter caenitepidi Gela4. M. marinum S8 oxidizes methane and supports syntrophic growth of M. caenitepidi Gela4 on methane-derived carbon. Transcriptome and chemical analyses indicate that acetate, rather than methanol alone, is likely a major cross-fed carbon source in this model methanotroph-methylotroph community.
Methylocystis-Rhodococcus Methane VFA PHBV Coculture
A defined synthetic coculture pairing the type II methanotroph Methylocystis parvus with the heterotrophic bacterium Rhodococcus opacus for methane-linked polyhydroxyalkanoate production. The coculture was first evaluated for methane-to-poly(3-hydroxybutyrate) conversion and then used in a two-stage PHBV accumulation strategy with nutrient starvation, methane, oxygen or air, valeric acid, and a volatile fatty acid mixture containing acetic, propionic, butyric, and valeric acids. The system is relevant to methane valorization, waste-derived volatile fatty acid upgrading, and biopolymer production.
Methylomicrobium-Chlorella Methane Sequestration Coculture
A defined halotolerant methanotroph-microalga coculture pairing Methylomicrobium alcaliphilum 20Z, currently represented by NCBI as Methylotuvimicrobium alcaliphilum 20Z, with Chlorella sp. HS2. The two-member system was assembled to test biological methane and carbon dioxide mitigation through metabolic coupling in saline culture, with increased methane removal, improved growth of both members, pH recovery, and greater biomass carbon sequestration reported in coculture. The system is relevant to DOE interests in methane mitigation, carbon capture and utilization, photosynthetic-methanotrophic consortia, and C1 bioconversion.
Methylotuvimicrobium-Synechococcus Gas Feedstock Coculture
A defined synthetic methanotroph-cyanobacterium coculture developed at Pacific Northwest National Laboratory for simultaneous use of methane and carbon dioxide gas feedstocks. The methanotrophic bacterium Methylomicrobium alcaliphilum 20z, currently represented by NCBI as Methylotuvimicrobium alcaliphilum 20Z, is coupled to the cyanobacterium Synechococcus PCC 7002, currently represented by NCBI as Picosynechococcus sp. PCC 7002. The coculture converts CH4 and CO2 into microbial biomass through oxygenic photosynthesis-driven O2 supply to the methanotroph and respiratory CO2 supply to the photoautotroph, with follow-up work using the same species pair for quantitative coculture characterization.
Microalgae-Cyanobacteria Bioactive Peptide Consortia
A bounded controlled-photobioreactor biomass panel comprising two marine microalgae-cyanobacteria consortia supplied by Microalgae Solutions S.L. for protein extraction, LC-MS/MS proteome identification, and Alcalase hydrolysis. Consortium C1 combined Chlorella vulgaris with Arthrospira platensis, while consortium C2 combined Kamptonema sp., Nannochloropsis oculata, Tetraselmis suecica, and Chlorella vulgaris. Both biomasses were grown in flat photobioreactors in modified Guillard F/2 medium, lyophilized, characterized for macromolecular composition, extracted at pH 10/pH 5, and hydrolyzed to evaluate release of antioxidant peptides.
Microbacterium-Terrabacter Sulfadiazine Cross-Feeding Coculture
A two-member synthetic bacterial coculture pairing Microbacterium sp. BR1 with Terrabacter sp. 2APm3/DSMZ 28514 for sulfadiazine degradation. Xue et al. 2026 traced 13C,15N-labeled sulfadiazine through the coculture and showed a sequential commensal pathway in which Microbacterium sp. BR1 cleaves sulfadiazine to release 2-aminopyrimidine and Terrabacter assimilates and degrades the 2-aminopyrimidine intermediate that accumulated in Microbacterium monoculture.
Microcoleus-Massilia Cyanosphere Urea Mutualism
A defined biological soil crust cyanosphere coculture pairing the pioneer cyanobacterium Microcoleus vaginatus PCC 9802 with the heterotrophic cyanosphere isolate Massilia sp. METH4. Across repeated studies of the same exact strain pair, M. vaginatus provides photosynthetically fixed organic carbon while the diazotrophic Massilia partner supports nitrogen acquisition through a specific carbon-for-nitrogen mutualism, including urea-mediated nitrogen transfer and GABA/glutamate signaling that organizes close spatial association.
Microhabitat Mineral Fungal-Bacterial SOM SynCom
A four-member artificial soil-organic-matter microcosm inoculum consisting of Curtobacterium sp. PTCC 1316, Trichoderma harzianum IBRC-M30059, Phanerochaete chrysosporium IBRC-M30144, and Pseudomonas fluorescens IBRC-M10752. Maqami et al. 2026 used the synthetic fungi-plus-bacteria consortium as an experimentally simplified alternative to a native agricultural-soil microbiome in 500 mL glass-jar microcosms containing sterilized bentonite or palygorskite clay, calcium carbonate, quartz sand, and wheat-straw or alfalfa-shoot litter, then quantified respiration kinetics and microbial biomass carbon over a 90-day incubation.
Miscanthus REE Tailings Nitrogen SynCom10
A ten-strain Miscanthus root-derived SynCom with nitrification and denitrification capabilities for ammonia nitrogen removal in rare earth mine tailings.
Mixed Gallium LED Recovery Consortium
An engineered acidophilic microbial consortium specifically designed for recovering gallium from waste light-emitting diodes (LEDs) through non-contact bioleaching. This mixed community consists of three iron- and sulfur-oxidizing bacteria in equal proportions (1:1:1 ratio): Acidithiobacillus thiooxidans, Acidithiobacillus ferrooxidans, and Leptospirillum ferrooxidans. The consortium produces biogenic lixiviants - primarily sulfuric acid (H₂SO₄) from sulfur oxidation and ferric iron (Fe³⁺) from iron oxidation - that solubilize gallium from GaN-based LED materials without direct contact between microbes and solid waste. Operating at pH 1.0-1.5 and 15 g/L pulp density, the system achieves exceptional 99.5% gallium leaching efficiency within just 3 days. The non-contact bioleaching approach separates the bioreactor (where microbes generate lixiviants) from the leaching reactor (where acids attack LED waste), preventing microbial inhibition by toxic LED components while enabling gallium recovery. In addition to gallium, the process recovers copper and nickel from LED substrates and interconnects. This biotechnological platform offers a sustainable alternative to harsh chemical leaching methods, utilizing microbial metabolism to extract critical materials from electronic waste while avoiding toxic emissions and reducing environmental impact.
Model Cyanobacterial Consortia Core Microbiome
A laboratory framework of 108 stable cyanobacteria-heterotroph consortia generated by coculturing five well-characterized model cyanobacterial strains with microorganisms filtered from three distinct freshwater sources. Metagenomic analysis across the 108 consortia identified a 25-species noncyanobacterial core microbiome that recurred independently of cyanobacterial host species or inoculum source, with statistically supported core functions in micronutrient biosynthesis, metabolite transport, and anoxygenic photosynthesis, and a significant enrichment of plasmids in core species suggesting plasmid-mediated symbiotic roles.
Model Lignocellulose Formaldehyde Cross-Feeding Community
A synthetic model lignocellulose-degrading community developed to study plant-biomass transformation and mitigation of toxic formaldehyde produced during breakdown of methoxylated aromatic compounds. The system includes Pseudomonas putida as a lignin degrader, Cellulomonas fimi as a cellulose degrader, Methylorubrum extorquens as a methylotrophic formaldehyde consumer, and Yarrowia lipolytica as an oleaginous yeast included in some consortium variants.
Model Soil Consortium-2 (MSC-2)
Reduced-complexity model soil consortium assembled from MSC-1 isolates to study community-level chitin decomposition, interspecies interactions, and emergent phenotypes in soil. MSC-2 contains eight bacterial members spanning diverse phyla and was used for isolate genome sequencing, 16S profiling, metatranscriptomics, metabolomics, and KBase-enabled metabolic modeling in the Hofmockel Soil Microbiome SFA context.
Moss-Microbe Complex Regolith Biofertilizer
A moss-microbe complex evaluated as a bio-based biofertilizer for improving crop growth on lunar and Martian soil simulants. The complex comprises the moss Hypnum plumaeforme together with plant growth-promoting bacteria isolated from it — Pseudomonas monteilii and Bacillus cereus — selected for phosphate solubilization, indole-3-acetic acid (IAA) production, and siderophore synthesis. Using barley (Hordeum vulgare) as a model crop, the study compared moss alone, microbes alone, and their combined application under extreme edaphic conditions represented by lunar (LHS) and Martian (MGS) soil simulants. The moss-microbe co-treatment significantly enhanced shoot biomass, dry weight, organic matter, available phosphate, and cation exchange capacity; in the dense, low-porosity Martian simulant the moss functioned as a biological buffer that facilitated microbial colonization and restored plant growth. 16S rRNA profiling confirmed the stable presence of the genera Pseudomonas, Bacillus, and Devosia in moss-treated soils, and metabolite profiling revealed accumulation of growth-related compounds (D-ribose, D-gluconate), suggesting the complex reprograms rhizosphere metabolism. The system is an In-Situ Resource Utilization model for extraterrestrial farming and land restoration.
MSC-1 Dominant Core
A naturally evolved dominant core subset of Model Soil Consortium-1 (MSC-1), an arid-grassland soil consortium enriched through serial dilution and passaging on chitin as the primary carbon and nitrogen source. MSC-1 retained 31 bacterial OTUs, was dominated by 13 OTUs, and was later analyzed through N-acetylglucosamine co-cultures and soil co-abundance networks that highlighted Rhodococcus, Mycobacterium, and Rhizobiales lineages.
MUC2 Human Gut Commensal Defined Consortium
A 14-strain, commercially sourced synthetic consortium of human gut commensals assembled to span low, moderate, and extensive mucin-glycan degradation capacities. The consortium was grown anaerobically in ZMB1 chemically defined medium in 150 mL bioreactors with either vehicle or 0.5 mg/mL porcine MUC2. After 72 h of semi-continuous cultivation, MUC2 supplementation shifted group-level qPCR profiles by expanding Akkermansia and reducing Prevotella, and it remodeled extracellular metabolism by lowering acetate while increasing propionate, butyrate, and formate.
MUCC Freshwater Wetland Methane-Cycling Network Community
A multi-site terrestrial freshwater wetland microbial community synthesis curated around the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. The study integrates 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual methane flux measurements across nine wetlands to link microbial community structure, methane-cycling guilds, decomposition networks, and methane emissions. It identifies eight methane-cycling genera shared across wetlands, highlights wetland-specific metabolic interactions in marshes, and reports Methanoregula as a hub methanogen and predictor of methane flux. The record is DOE-relevant because the study was supported by DOE Office of Science BER awards and included metagenomic and metatranscriptomic sequencing at the DOE Joint Genome Institute.
Mucin Glycan-Degrading MDSC Synthetic Gut Community
A 14-strain in vitro synthetic community of human colonic mucus-associated mucin glycan degraders, secondary degraders, and hydrogen consumers. The MDSC was assembled from Akkermansia, Bacteroides, Phocaeicola, Ruminococcus, Lachnospiraceae, Faecalibacterium, and Desulfovibrio type strains, grown anaerobically in sequential 24 h serum-bottle batches at 37°C, and compared across porcine gastric mucin, bovine submaxillary mucin, mixed PGM/BSM, and PGM supplemented with two sialylated glycans. Mucin type drove distinct stabilized community compositions, mucin glycan degradation patterns, and metabolite profiles after four transfers.
Mulberry-Distillers Grains Feed A/B/C Fermentation Panel
A designed Bacillus-yeast-LAB solid-state fermentation panel that mixed Bacillus subtilis, Saccharomyces cerevisiae, Levilactobacillus brevis, and Lactiplantibacillus plantarum as two three-species 1:1:1 recipes and one four-species 1:1:1:1 recipe to convert mulberry leaves and distillers' grains into higher-nutrient animal feed. Zhang et al. compared the three A/B/C inoculation recipes across mulberry leaves, distillers' grains, and mixed ML&DG substrates under 10% inoculation and five days of anaerobic solid-state fermentation.
Multi-stage Anaerobic-Digestion SynCom-YSJ and SynCom-J
Two function-driven synthetic microbial communities (SynComs) constructed for bioaugmentation of food-waste anaerobic digestion. SynCom-J is a methanogen-only consortium, whereas SynCom-YSJ is a multi-stage consortium comprising hydrolytic, acidogenic, and methanogenic members. Both were introduced into semi-continuous reactors already harboring a metabolically complete native microbiome. The multi-stage SynCom-YSJ increased methane yield by 22% (vs 8% for SynCom-J), nearly eliminated the start-up lag phase, reduced propionate accumulation, and reshaped the digester microenvironment (elevated acetate, reduced propionate), upregulating genes for hydrolysis, acidogenesis, interspecies electron transfer, energy metabolism, and acetoclastic/hydrogenotrophic methanogenesis. Individual member species are not named in the source abstract, so no NCBITaxon-grounded members are asserted here.
Multiomics Corn Straw Degradation SynCom
A core synthetic microbial community designed by multiomics linkage technology to degrade corn straw lignocellulose.
Mushroom Spring Hot-Spring Phototrophic Mat Community
A natural alkaline geothermal microbial mat community from Mushroom Spring in Yellowstone National Park. The community is structured around thermophilic Synechococcus cyanobacteria, filamentous anoxygenic phototrophs related to Roseiflexus and Chloroflexus, and an undermat community that includes Thermodesulfovibrio-like sulfate reducers. It is a DOE-relevant model for high-temperature photosynthesis, diel carbon and nitrogen cycling, metagenome-resolved community metabolism, and carbon flow in phototrophic microbial mats.
MWF001 Four-Species Cross-Feeding Consortium
A defined synthetic model community of four bacterial strains originally isolated from toxic metal-working fluids: Agrobacterium tumefaciens MWF001, Comamonas testosteroni MWF001, Microbacterium liquefaciens MWF001, now classified as Microbacterium maritypicum, and Ochrobactrum anthropi MWF001, now classified as Brucella anthropi. Sulheim et al. assembled the four strains into M9 minimal media with chemically diverse single or paired carbon sources, followed individual members by colony counts on selective media across eight 72 h growth-and-dilution cycles, and found that metabolic byproduct cross-feeding and niche partitioning let all four members coexist in nearly every tested nutrient condition.
N-Cycle Bioflocculation Model Consortium
A reduced-complexity N-cycle model consortium of nitrifiers and denitrifiers used to study bioflocculation mechanisms in biological wastewater treatment.
Naica Deep Subsurface Thermophilic Community
Deep saline hydrothermal waters from the Naica Mine crystal cave system in Chihuahua, Mexico. The assayed water samples were collected from the deepest accessible mineshafts, at approximately 700-760 m, and yielded a low-diversity prokaryotic community that included basal Thaumarchaeota, Thermoplasmatales- affiliated Euryarchaeota, Candidate Division OP3, Firmicutes, and Alpha/Beta-proteobacteria. Archaeal ammonia monooxygenase genes supported nitrification by thermophilic chemolithoautotrophic Thaumarchaeota, while unsuccessful sulfate-reducer marker amplification and low electron-donor availability argued against sulfate reduction as a dominant metabolism.
Nasal SynCom C Bioreactor
A nine-strain synthetic nasal community assembled from LaCa collection isolates recovered from Volunteer 1 and cultivated in a continuously fed glass bioreactor with synthetic nasal medium to maintain a stable S. aureus-free nasal microbiome before Day-20 S. aureus strain challenges.
NDC-6 Psychrotolerant Nitrogen Removal SynCom
A six-strain psychrotolerant composite microbial agent for low-temperature nitrogen removal, generated by coculturing nitrifying consortium NC1 (Pseudomonas veronii HN1, Pseudomonas poae HN2, and Pseudomonas peli HN3) with aerobic-denitrifying consortium DC1 (Aeromonas sp. AD1, Pseudomonas extremaustralis AD2, and Serratia liquefaciens AD3) at a 1:1 inoculation ratio.
Neocallimastix-Methanobrevibacter Xylanolytic Coculture
A defined anaerobic rumen-derived coculture in which the xylan-degrading fungus Neocallimastix frontalis PNK2 is grown with the hydrogenotrophic archaeon Methanobrevibacter smithii on xylan. The methanogen removes fermentation products through interspecies hydrogen transfer, shifting fungal metabolism toward acetate formation and increasing xylan utilization and extracellular hemicellulase activities.
Ngawha Geothermal Acidic Springs Mercury Cycling Community
An acidic warm spring microbial community from the Ngawha Geothermal Field (Northland Region, Aotearoa New Zealand) characterized by genome-resolved metagenomics and mercury speciation analysis. Two adjacent springs differ in mercury speciation, with dissolved total and methylated mercury concentrations among the highest reported from natural sources (250 to 16,000 ng/L total; 0.5 to 13.9 ng/L methylmercury). Sediment total mercury ranges from 1,274 to 7,000 ug/g. Despite ultrahigh mercury levels, the geothermal microbiome is unexpectedly diverse and dominated by acidophilic and mesophilic sulfur- and iron-cycling bacteria, mercury- and arsenic- resistant bacteria, and thermophilic and acidophilic archaea. A conceptual model integrates community structure and metagenomic potential with abiotic and biotic controls on Hg methylation, demethylation, and reduction to volatile Hg(0).
Nitratireductor-Gordonia Z123 LDPE-Degradation SynCom
A defined three-isolate synthetic consortium, Z123, reconstructed from a polyethylene-degrading enrichment isolated from marine plastic debris. Z123 comprises Nitratireductor sp. Z-1 and two Gordonia isolates, Gordonia sp. Z-2 and Gordonia sp. Z-3. In 30-day biodegradation assays with pristine low-density polyethylene, Z123 achieved 9.98% polymer weight loss and 50.88% molecular-weight reduction. Integrated genomic and proteomic data suggested a division of labor across oxidative activation, chain scission, and downstream metabolism, while GC-MS detected extracellular LDPE-associated products consistent with oxidative polymer modification.
Nitrifying Wastewater Ammonia-Oxidizing Consortium
A top-down, model aerobic ammonia-oxidizing consortium for wastewater treatment risk and performance assessment. Long-read metagenomics recovered 64 high-quality bacterial MAGs from the starting material, which was dominated by an unclassified Nitrosospira MAG carrying expected ammonia-oxidation capabilities and also contained a lower-abundance Nitrobacter MAG and Legionella MAGs monitored during virulence-gene risk assessment. The consortium was grown in synthetic pond water under an aerobic/anoxic redox gradient to test nitrogen cycling, community composition, and activity by metagenomics, metatranscriptomics, and nitrogen chemistry.
Oak Ridge FRC Uranium-Nitrate Groundwater Community
A natural contaminated-groundwater microbial community from the U.S. DOE Oak Ridge Field Research Center, where groundwater wells span strong gradients in acidity, nitrate, uranium, and other metal contaminants. Clone-library and isolate studies link geochemistry to community structure, with lower diversity in highly contaminated wells and enrichment of organisms capable of uranium, nitrate, and iron reduction. This record represents the field community, distinct from existing defined ENIGMA denitrifying SynCom records derived from Oak Ridge isolates.
Ogataea Met10-Str3 Sulfur Cross-Feeding Coculture
A defined two-member Ogataea polymorpha synthetic yeast coculture pairing a met10Δ-mCherry auxotroph, FY34, with a str3Δ-EGFP auxotroph, FY31. The pair was selected from systematic auxotroph screening because it showed reproducible growth restoration in Delft minimal medium with glucose or methanol; single-strain supplementation assays supported an asymmetric sulfur-metabolite dependency in which met10Δ could use multiple sulfur-containing intermediates while str3Δ depended on homocysteine.
Okeke-Lu Cellulolytic-Xylanolytic Consortium
A defined 5-member bacterial consortium from Alabama soil capable of dual cellulose and hemicellulose degradation. The consortium consists of Pseudoxanthomonas byssovorax DB1, Microbacterium oxydans DB2, Bacillus sp. DB7, Ochrobactrum sp. DB8, and Klebsiella sp. DB13. Isolates DB1 and DB2 display the highest cellulase activity (27.83 and 31.22 U/mg), producing a complete enzyme system including filter paper cellulase, β-glucosidase, xylanase, and β-xylosidase for comprehensive lignocellulose bioprocessing.
OMM12 Gnotobiotic Mouse Gut Community
OMM12, also called Oligo-MM12 or Oligo-Mouse-Microbiota, is a defined 12-strain murine intestinal bacterial community used to colonize germ-free mice for reproducible microbiome research. The community includes Lactobacillus reuteri I49, Enterococcus faecalis KB1, Blautia coccoides YL58, Clostridium innocuum I46, Flavonifractor plautii YL31, Clostridium clostridioforme YL32, Acutalibacter muris KB18, Bacteroides caecimuris I48, Muribaculum intestinale YL27, Bifidobacterium longum subsp. animalis YL2, Akkermansia muciniphila YL44, and Turicimonas muris YL45. It is used as a reduced, genome-characterized model of the mouse gut microbiota for colonization resistance, mucosal immunology, microbial ecology, host-microbiome metabolic cross-talk, and facility-to-facility reproducibility studies.
Optimized Rumen Fiber-Degrading SynCom 3
A five-strain synthetic rumen bacterial consortium optimized from dairy-cattle culturomics isolates to increase fiber degradation of a total-mixed-ration substrate. The Streptococcus equinus 5640, Lactobacillus delbrueckii 5812, Proteiniphilum acetatigenes 6076, Enterococcus lactis 6088, and Petrimonas mucosa 6360 SynCom 3 derivative was dose-optimized by a Box-Behnken in vitro design and then dosed into fistulated Huaxi cattle as a mixed bacterial suspension.
ORNL Clostridium-Desulfovibrio-Geobacter Trophic Model Community
A three-species anaerobic continuous-culture model community established to study trophic and electron-acceptor interactions relevant to subsurface anaerobic environments. Clostridium cellulolyticum ferments cellobiose, while Desulfovibrio vulgaris Hildenborough and Geobacter sulfurreducens depend on fermentation products and use sulfate and fumarate, respectively, as supplied electron acceptors.
ORNL PMI Populus PD10 SynCom
A 10-member synthetic bacterial community (PD10) assembled by the Oak Ridge National Laboratory Plant-Microbe Interfaces (PMI) team from Populus deltoides rhizosphere isolates. The community was used as a bottom-up model system to study assembly dynamics, medium-dependent community structure, metabolic exchange, and antagonistic interactions during stable community formation.
Ostreococcus-Dinoroseobacter B-Vitamin Mutualism
A defined marine algal-bacterial coculture in which the picoeukaryotic alga Ostreococcus tauri OTH95 and the roseobacter Dinoroseobacter shibae DF-12 form a reciprocal B-vitamin mutualism. D. shibae supplies cobalamin and thiamine needed by O. tauri, while O. tauri satisfies bacterial requirements for other B vitamins in a stable long-term coculture; the interaction is experimentally tractable under controlled light, temperature, and vitamin-amendment regimes.
Panax Bacillus-Serratia Root-Rot Biocontrol SynCom
A two-member Bacillus subtilis/Serratia marcescens synthetic microbial consortium, BS, pairing the antagonistic strains XY-6 and XB-7, isolated from root-rot-affected Panax notoginseng plantation soil, for Fusarium root-rot biocontrol. Deng et al. 2026 selected Bacillus subtilis XY-6 as the core strain after antagonistic screening, combined compatible strains with XY-6 in 1:1 volume ratios, and found that the XY-6/XB-7 consortium improved greenhouse disease suppression beyond the single strains, directly inhibited Fusarium solani LP2 through cell-free filtrates, activated host antioxidant defenses, and reshaped the P. notoginseng rhizosphere mycobiome.
Panzhihua Vanadium Titanium Tailings Community
A perturbed indigenous microbial community from vanadium-titanium magnetite mine tailings in Panzhihua, Sichuan, China, the world's largest V-Ti magnetite deposit and largest vanadium production city. This community comprises nitrogen-fixing rhizobia (Bradyrhizobium pachyrhizi, Rhizobium species), metal-reducing bacteria, and indigenous microbiota that facilitate phytoremediation of polymetallic tailings containing vanadium (340 mg/kg), titanium, iron, copper, nickel, manganese, and zinc. The Panzhihua deposit has generated approximately 570 million tons of tailing slurries from mining activities, creating a massive contamination challenge requiring sustainable bioremediation. The indigenous microbial community has adapted to extreme metal stress through nitrogen fixation coupled with plant growth promotion, enabling successful legume-based phytoremediation with Pongamia pinnata and Leucaena leucocephala. Bradyrhizobium species demonstrate exceptional heavy metal tolerance while maintaining nitrogen-fixing capacity (increasing plant nitrogen content by 10-145%), promoting plant growth through IAA production, and facilitating metal phytoextraction (enhancing Cu and Ni uptake by 600%). Metal-reducing bacteria contribute to vanadium detoxification through dissimilatory V(V) reduction to less soluble V(IV), decreasing vanadium bioavailability and mobilization risk. The community drives transformation of soil organic carbon, increasing active carbon components and carbon transformation enzymes during revegetation, improving overall tailings soil quality. This system represents a critical model for coupling nitrogen fixation, metal tolerance, and phytoremediation in polymetallic mine tailings, addressing both resource recovery and environmental remediation challenges in the world's largest vanadium-titanium deposit.
Parachlorella kessleri + Saccharomyces cerevisiae Mutualistic Co-culture
Two-member engineered co-culture of the green microalga Parachlorella kessleri and the yeast Saccharomyces cerevisiae, established to enhance microalgal lipid productivity. The partners form a mutualistic relationship based on reciprocal oxygen/carbon dioxide gas exchange. Under co-culture, biomass and lipid production increased 4-fold relative to microalgal monoculture. Yeast sustained microalgal growth during the transition to phototrophy after glucose depletion and promoted lipid accumulation through nutrient competition, while microalgae are inferred to provide metabolic support to the yeast via exopolysaccharide (EPS)-derived molecules. Nanomechanical analyses (AFM, FluidFM) showed increased EPS production and stronger, longer microalga-yeast cell-cell interactions in co-culture.
Parmigiano NWS Set 2 LAB Triculture
A defined three-strain lactic-acid-bacterial triculture assembled from Parmigiano Reggiano natural whey starter isolates. Cristofolini et al. 2026 combined Lactobacillus helveticus LBB04, Streptococcus thermophilus C001.27, and Lactobacillus delbrueckii subsp. lactis C5I3 in a 1:1:1 milk triculture to test whether natural-whey-starter partners could enhance the impaired cultivability and acidification activity of L. delbrueckii subsp. lactis. Across the milk cross-feeding panel, tricultures showed the highest maximum acidification rates and total lactic acid production, with positive S. thermophilus-linked effects and weaker L. helveticus/L. delbrueckii pair performance in set 2.
Peanut Seed Bacterial CS SynCom
A combined peanut seed-borne bacterial synthetic community that suppresses Aspergillus flavus and Fusarium oxysporum while promoting seedling growth.
Pelagerythrobacter-Salinicola PES Pyrene-Degradation SynCom
A defined two-member halophilic synthetic consortium, PES, assembled from Pelagerythrobacter sp. N7 and Salinicola sp. A11, which were isolated from a PAH-degrading consortium enriched from saline PAH-polluted soil in Shanxi Province, China. Washed suspensions of the two isolates were mixed 1:1 and assayed in 5% sea-salt defined medium with 50 mg/L pyrene as the sole carbon source. N7 alone initiated pyrene oxidation but incompletely removed pyrene and accumulated 4,5-dicarboxyphenanthrene, whereas A11 alone had no detectable direct pyrene-degrading capability. In the PES consortium, A11 supplied a proposed hphtC-5-encoded aromatic-acid decarboxylase/downstream C12O arm and extracellular emulsan-like bioemulsifier activity, together enabling complete removal of 50 mg/L pyrene within 10 days at 5% salinity.
Pelotomaculum-Methanocella Propionate RNA-Seq Coculture
A defined anaerobic syntrophic coculture pairing the propionate-oxidizing bacterium Pelotomaculum thermopropionicum with the hydrogenotrophic methanogen Methanocella conradii. RNA-seq comparisons against monocultures showed coordinated transcriptional shifts in catabolism, methanogenesis, electron bifurcation/confurcation, formate handling, signal transduction, and amino acid exchange. The system is relevant to DOE interests in anaerobic carbon cycling, methane production, syntrophic propionate degradation, and transcriptome-guided bioreactor microbiology.
Pelotomaculum-Methanothermobacter Syntrophic Consortium
A thermophilic syntrophic, obligate two-member anaerobic consortium consisting of Pelotomaculum thermopropionicum, which oxidizes propionate and other organic acids (ethanol, lactate, alcohols) to acetate, CO2, and H2, and Methanothermobacter thermautotrophicus, a hydrogen-utilizing thermophilic methanogen. P. thermopropionicum oxidizes propionate only in coculture with H2-using methanogens, as it uses protons as the electron acceptor with H2 as the electron sink product. The removal of H2 by M. thermautotrophicus is thermodynamically essential for continued propionate oxidation by P. thermopropionicum. This thermophilic syntrophic relationship is fundamental to understanding propionate degradation and methane production at elevated temperatures (55°C) in anaerobic environments such as thermophilic digesters and hot springs.
Pepper Growth Rhizosphere SynCom
A pepper seedling SynCom treatment that enhances growth and root morphology by modulating rhizosphere microbial communities.
Pepper Phytophthora-Resistance SynCom5
A five-isolate pepper rhizosphere SynCom that reduces Phytophthora capsici disease severity and enhances pepper growth.
PET Artificial Four-Species Degradation Consortium
An engineered artificial consortium for polyethylene terephthalate (PET) biodegradation composed of two metabolically engineered Bacillus subtilis 168 strains that secrete PETase and MHETase, plus Rhodococcus jostii RHA1 and Pseudomonas putida KT2440. The design partitions PET depolymerization, terephthalic acid utilization, and ethylene glycol utilization across different members to reduce product inhibition during PET degradation.
PGM Spent Catalyst Bioleaching Consortium
An acidophilic bioleaching system for recovery of platinum group metals (PGMs) from spent automotive catalysts and hydroprocessing catalysts. Acidithiobacillus thiooxidans is the only organism the cited sources name: it generates sulfuric acid that dissolves the alumina support. The thiosulfate used for PGM complexation was sourced separately, from a biogas biodesulfurization bioreactor whose community the source does not characterise taxonomically. Spent three-way catalysts (TWC) from automotive exhaust systems contain precious metals (Pt, Pd, Rh) deposited on alumina (Al₂O₃) supports, while spent petroleum refinery hydroprocessing catalysts contain Pd, Ni, Mo, and Al. The consortium operates under acidic conditions in column bioreactors, achieving exceptional recovery rates: 93.2% Pd extraction, 82.9% Ni, 33.4% Al, and 22.7% Mo from spent petroleum catalysts. The bioleaching mechanism proceeds in two stages: (1) At. thiooxidans generates sulfuric acid that dissolves the alumina support matrix, exposing embedded PGM particles, and (2) biogenic thiosulfate (S₂O₃²⁻) produced during sulfur oxidation forms stable complexes with Pd and other PGMs in the presence of copper and ammonia, mobilizing them from the catalyst surface. The thiosulfate-copper-ammonia system enables selective PGM leaching without harsh cyanide reagents. This biotechnological approach offers an environmentally sustainable alternative to conventional pyrometallurgical PGM recovery (high-temperature smelting) and aggressive chemical leaching (aqua regia, cyanide), while addressing circular economy needs for critical materials recovery from automotive and industrial waste streams. The technology represents a significant advance in green metallurgy for spent catalyst recycling.
Phaeodactylum-Aliivibrio Diel Co-culture
A defined two-member marine algae-bacteria co-culture pairing the model diatom Phaeodactylum tricornutum CCAP 1055/1 with the heterotrophic marine bacterium Aliivibrio fischeri MCCC 1H00019. Chen et al. 2026 grew the pair in EASW medium supplemented with 30% marine broth under a 12 h light/12 h dark cycle and used 4-day and 8-day samples to show bacterial surface colonization, competitive rather than growth-promoting behavior, a day-6 extracellular-polymeric-substance peak followed by day-8 depletion, and time-dependent rewiring of P. tricornutum photosynthetic physiology, transcriptomic rhythmicity, and model-inferred biomass flux.
Phenol Carboxylation Consortium
A purified two-member anaerobic syntrophic coculture in which Syntrophorhabdus aromaticivorans strain UI(T) oxidizes phenol, p-cresol, 4-hydroxybenzoate, isophthalate, and benzoate in association with the hydrogenotrophic methanogen Methanospirillum hungatei DSM 864. The M. hungatei partner supplies the H2-scavenging methanogenic sink needed for strain UI(T) to mineralize aromatic substrates to acetate and methane, and blocking methanogenesis or raising hydrogen partial pressure halts phenol and 4-hydroxybenzoate degradation.
Phormidium Alkaline Consortium
A natural cyanobacterial-heterotrophic consortium dominated by Candidatus Phormidium alkaliphilum, isolated from soda lakes. This consortium represents a robust, stable community optimized for carbon sequestration in high-pH environments (pH >11). The community includes 8-12 core members with 29 identified heterotrophic metagenome-assembled genomes spanning Bacteroidota, Alphaproteobacteria, Gammaproteobacteria, Verrucomicrobiota, Patescibacteria, and Planctomycetota. The consortium demonstrated exceptional stability with 4 years of crash-free growth in laboratory culture, maintaining biomass productivity of 15.2 g/m²/day. Ecological interactions include carbon transfer from cyanobacteria to heterotrophs, nutrient remineralization, vitamin provision (B12, B1, B7), and functional niche partitioning that enhances community robustness. The consortium enables direct CO2 capture from air at alkaline pH, making it highly relevant for biotechnological carbon sequestration applications. Stable isotope probing with ¹³C-bicarbonate revealed tight coupling of carbon flux from primary production to heterotrophic populations, particularly Wenzhouxiangella species.
Phosphitivorax-Methanoculleus Lithosyntrophic Phosphite-Oxidizing Methanogenic Culture
An anoxic, methanogenic enrichment culture defining "lithosyntrophy," an obligate syntrophic interaction in which the electrons driving hydrogenotrophic methanogenesis originate from an inorganic compound. Candidatus Phosphitivorax anaerolimi Phox-21 oxidizes phosphite (oxidation state +3) to phosphate coupled to hydrogenogenesis, in an obligate energetic dependency on a hydrogenotrophic methanogen, Methanoculleus sp. Electrons derived from phosphite drive H2 production via an electron-confurcating hydrogenase; the methanogen consumes the H2 to keep the reaction thermodynamically favorable, establishing interspecies electron transfer that links the phosphorus and carbon redox cycles in anoxic ecosystems.
Phylogenetically Diverse Denitrifying SynCom
Closely related and distantly related synthetic denitrifying communities used to test how phylogenetic diversity affects denitrification and stability.
Pichia-Lactiplantibacillus CCMA Plant Beverage Coculture
A defined bacterial-yeast co-culture pairing Lactiplantibacillus plantarum CCMA 0743 with Pichia kluyveri CCMA 0615 to ferment a non-dairy beverage made from oats, almonds, and sunflower seeds. After 24 h of fermentation both partners remained highly viable, with 9.32 log CFU/mL L. plantarum and 7.05 log CFU/mL P. kluyveri. The co-culture acidified the plant-based substrate, utilized carbohydrates, generated bioactive metabolites, increased linoleic acid, short-chain fatty acids, phenolic acids, vitamins B2 and B12, and GABA, and its fermented beverage promoted gut-microbiota recovery in a BALB/c mouse vancomycin-induced dysbiosis model.
Picocystis Activated-Sludge Refinery SWW Consortium
A laboratory algae-bacteria consortium combining Picocystis sp. with an aerobic activated-sludge bacterial consortium to treat petroleum refinery stripped wastewater (SWW). The study compared Picocystis monoculture and Picocystis plus bacteria in 2 L photobioreactors containing 10% or 25% SWW. The Pico-Bac consortium reached 72% COD reduction and 96.4% polyphenol reduction in 10% SWW, while hydrocarbon removal was highest at 80.4% in 25% SWW.
Pinus armandii Endophytic Biocontrol SynCom
A five-strain synthetic bacterial community (SynCom) assembled from endophytic bacteria isolated from multiple tissues of Pinus armandii to promote seedling growth and prime blister rust-associated defense responses. The optimized, functionally complementary SynCom comprises Pseudomonas koreensis RC1, Paenibacillus terrae RE7, Bacillus velezensis OB3 and NA3, and Bacillus subtilis NA11, selected for plant growth-promoting traits (nitrogen fixation, phosphate and potassium solubilization, IAA production) and antagonism of the rust pathogen. In pot experiments the SynCom increased seedling height and biomass and raised defense-related polyphenol oxidase and peroxidase activities relative to the control.
Pleuromutilin-degrading Artificial Consortium (5-strain)
A defined five-strain artificial microbial consortium constructed to degrade the antibiotic pleuromutilin, assembled from bacteria isolated out of a natural consortium (En4) that was itself developed by gradient enrichment and domestication under pleuromutilin stress. The consortium comprises Stenotrophomonas pavanii, Stenotrophomonas maltophilia, Lysinibacillus sphaericus, Lysinibacillus mangiferihumi, and Pseudomonas songnenensis, and achieves a pleuromutilin degradation rate of 91.97%. In the parent natural community, pleuromutilin stress reduced microbial diversity and selected core taxa with functional specialization (notably Proteobacteria, and enriched pollutant-degrading genera such as Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium and Cupriavidus), and potential degradation products and metabolic pathways were proposed for the artificial consortium.
PMI Variovorax Thermotolerance Collection
A 25-strain Variovorax collection from Populus roots, screened for bacterial effects on Arabidopsis thaliana thermotolerance using a rapid hydroponic assay. Six strains (CF313, YR634, GV004, GV035, YR752, OV084) significantly improve plant heat tolerance at 45C. CF313 was selected for detailed follow-up study. The thermal benefit requires direct contact with living bacteria; heat-killed bacteria and culture supernatants provide no protection.
PMSX Carbon-Substrate Biofilm SynCom
A defined four-member bacterial SynCom, abbreviated PMSX, containing Paenibacillus amylolyticus, Microbacterium oxydans, Stenotrophomonas rhizophila, and a strain reclassified as Stenotrophomonas maltophilia. Zhu et al. grew the soil isolates in M9 media and chemically defined 3D-printed hydrogels with diffusible sugars or polymeric cellulose/xylan carbon sources, measured crystal-violet biofilm biomass and FISH spatial patterning, and found that the complete SynCom robustly formed more biofilm than subsets while polymer-rich carbon sources drove self-organization around the Paenibacillus member.
Polaromonas Vanadium Reduction Community
A microbial community from vanadium mine tailings in northern China capable of reducing toxic soluble vanadate [V(V)] to less soluble vanadyl [V(IV)], facilitating vanadium detoxification and immobilization. This community is dominated by Polaromonas species (Burkholderiaceae family, up to 46% relative abundance in tailings) that perform dissimilatory V(V) reduction using genes homologous to iron and metal reduction pathways (cymA, omcA, narG). The tailings harbor diverse metal-reducing bacteria including sulfate reducers (Desulfovibrio, Desulfitobacterium) and iron-reducing Proteobacteria (Geobacter-related organisms) that contribute to reductive immobilization of vanadium and co-occurring metals. V(V) reduction to V(IV) decreases vanadium solubility by 2-3 orders of magnitude, transforming mobile vanadate into sparingly soluble vanadyl species and V(IV)-containing minerals. The community is enriched from highly contaminated mine tailings with total vanadium concentrations reaching 10,500 mg/kg and bioavailable V(V) at 15-25 mg/L in pore water. Under anaerobic conditions with electron donors (lactate, acetate, hydrogen), the community achieves 60-85% V(V) reduction within 7-14 days. Genes encoding c-type cytochromes (cymA, omcA), nitrate reductases (narG, napA), and arsenate reductases (arrA) mediate V(V) reduction through outer membrane electron transfer pathways. This represents the first demonstration of microbial V(V) reduction in circumneutral pH mine tailings, providing a biological approach for vanadium immobilization and mine remediation. The system is particularly relevant for emerging vanadium contamination from steel production, petroleum processing, and vanadium redox flow battery manufacturing.
Polyhydroxyalkanoate-Producing Mixed Microbial Culture Under Phage Predation
Five parallel 2 L sequencing batch reactors enriched from municipal activated sludge under an aerobic dynamic feeding regime, each on a single volatile fatty acid or lactate as sole carbon source, and followed for 145 days by paired metagenomics and metatranscriptomics. The polyhydroxyalkanoate-producing mixed microbial cultures (PHA-MMCs) include dominant Azoarcus, Paracoccus, Azomonas, Thauera, and Brevundimonas populations across the different reactors. The study recovered 963 metagenome-assembled genomes and 4,294 phage operational taxonomic units. Bacterial and phage community turnover are statistically associated. Structural equation modeling estimates a negative association of phage abundance with bacterial alpha diversity and activity. The authors propose kill-the-winner predation as an explanation for alternating dominance; this is a model-inferred mechanism, not a controlled phage perturbation or direct demonstration of host lysis. Predicted host links and defense systems are sequence-derived. Predicted phage auxiliary metabolic genes are transcribed, but transcription does not establish a contribution to PHA yield or productive lytic infection. This many-phages-on-many-bacteria system complements the experimentally manipulated four-species community in CommunityMech:000467. The two records preserve the distinction between inferred phage effects and experimental intervention.
Populus Salt-Tolerant Rhizosphere SynComs
Function-driven Populus rhizosphere SynComs selected from high-salt soil to improve salt resistance in hybrid poplar.
Poultry-Wastewater Three-Strain Electroactive Consortium
A defined equal-volume consortium of Lysinibacillus sphaericus A1, Bacillus cereus A2, and Lactococcus lactis A4 tested in dual-chamber microbial fuel cells containing amended, sterilized poultry slaughterhouse wastewater. The consortium produced more power and removed more chemical oxygen demand than the constituent strains tested separately during the 30-day experiment.
PPCP Wastewater Sphingopyxis-Ochrobactrum-Apiotrichum SMC
A three-member synthetic microbial community comprising Sphingopyxis sp. GC21, Ochrobactrum sp. TCC-2, and Apiotrichum sp. IB-1. Xu et al. assembled the two bacterial strains and one fungal strain to enhance simultaneous removal of the pharmaceutical and personal care products chloramphenicol, triclocarban, and naproxen from simulated wastewater and real domestic wastewater under aerobic and anoxic conditions.
PPHET Hybrid Photosynthetic PHB Microbiome
A hybrid photosynthetic microbiome that combines the engineered polyhydroxybutyrate-producing cyanobacterium Synechocystis sp. PCC 6803 PPT1 with the non-cyanobacterial fraction of a wild cyanobacteria-rich microbiome (WCRM). The engineered phototroph replaced the native cyanobacterial component of WCRM while retaining a heterotrophic community dominated by Proteobacteria/Pseudomonadota and Bacteroidota. PPHET accumulated up to 48% PHB per cell dry weight in nitrogen-limited small-scale photoautotrophic cultures, continued to accumulate PHB under dark acetate-fed conditions in which PHB granules localized primarily to heterotrophic members, and retained PHB production in non-sterile 4 L flat-panel and 8 L dark scaled reactors.
Prairie Pothole Wetland Sulfur-Carbon Virus-Host Community
Natural wetland sediment microbial and viral communities from the Prairie Pothole Region of North America, curated around genome-resolved metagenomic evidence for high-rate sulfur and carbon cycling. The study recovered sulfate-reduction marker genes, candidate sulfate-reducing genomes, methanogenesis marker genes, putative methanogen genomes, and abundant novel viral populations predicted to target dominant sulfate reducers and methanogens. The community is DOE-relevant because DNA sequencing and analysis were conducted by the DOE Joint Genome Institute and because the system links wetland methane emissions, sulfate reduction, carbon mineralization, and virus-host controls.
Premature Infant Gut Escherichia In-Situ Physiological-Condition Community
A premature infant gut microbiome study that combines metagenomic and metatranscriptomic sequencing to probe the in situ physiological conditions experienced by Escherichia spp. in four premature infants (two of whom developed necrotizing enterocolitis, NEC). Twenty fecal samples spanning 4-6 time points per infant were analyzed using sample-specific metagenome-assembled genomes (MAGs) as references for transcript mapping, and a "diametric ratio" method that compares transcript ratios of genes with opposite transcription responses to eliminate biases related to organism abundance. Diametric ratios of genes associated with low oxygen levels were significantly higher in samples from infants later diagnosed with NEC than in samples without NEC, and the method extends to other physiological conditions such as nitric oxide exposure and osmotic pressure.
Priestia-Pseudomonas Rice Arsenic-Stress SynCom
A defined two-member synthetic microbial community composed of Priestia flexa and Pseudomonas putida that mitigates arsenic toxicity in rice (Oryza sativa var. Sarju-52). In arsenite- and arsenate-stressed paddy-soil assays, SynCom inoculation restored plant photosynthetic and metabolic balance, limited oxidative-stress responses, reduced arsenic accumulation in roots, shoots and grains, and coordinately down-regulated rice arsenic-transporter genes including Lsi1, Lsi2, Lsi3, OsNIP1;1, and OsNIP3;3.
Prochlorococcus-Alteromonas Helper Coculture
A defined marine phototroph-heterotroph coculture in which the cyanobacterium Prochlorococcus marinus MIT9312 is paired with the heterotrophic helper bacterium Alteromonas macleodii EZ55. The system models an ocean-surface interaction where Prochlorococcus is vulnerable to hydrogen peroxide because it lacks catalase, while Alteromonas removes reactive oxygen species and thereby expands the conditions under which Prochlorococcus can grow. Elevated carbon dioxide perturbs this interaction by reducing Alteromonas catalase expression and hydrogen peroxide removal.
Propanotrophic Chlorinated Ethene Cometabolism Enrichment Cultures
Propane-enriched aerobic mixed cultures derived from three Michigan State University Long-Term Ecological Research agricultural soils (Soils T2, T3, T4) and from impacted-site sediment at a West Coast Naval Station (Site 1), evaluated for cometabolic biodegradation of three chlorinated ethenes - trichloroethene (TCE), cis-1,2-dichloroethene (cDCE), and 1,1-dichloroethene (1,1-DCE) - in the presence of propane as growth substrate. Substrate-specific selection drove distinct dominance patterns: cDCE-amended cultures were dominated by Mycolicibacterium followed by Mycobacterium, TCE-amended cultures were dominated by Rhodococcus (R. opacus or R. wratislaviensis from agricultural soils; Mycolicibacterium/Mycobacterium/Rhodococcus mixture from the impacted site sediment), and the subset of 1,1-DCE-degrading cultures was dominated by Pseudonocardia (with a truncated propane monooxygenase alpha subunit suggesting alternative enzymes drive 1,1-DCE transformation). The enrichments express group 5 (prmABCD) and putative group 6 propane monooxygenases. The system supports development of propane-based bioaugmentation strategies for mixed chlorinated solvent contamination under aerobic conditions.
Prymnesium parvum B12-Limited SynCom
A defined 16-member marine algal-bacterial holobiont in which Prymnesium parvum CCAP 646/6 was cocultured in L1 medium with a 15-strain synthetic bacterial community and monitored under nitrogen, phosphorus, or vitamin B12 limitation. Patron et al. (2026) inoculated all SynCom bacteria in equal proportions and compared photobioreactor cultures with and without the SynCom for 14 days. Nitrogen and phosphorus limitation did not reveal a major growth benefit from the SynCom, whereas B12 limitation triggered a mutualistic state in which bacterial cobalamin provisioning rescued algal growth, B12-producing bacteria upregulated cobalamin biosynthesis, and B12-auxotrophic bacteria induced vitamin transport and B12-dependent enzymes.
Pseudo-nitzschia-Sulfitobacter Marine Association
A mutualistic marine diatom-bacteria association between Pseudo-nitzschia multiseries and Sulfitobacter sp. SA11, mediated by auxin and tryptophan signaling. The bacterium synthesizes the auxin indole-3-acetic acid (IAA) from diatom-secreted and endogenous tryptophan, promoting diatom cell division as part of a complex nutrient exchange that also includes diatom organosulfur compounds and bacterial ammonia.
Pseudomonas aeruginosa Eight-Strain Full-Factorial SynCom
A full-factorial synthetic community panel built from eight Pseudomonas aeruginosa mutants: pAOV, PA14, NfxB, ParR-CAZ, mexZ, OrfN, NfxB-CAZ, and MDR6-CAZ. Diaz-Colunga et al. assembled all 256 strain combinations in LB medium in 96-well plates, measured post-growth absorbance spectra after 40 h at 37 C, and identified the three-member 00001101 consortium containing strains 1, 3, and 4 as the highest-Abs600 combination.
Pseudomonas putida Pp-TE + Rhodococcus sp. RDK17 Terephthalic-acid Consortium
Two-strain synthetic consortium of an engineered degrader (Pseudomonas putida strain Pp-TE) and a native degrader (Rhodococcus sp. strain RDK17) grown with terephthalic acid (TPA), a primary polyethylene terephthalate (PET) monomer, as the sole carbon and energy source. Although both strains utilize TPA at comparable rates in monoculture, Pp-TE consistently outcompetes RDK17 in batch and multitransfer coculture fermentations. Dominance is driven jointly by exploitative competition for TPA and by interference competition through the Pp-TE type VI secretion system, which impairs RDK17 growth via contact-dependent inhibition. Loss of TPA metabolism in Pp-TE abolishes its dominance, illustrating how interspecies interaction and metabolic capability co-determine consortium structure and overall TPA degradation.
Pseudomonas stutzeri + Rhodococcus Naphthalene-degrading Biochar-bridged Engineered Consortium
Two-member engineered bioremediation consortium in which genetically engineered Pseudomonas stutzeri (overexpressing nahAc and nahB) and a Rhodococcus strain (overexpressing nahH and catA) are co-anchored on S-N-doped biochar to mineralize naphthalene. Pseudomonas stutzeri acts as an oxidative bio-anode that initiates naphthalene degradation and releases electrons, while the conductive biochar matrix mediates direct interspecies electron transfer (DIET) and extracellular electron transfer (EET) to Rhodococcus, which serves as a reductive bio-cathode driving oxygenolytic ring-cleavage catalysis. The resulting bioelectrochemical syntrophic circuit achieved >98.3% naphthalene removal and 89.5% mineralization by circumventing diffusive bottlenecks.
Pseudomonas, Achromobacter, and Stenotrophomonas Prometryn-Degrading Consortium
Defined 1:1:1 synthetic bacterial consortium composed of Pseudomonas sp. ZM-1, Achromobacter sp. ZM-2, and Stenotrophomonas sp. ZM-3 isolated from long-term prometryn-contaminated cornfield soil in Harbin, China. The consortium synergistically degrades the methylthio-s-triazine herbicide prometryn (96.87% removal in 12 h in liquid culture and 96.3% removal over 30 days in soil microcosms) and alleviates prometryn phytotoxicity in maize (Zea mays).
Pseudomonas-Acidovorax Aniline-Degradation SynCom
A two-member Pseudomonas sp./Acidovorax sp. synthetic microbial consortium, RF-PH, assembled from the aniline-degrading strains RF and PH isolated from heavily aniline-contaminated soil in a Dalian chemical industrial park. Pan et al. 2026 identified Pseudomonas and Acidovorax isolates by 16S rRNA sequencing, optimized their inoculation ratio in mineral-salts medium containing aniline, and designated a 3:1 RF:PH mixture as RF-PH after the consortium outperformed either monoculture in aniline shake-flask assays.
Pseudomonas-Bacillus Waxy Oil Biodegradation Consortium
A defined two-member consortium of Pseudomonas aeruginosa PA12 and Bacillus subtilis G1 engineered to biodegrade waxy crude oil. Bacillus improves access to the oil-water interface and supplies metabolic precursors, while Pseudomonas performs deeper oxidation of long-chain alkanes and aromatics.
Pseudomonas-Klebsiella-Alcaligenes Fe2+ Nitrogen-Removal SynCom
A defined three-member synthetic bacterial consortium composed of the aerobic denitrifier Pseudomonas stutzeri, the facultative anaerobic denitrifier Klebsiella sp., and the heterotrophic nitrifying-aerobic denitrifying bacterium Alcaligenes sp. for Fe2+-regulated deep nitrogen removal. The 2026 Environmental Research abstract reports that the Fe2+ treatment increased nitrate-N removal efficiency by 20-30% relative to other iron species and that metagenomic analysis associated Fe2+ with a shift in carbon and nitrogen metabolic networks, including higher dissimilatory nitrate reduction to ammonium pathway abundance and lower denitrification pathway abundance.
Pseudomonas-Paracoccus Bifenthrin-Degrading Consortium
A defined two-strain consortium of Pseudomonas aeruginosa PA and Paracoccus pantotrophus PP assembled from contaminated-soil isolates for bifenthrin biodegradation. P. aeruginosa PA hydrolyzes bifenthrin, while P. pantotrophus PP oxidizes the resulting bifenthrin-alcohol intermediate; PA extracellular polymeric substances also modify the local chemical microenvironment.
Pseudomonas-Pedobacter Social Spreading Coculture
A two-species soil-bacterial model community composed of Pseudomonas fluorescens Pf0-1 and Pedobacter sp. V48. When mixed on low-nutrient, high-salt hard agar, the two sessile monocultures produce an emergent interspecies social spreading phenotype in which both bacteria comigrate across the agar surface. The system is used to study contact-dependent and environment-dependent emergent motility in small soil microbial communities.
Pseudomonas-Rahnella native rhizosphere SynCom for Artemisia argyi phytoremediation
A simplified, native rhizosphere synthetic microbial community (SynCom) pairing a Pseudomonas isolate with a Rahnella isolate, assembled by a top-down design from rhizobacteria isolated from cadmium (Cd)-contaminated agricultural soil to partner with the perennial medicinal plant Artemisia argyi. The Pseudomonas-Rahnella pair shows strong Cd tolerance (~2 mM), plant growth-promotion (PGP) traits, and carbon fixation capacity, and was chosen for functional complementarity with minimal antagonism. Under Cd stress the SynCom establishes stable endophytic colonization (10-15%) rather than rhizoplane colonization, improving root biomass, Cd uptake, soil organic carbon accumulation, and essential-oil precursors, thereby coupling phytoremediation, productivity, and carbon sequestration.
Pseudomonas-Rhodococcus Chloronitrobenzene Coculture
A defined two-member aerobic laboratory coculture for chloronitrobenzene bioremediation. Pseudomonas putida HS12 was isolated using nitrobenzene enrichment and performs the first partial reductive and acetylation steps on 3- and 4-chloronitrobenzene. Rhodococcus sp. strain HS51 degrades the chlorohydroxyacetanilide intermediates, allowing the coculture to mineralize 3- and 4-chloronitrobenzenes when an additional carbon source is supplied.
PSY Transgenic Rice Rhizosphere Methane-Mitigating Community
A rice rhizosphere microbial community whose H2 cycling and methanogenesis are reshaped by host overexpression of PLANT PEPTIDES CONTAINING SULFATED TYROSINE (PSY) genes. Two independent transgenic rice genotypes (PSY1 and PSY2) reduced cumulative CH4 emissions by 38 percent and 58 percent over 70 days relative to controls. Genome-resolved metatranscriptomic, metagenomic, metabolomic, and metabolic modeling data from PSY rhizosphere soils show lower ratios of CH4 production versus consumption gene activities (largely hydrogenotrophic), decreased H2-producing gene activity, and increased bacterial H2 oxidation pathways. Assembled genomes of rhizosphere H2-oxidizing bacteria are enriched in gluconeogenic-acid utilization genes, and their activity is likely stimulated by elevated gluconeogenic-acid amino acids in PSY rice root exudates, lowering H2 available for hydrogenotrophic methanogens.
Pu'er Floral-Fruity Fungal SynCom
A defined three-fungus starter for controlled ripe Pu'er tea pile fermentation. Yan et al. 2026 inoculated sun-dried green tea leaves with a patented Saccharomyces cerevisiae, Rhizopus arrhizus, and Aspergillus niger starter at a 2:1:2 weight ratio, then integrated sensory evaluation, physicochemical measurements, volatile and non-volatile metabolomics, and metagenomic sequencing across six fermentation stages to profile the emergence of a floral-fruity aroma.
Quinoa SCDY1 Salt-Stress SynCom
A nine-isolate synthetic bacterial community discovered by cube-based screening of quinoa-associated isolates for Arabidopsis salt-stress growth promotion. Dangjarean et al. divided 135 quinoa isolates into five 3 x 3 x 3 cubes, treated each layer as a nine-isolate SynCom, and identified SynCom DY1 (SCDY1) as the 100 mM NaCl screening hit. SCDY1 combined Pseudomonas panipatensis-like isolate 82, Stenotrophomonas bentonitica-like isolate 85, Fictibacillus enclensis-like isolate 88, Novosphingobium subterraneum-like isolate 91, Herbaspirillum frisingense-like isolate 94, Acidovorax facilis-like isolate 97, Bacillus atrophaeus-like isolate 100, Priestia megaterium-like isolate 103, and Bacillus subtilis-like isolate 106.
QY2-S1 Dehalogenimonas-Rich Brominated-Flame-Retardant Consortium
A Dehalogenimonas-containing anaerobic enrichment culture obtained from e-waste-contaminated pond sediments in Longtang Town, Qingyuan, China, re-inoculated as QY2-S1, and assayed in anaerobic serum bottles for reductive debromination of the legacy brominated flame retardant BDE 99 and the novel cycloaliphatic flame retardant beta-TBCO. Zhang et al. showed that QY2-S1 transformed both substrates singly, that co-exposure reduced first-order transformation rates by 3- to 5-fold, and that Dehalogenimonas was the only detected organohalide-respiring genus in a stable consortium whose dominant fermenters and methanogens can supply H2, carbon, and cofactors for reductive dehalogenase activity.
Rammelsberg Cobalt-Nickel Tailings Consortium
A mesophilic acidophilic bacterial consortium applied to bioleach cobalt, copper, and other valuable metals from sulfidic mine tailings at the Rammelsberg polymetallic massive sulfide deposit in the Harz Mountains, Germany. This consortium represents one of the only industrial-scale cobalt bioleaching processes globally and demonstrates exceptional efficiency in recovering critical battery materials from low-grade mine tailings. The adapted microbial community consists mainly of Acidithiobacillus ferrooxidans (iron-oxidizing) and Acidithiobacillus thiooxidans (sulfur-oxidizing), achieving 91% cobalt and 57% copper extraction from bulk tailings (Co 0.02%, Cu 0.12%) after 13 days in stirred tank reactors at 10% pulp density. The consortium exhibits synergistic cooperation between iron and sulfur oxidizers, where iron oxidation by At. ferrooxidans generates ferric iron that chemically oxidizes sulfide minerals, while sulfur oxidation by At. thiooxidans prevents elemental sulfur passivation and maintains low pH through sulfuric acid production. Mineralogical analysis revealed that cobalt occurs on the surface of framboidal pyrite and is mobilized through microbial attack. This system demonstrates the biotechnological potential for recovering critical materials (cobalt, copper, nickel) from mine waste through environmentally sustainable bioprocessing, addressing both resource recovery and mine tailings remediation challenges relevant to the circular economy and battery supply chains.
RH1 Glyphosate Streptomyces Consortium
A defined four-member actinobacterial consortium assembled from Streptomyces sp. SPA2, Streptomyces rochei IT, Streptomyces variabilis Herb, and Streptomyces griseoincarnatus SC for laboratory glyphosate biodegradation. The strains were mixed at a 1:1:1:1 ratio after separate ISP2 pre-culture and OD590 normalization, then incubated in mineral salt medium with glyphosate as the only carbon source. In 15-day 30 C shake-flask assays, RH1 removed glyphosate across 1-200 mg/L initial concentrations, reached 92.06% glyphosate removal and 91.03% total organic carbon reduction at 50 mg/L, and outperformed the matching single-strain treatments at that concentration. Higher glyphosate doses inhibited consortium growth and degradation, and the Haldane-Andrews model was the best fit to the initial-concentration growth-rate response.
Rhizorhabdus-Cupriavidus BDE-47 Degradation SynCom
A defined aerobic two-isolate synthetic consortium pairing Rhizorhabdus wittichii YL-JM2C with the chloroaromatic-degrading strain reported as Cupriavidus necator JMP134 for 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) degradation. YL-JM2C uses the dioxygenase TcsAaAb to initiate BDE-47 conversion to 2,4-dibromophenol and 3,5-dibromocatechol; JMP134 hydroxylates the YL-JM2C dead-end 2,4-dibromophenol intermediate to 3,5-dibromocatechol, which can then enter an ortho-cleavage pathway in either strain. The bottom-up consortium removed BDE-47 from minimal salts medium and real wastewater microcosms.
Rhodococcus-Acinetobacter RAMC Mixed Plastic Upcycling SynCom
A bottom-up, two-member synthetic bacterial consortium, termed RAMC, that couples Rhodococcus jostii strain PET aromatic-carboxylate metabolism with Acinetobacter baylyi ADP1 aliphatic-carboxylate metabolism to consume oxygenated products from post-consumer mixed plastic deconstruction. The platform was optimized across SR:SA starting ratios of 9:1 through 1:9, completely consumed aromatic plus aliphatic model oxygenates that neither monoculture fully depleted, and supported an engineered RAMC-P_9/1 derivative that converted real mixed-plastic effluents into lycopene and microbial lipids.
Rhodococcus-Pseudomonas Plastic Pyrolysis Oil Waste Consortium
A defined three-member synthetic bacterial consortium composed of Rhodococcus opacus DSM 43250, Pseudomonas putida KT2440, and Pseudomonas sp. VLB120 for aerobic degradation of CARBOLIQ-derived plastic pyrolysis oil waste in a 2-nonanone organic-aqueous biphasic system. The consortium was rationally assembled to couple long-chain alkane degradation with aromatic-catabolism and solvent-tolerance functions, and its highest measured activity used an initial R. opacus:P. putida:VLB120 ratio of 1:1:2 at 30 C, 1:5 organic-to-aqueous phase ratio, and 20% v/v PPOW in the organic phase.
Rhodopseudomonas palustris and Escherichia coli Multilayered Cross-Feeding Coculture
Defined synthetic bacterial coculture pairing phototrophic nitrogen-fixing Rhodopseudomonas palustris CGA676 with fermentative Escherichia coli PFM2 in an obligate bidirectional carbon-and-nitrogen cross-feeding relationship evolved for 650-800 generations alongside matched monocultures. Beyond engineered carbon (organic acids from glucose fermentation) and nitrogen (ammonium from N2 fixation) exchange, the coculture engages in additional cross-feeding of adenine and iron that represses biosynthesis and scavenging gene expression in the recipient and limits rather than promotes emergent metabolic dependencies.
Rhodopseudomonas-E. coli Cross-Feeding Coculture
A reciprocal cross-feeding coculture pairing N2-fixing Rhodopseudomonas palustris with fermentative Escherichia coli.
Rhodopseudomonas-Geobacter Magnetite Redox Coculture
A defined laboratory coculture in which the phototrophic Fe(II)-oxidizing bacterium Rhodopseudomonas palustris TIE-1 and the anaerobic Fe(III)-reducing bacterium Geobacter sulfurreducens cycle electrons through magnetite. The system demonstrates that mixed-valence magnetite can act as a recyclable electron donor and electron acceptor, effectively functioning as a naturally occurring biogeochemical battery under changing light and redox conditions. This community is DOE-relevant because mineral-mediated electron flow shapes subsurface elemental cycling and can influence contaminant fate in sediments, aquifers, and engineered remediation settings.
Rice Acid Soil Bioinoculant SynCom
A customized rhizosphere-competent bacterial SynCom used as a bioinoculant to improve rice production in acid soils.
Rice FSQN Rhizosphere Microbiome SynCom
A four-strain synthetic microbial community, FSQN, applied to the rhizosphere soil and root microbiomes of rice (Oryza sativa) and compared with the single-strain Brevundimonas diminuta NH1 inoculant. FSQN was composed of Bacillus amyloliquefaciens FH1, Ochrobactrum tritici S112, Gluconacetobacter liquefaciens QZR14, and Brevundimonas diminuta NH1; after inoculation, high-throughput sequencing showed altered beta-diversity in rhizosphere soil and roots and functional predictions indicated enhanced ectomycorrhizal, endomycorrhizal, and plant-saprotrophic functions.
Rice Phosphorus Uptake Intercropping SynCom4
A four-strain rice rhizosphere SynCom from intercropping systems that enhances biomass and phosphorus uptake.
Rice-Duckweed Bacillus Biocontrol SynCom
An 8-member, Bacillus-dominated synthetic community (SynCom) assembled from a rice-duckweed agroecosystem by targeting taxa consistently shared across soil, root and shoot niches. The SynCom concurrently promotes rice growth and suppresses sheath blight caused by Rhizoctonia solani, reducing the final disease index by 70% without detectable phytotoxicity. Leave-one-member perturbations reveal a division-of-labor architecture: individual strains specialize in auxin production, siderophore-linked iron mobilization, or lipopeptide/polyketide-based antagonism, yielding complementary yet partially redundant contributions that render community performance resilient to single-member loss. 8 members total; strain-level identifiers available in supplementary data.
Richmond Mine AMD Biofilm
A thick, subaerial biofilm community from the Richmond Mine at Iron Mountain, California, representing one of the most extreme acid mine drainage (AMD) environments on Earth. This predominantly lithotrophic biofilm thrives at extraordinarily low pH (0.5-1.0) with temperatures ranging from 30-50°C and metal ion concentrations in the decagrams per liter range. The community is dominated by iron-oxidizing bacteria (Leptospirillum spp.) and archaea (Ferroplasma acidarmanus) that drive pyrite dissolution through ferric iron generation. Leptospirillum group II comprises 71% of detected clones, with Ferroplasma reaching up to 85% of cells in highly acidic microniches. The biofilm also contains nitrogen-fixing Leptospirillum group III (L. ferrodiazotrophum), making it a keystone species in this nitrogen-limited ecosystem. Ultra-small ARMAN archaea (Micrarchaeota and Parvarchaeota) with genome sizes ~1 Mb represent novel lineages found at 5-25% relative abundance. The community oxidizes approximately 1-2 × 10⁵ moles of pyrite per day, generating extreme acidity and solubilizing metals including iron (up to 24 g/L), zinc (several g/L), and copper (hundreds mg/L). This natural biofilm serves as a model system for understanding microbial life at pH extremes and has implications for biomining, bioremediation, and astrobiology.
Rifle Aquifer Bioanode Extracellular Electron Transfer Community
An electroactive microbial community established and maintained for almost four years in microbial electrochemical cells (MXCs) inoculated with a well-studied aquifer near Rifle, CO. Anodes were poised mostly at -0.2 to -0.25 V vs SHE to mimic iron-oxide mineral redox potentials, with acetate as the sole carbon source. Genome-resolved metagenomics of two biofilm and 26 planktonic samples yielded 84 bacterial and 2 archaeal near-complete draft genomes. A novel Geobacter sp. with at least 72 putative multiheme c-type cytochromes dominated the electrode-attached community, while diverse other organisms (Actinobacteria, Ignavibacteria, Chloroflexi, Acidobacteria, Firmicutes, Beta- and Gammaproteobacteria) also encoded multiheme cytochromes, porin-cytochrome complexes, and electrically conductive pili (e-pili), identifying a small subset of Rifle aquifer organisms that may mediate mineral redox transformations.
Rifle Uranium-Reducing Community
A microbial community stimulated for in situ bioremediation of uranium-contaminated groundwater at the Old Rifle site in Rifle, Colorado. This aquifer community demonstrates sequential reduction processes following acetate biostimulation at 1-3 mM concentrations. The community transitions through distinct metabolic phases: Phase I (days 0-50) dominated by Geobacter species (up to 89% of community) performing Fe(III) reduction coupled to U(VI) reduction, achieving 70% uranium removal within 50 days and reducing concentrations below the EPA treatment goal of 0.18 μM in some wells. Phase II (>50 days) shifts to sulfate-reducing bacteria including Desulfobacteraceae (45% by day 80), Desulfosporosinus, and Desulfotomaculum acetoxidans as Fe(III) becomes depleted. Geobacter metallireducens and Anaeromyxobacter dehalogenans reduce soluble U(VI) to insoluble U(IV), forming biogenic uraninite nanoparticles that immobilize uranium. Desulfovibrio species contribute to uranium reduction through enzymatic pathways while generating hydrogen sulfide that can chemically reduce uranium. This represents the first successful field demonstration of uranium bioremediation via stimulating subsurface Geobacter populations, providing an alternative to pump-and-treat remediation. Groundwater flow rate is 0.82 m/day, creating dynamic conditions where microbial metabolism must outpace uranium advection.
Rumen Substrate-Adapted Lignocellulose Enrichment Consortia
A laboratory panel of rumen-derived anaerobic enrichment consortia selected for 10 serial 72 h generations on four lignocellulosic substrates: alfalfa, barley straw, carboxymethyl cellulose, or a 1:1 arabinoxylan/acetylated-xylan mixture. The enrichments were derived from pooled rumen fluid from cannulated beef heifers in MC medium and were tracked by gas production, volatile fatty acids, and 16S V1-V2 amplicon sequencing. Substrate-specific late consortia showed divergent bacterial profiles, including Prevotella-dominated barley-straw enrichments, Bacteroides-rich CMC enrichments, and xylan enrichments associated with Caproiciproducens, Megasphaera, Lactobacillus, and caproate accumulation; alfalfa and xylan G10 cultures also retained core community structure after one month of cryopreservation and revival.
Saanich Inlet Oxygen Minimum Zone Redox-Gradient Community
A natural marine water-column microbial community from Saanich Inlet, a seasonally anoxic fjord on Vancouver Island, Canada that serves as a model oxygen minimum zone. Integrated geochemistry, rate measurements, metagenomics, metatranscriptomics, metaproteomics, and qPCR link community structure to coupled carbon, nitrogen, and sulfur cycling across a redox gradient, including SUP05-driven incomplete sulfide-dependent denitrification, nitrite leakage supporting anammox, and a complementary nitrous oxide reduction niche.
Saccharomyces Met-Trp4 FLO1 Resveratrol Coculture
A defined two-member synthetic Saccharomyces cerevisiae coculture that combines Met-Trp4 coauxotrophic cross-feeding, FLO1-mediated cell adhesion, and division of labor across the de novo resveratrol pathway. In the Met-Trp4 A-B:FLO1 configuration, a met14 knockout derivative of the nonflocculating 007 deletion background carries the FjTAL upstream module that converts L-tyrosine to p-coumaric acid, while a trp4 knockout partner carries the At4CL and VvVST1 downstream module that converts p-coumaric acid to resveratrol. After 48 h in SM medium, the FLO1 adhesion variant produced more resveratrol than the no-FLO1 Met-Trp4 A-B coculture, noncross-feeding controls, and a monoculture carrying the full pathway.
Saccharomyces-Acinetobacter Lignocellulose Hydrolysate Detoxification Coculture
A defined two-member synthetic coculture pairing engineered Saccharomyces cerevisiae and engineered Acinetobacter baylyi ADP1 for upgrading a synthetic lignocellulosic hydrolysate. A. baylyi ADP1 bioconverts the furan aldehyde inhibitors furfural and 5-hydroxymethylfurfural that are present in lignocellulose hydrolysates without competing with S. cerevisiae for substrates, while also redirecting S. cerevisiae's residual carbon sources and byproducts into wax esters. The detoxification function raises S. cerevisiae's lactic acid productivity approximately 1.5-fold compared to a monoculture, making the coculture a candidate platform for inhibitor-tolerant lignocellulose conversion.
Saccharomyces-Chlamydomonas Fungal-Algal Mutualism
A two-member synthetic fungal-algal community pairing Saccharomyces cerevisiae with Chlamydomonas reinhardtii under engineered laboratory conditions that force reciprocal carbon and nitrogen exchange. Yeast metabolizes glucose and supplies carbon dioxide to the alga, while the alga photosynthetically releases oxygen and converts nitrite into reduced nitrogen that supports yeast growth.
Salar de Atacama Lithium Brine Community
A halophilic archaeal-bacterial consortium from the world's largest lithium reserve in the Salar de Atacama, Chile. This community thrives in extreme hypersaline brines with lithium concentrations up to 1,500 ppm (1.5 g/L) and total salinity ranging from 34.7% (natural brine) to 55.6% (concentrated brine during industrial processing). The community is strongly dominated by halophilic archaea of the family Halobacteriaceae, with natural brines showing higher archaeal diversity (Halovenus 26.8%, Natronomonas 20.1%, Haloarcula 14%, Halobacterium 13%) compared to concentrated brines where Halovenus becomes even more dominant (41%). Bacterial diversity is phylogenetically richer in concentrated brines, with Rhodothermaceae (represented solely by Salinibacter, 56% in natural brine) being the most abundant bacterial family. The community demonstrates remarkable lithium tolerance and adaptation to chaotropic stress, making it highly relevant for understanding microbial ecology in extreme saline environments and potential biotechnological applications in lithium extraction and critical mineral bioprocessing. Lithium acts as a modulator of microbial richness and diversity, with bacterial diversity increasing and archaeal diversity decreasing as lithium concentration rises during industrial processing.
San Francisco Bay Area Sewage SARS-CoV-2 Metagenomic Surveillance Community
A metatranscriptomic surveillance community in municipal sewage from the San Francisco Bay Area used to detect regionally prevalent SARS-CoV-2 variants during the COVID-19 pandemic. RNA was sequenced directly from sewage collected by municipal utility districts to generate complete and nearly complete SARS-CoV-2 genomes. The major consensus SARS-CoV-2 genotypes detected in sewage were identical to clinical genotypes, showing that wastewater metatranscriptomics can profile viral genetic diversity at the community scale.
Sclerotinia Sclerotia 12-Strain Biocontrol SynCom
A twelve-strain bacterial synthetic community assembled from isolates recovered from Sclerotinia sclerotiorum sclerotia after 5 days in flooded non-autoclaved soil. The SynCom spans Caballeronia, Cupriavidus, Massilia, Paraburkholderia, Ralstonia and Trinickia isolates, was co-cultured with mature fungal sclerotia in 10 mL tubes, and was resolved spatiotemporally by a 10x Genomics Xenium panel targeting all twelve members. Sclerotia inoculated with the full SynCom reached 100% mortality by day 14, and the dropout design identified Trinickia sp. MC, proposed in the paper as Trinickia sclerotiorum sp. nov. type strain MC, as the apparent key bacterial contributor.
Sedimenting Arabinose-Glucose Saccharomyces Coculture
A defined two-member Saccharomyces cerevisiae coculture that partitions glucose and arabinose fermentation between specialist strains. ACE2 deletion gives the arabinose specialist a multicellular, fast-sedimenting phenotype, allowing selective biomass retention during sequential-batch cultivation and faster mixed-sugar conversion.
Sesame-flavor Baijiu Fuqu SynCom (13-genus)
Thirteen-genus synthetic microbial community (SynCom) designed for Fuqu, the fermentation starter used in sesame flavor-type baijiu (Chinese liquor) production. Multi-omics analysis identified 13 core genera - the fungal/yeast genera Aspergillus, Pichia, Saccharomyces, Trichosporon, Candida, Torulaspora, Clavispora and Wickerhamomyces and the bacterial genera Bacillus, Lactobacillus, Leuconostoc, Pediococcus and Weissella - as the core microbiota driving flavor-compound formation. Assembled into a SynCom, these members yielded the highest flavor-compound diversity and 3-(methylthio)-1-propanal (a key sulfur-containing flavor compound) content in simulative fermentation, and outperformed commercial Fuqu at large scale. The community represents an engineered strategy to enhance sulfur-containing flavor compounds during baijiu fermentation.
SF356 Thermophilic Cellulose-Degrading Community
A stable thermophilic cellulose-degrading consortium (SF356) from composting systems, consisting of five bacterial strains: Clostridium straminisolvens CSK1, Clostridium sp. FG4, Pseudoxanthomonas sp. M1-3, Brevibacillus sp. M1-5, and Bordetella sp. M1-6. The community exhibits both functional and structural stability over 20 subcultures at 50°C. Synergistic interactions occur between the anaerobic cellulolytic Clostridium and aerobic bacteria, where aerobes create anaerobic conditions while receiving acetate and glucose from cellulose fermentation.
Shewanella Denitrifying Richness SynComs
A panel of synthetic denitrifying communities assembled from 12 Shewanella denitrifiers with richness spanning one to twelve species and evolved for 180 days to measure how biodiversity-ecosystem functioning relationships changed for productivity and nitrate-reduction activity.
Shewanella oneidensis + Pseudomonas aeruginosa Fe0-dependent Electro-syntrophic Denitrifying Consortium
Engineered two-member denitrifying consortium of the electroactive bacterium Shewanella oneidensis and the denitrifier Pseudomonas aeruginosa, operated in anaerobic conditions with metallic iron (Fe0) as the sole electron donor. S. oneidensis acts as a bio-engine, using its membrane-bound CymA-OmcA-MtrC complexes to harvest electrons from Fe0 biocorrosion and transfer them to P. aeruginosa. P. aeruginosa accepts these electrons for nitrate reduction, accomplishing microbial denitrification via a Fe0-S. oneidensis-P. aeruginosa electron-transfer system. This Fe0-dependent electro-syntrophy defines a metabolic window for denitrifier growth relevant to nitrate removal in water/wastewater treatment and the global nitrogen cycle.
Shewanella oneidensis MR-1 - Rhodopseudomonas palustris Electro-syntrophic Co-culture
Engineered two-species electro-syntrophic co-culture of Shewanella oneidensis MR-1 (the electron-donating partner) and Rhodopseudomonas palustris (the electron-accepting partner) built to study and enhance artificial interspecies electron transfer (IET). In-situ polydopamine (PDA) nano-encapsulation of the S. oneidensis MR-1 surface created a conductive, adhesive cell-to-cell interface that promoted stable coaggregation of the two partners and shifted the dominant IET mode from H2-mediated MIET toward contact-dependent direct electron transfer involving outer-membrane c-type cytochromes. Nitrogenase-derived CH4, used as a quantitative indicator of IET efficiency, increased by roughly 380% in the engineered community.
Shewanella-Acetogen Electrosynthetic Consortia for CO2-to-Acetate
Defined synthetic microbial electrosynthesis (MES) consortia constructed by pairing the model bidirectional electroactive bacterium Shewanella oneidensis MR-1 with either the electroactive acetogen Clostridium aceticum or the nonelectroactive acetogen Acetobacterium woodii, mimicking functional guilds of natural MES communities. Co-cultivation boosts CO2-to-acetate production by up to 88%. The two pairings use distinct interspecies electron transfer (IET) modes, namely direct interspecies electron transfer (DIET) via cytochrome c and riboflavin at the biofilm-electrode interface in the S. oneidensis-C. aceticum consortium, versus H2/formate-mediated IET in the planktonic phase for the S. oneidensis-A. woodii consortium. This metabolic stratification lets S. oneidensis act as an "ecosystem engineer" orchestrating electron flow across biofilm and suspension niches.
Shewanella-Geobacter Three-Species Exoelectrogenic Biofilm Community
A defined three-species anode-associated exoelectrogenic biofilm community composed of Shewanella oneidensis, Geobacter sulfurreducens, and Geobacter metallireducens. The community was assembled to study biofilm formation dynamics, strain interactions, redox potential resilience, and electron transfer activity in bioelectrochemical systems.
Shewanella-Streptococcus Starch-Fueled Microbial Fuel Cell Coculture
A defined starch-fed microbial fuel cell community pairing the exoelectrogen Shewanella oneidensis MR-1 with the starch-fermenting lactic acid producer Streptococcus bovis 148. The system was tested in two configurations: two-step fermentation, where S. bovis first converted starch to lactic acid before S. oneidensis generated electricity, and parallel fermentation, where cultivation and fermentation by both organisms occurred simultaneously. The community is relevant to DOE bioenergy and bioelectrochemical systems because it couples conversion of a polymeric biomass substrate to lactate cross-feeding and extracellular electron transfer in a microbial fuel cell.
Shrimp Vibrio-Resistance Gut-Enrichment SynCom Panel
A four-SynCom panel constructed from shrimp gut bacterial enrichment cultures screened for resistance to Vibrio parahaemolyticus infection. Shen et al. enriched gut consortia in R2A plus kanamycin, R2A, and Gauze's Synthetic Medium No.1, isolated eight corresponding key bacterial strains from enriched genera, and assembled SynComAll, SynCom R2A+Kan, SynCom R2A, and SynCom GM1; addition of these SynComs improved shrimp fitness and conferred protection against V. parahaemolyticus infection.
Sichuan Shai Vinegar Yeast Flavor SynCom
A defined yeast consortium model for early solid-state fermentation of Sichuan Shai vinegar. Zhu et al. 2026 compared four key yeast species by co-culturing, metabolomics, and simulated fermentation, then identified Pichia kudriavzevii, Kazachstania humilis, and Brettanomyces bruxellensis as a triple consortium with optimal synergy for total acid, acetic acid, and characteristic flavor-profile formation.
SIHUMIx Human Intestinal Model Community
SIHUMIx is an extended simplified human intestinal microbiota consisting of eight bacterial strains used as a reduced-complexity in vitro model of the human gut microbiome. The community includes common intestinal anaerobes and facultative bacteria spanning major gut-associated lineages, and it is maintained under anaerobic bioreactor conditions in complex intestinal medium. SIHUMIx supports controlled metaproteomic, metabolomic, metatranscriptomic, and community stability studies, including analysis of short-chain fatty acid output and community-specific small proteins.
SkinCom Synthetic Skin Community
A standardized synthetic skin microbial community for reproducible in vitro and in vivo studies of skin-associated microbe-metabolite interactions.
SO3-BS3 Lithium-ion Battery Bioleaching Consortium
A two-member engineered Shewanella oneidensis MR-1 and Bacillus subtilis 168 synthetic consortium for metal oxide leaching from spent LiNixCoyMn1-x-yO2 lithium-ion battery cathode black mass using Moutai brewing wastewater as the organic leaching medium. The final SO3-BS3 design pairs S. oneidensis SO3, engineered for riboflavin synthesis and Deinococcus IrrE-mediated metal-ion stress resistance, with B. subtilis BS3, engineered for ethanol detoxification, riboflavin production, and IrrE-mediated resistance. In anaerobic bottle cultures with 0.2 g/L black mass, the SO3-BS3 consortium increased total dissolved Li, Ni, Co, and Mn to 102.4 mg/L by reducing NCM through MtrC/OmcA- and riboflavin-mediated extracellular electron transfer.
Soil Biosynthetic Gene Cluster Phylum-Depth-Vegetation Community
A soil bacterial community surveyed for secondary-metabolite biosynthetic gene cluster (BGC) content across three sites in a northern California Critical Zone Observatory with varying vegetation and bedrock. 1,334 metagenome-assembled genomes were reconstructed and screened for BGCs, including genomes for prolific producers among Actinobacteria, Chloroflexi, and candidate phylum Candidatus Dormibacteraeota. One Candidate Phyla Radiation (CPR) bacterial genome encoded a ribosomally synthesized linear azole/azoline-containing peptide, a capacity also found in other publicly available CPR genomes. Bacteria with higher biosynthetic potential were enriched in shallow soils and grassland soils, with BGC-type patterns varying by taxonomy.
Soil Corrinoid Reservoir Microbial Community
A grassland soil microbial community in which the structurally diverse corrinoid (vitamin B12-related) cofactor pool serves as a key determinant of community structure. Analysis of metagenome-assembled genomes implicates Thermoproteota, Actinobacteria, and Proteobacteria as the principal corrinoid suppliers. Corrinoids accumulate adhered to the soil matrix at levels exceeding the requirements of cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids exhibit distinct shifts in bacterial community composition, supporting the hypothesis that corrinoid structure shapes communities, with environmental context modulating both community-level and taxon-specific responses.
Soil CPR Bacteria and Nanoarchaea Rare-Biosphere Community
A rare-biosphere community of Candidate Phyla Radiation (CPR) bacteria and DPANN archaea recovered from grassland soil by concentrating particles smaller than 0.2 micrometers prior to metagenomic sequencing. CPR and DPANN sequences were enriched 100- to 1,000-fold compared to bulk soil (estimated at roughly 1 to 100 cells per gram of soil for each lineage) and include Doudnabacteria (SM2F11) and Pacearchaeota - organisms rarely reported in soil - alongside Saccharibacteria, Parcubacteria, and Microgenomates as well as Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota. Most members likely live symbiotic anaerobic lifestyles, but some Saccharibacteria, Parcubacteria, and Doudnabacteria encode components of aerobic metabolism that may be particularly relevant in oxic soil habitats.
Sorghum SRC1 Subset Community
A simplified synthetic rhizosphere community (SRC1-subset) derived from the larger SRC1 consortium for enhancing sorghum bioenergy crop productivity. The subset consists of 16-20 bacterial strains selected from the full 57-strain SRC1 community, including multiple Pseudomonas, Bacillus, and Arthrobacter strains. This engineered community was designed using network analysis to identify hub taxa and strains capable of utilizing sorghum-specific root exudate compounds. Field-tested studies demonstrate that the community effectively colonizes sorghum rhizosphere and roots, leading to increased shoot biomass and improved yield performance under field conditions. The growth enhancement correlates with transcriptional dampening of lignin biosynthesis in the host plant.
Sorghum SRC2v4 Root Colonization SynCom
A 15-member reduced-complexity Sorghum bicolor synthetic root community rationally derived from the 57-member Sorghum Root Consortium 1 (SRC1). SRC2v4 was designed by ranking SRC1 strains by cumulative root abundance in a prior permutational membership experiment, prioritizing known sorghum root-exudate users when abundance rankings were highly similar, and selecting 15 high-colonization isolates with unique 16S rRNA gene sequences in the V3-V4 region. In gnotobiotic 5-l sterile microboxes, SRC2v4 showed exceptional compositional fidelity relative to its inoculum, stably colonized roots and rhizospheres, promoted plant growth as a live community but not as a heat-killed inoculum, and induced coordinated S. bicolor transcriptional and metabolomic responses centered on flavonoid biosynthesis.
South Bay Salt Pond Methane Restoration Microbial Community
Natural sediment microbial communities from former industrial salt ponds, a restored salt pond, and a reference tidal wetland in the San Francisco South Bay Ravenswood complex. DOE JGI-supported 16S rRNA amplicon and shotgun metagenomic analyses linked wetland restoration state to microbial composition, metabolic potential, and methane flux. Unrestored salt ponds had elevated methane emissions that were positively correlated with salinity and sulfate, while the restored pond resembled the reference wetland more closely and showed lower salinity, sulfate, and methane emissions. The study implicates archaeal methanogenesis and bacterial methylphosphonate degradation as methane-generating mechanisms in these coastal wetland sediments.
Soy Sauce Temporal Seven-Species SynCom
A laboratory-scale temporal synthetic microbial community for soy sauce moromi fermentation. Chen et al. 2026 distilled a nine-member candidate set to seven core species and tested delayed inoculation schemes in which Aspergillus oryzae 3.042 made koji, Weissella paramesenteroides WP-8 was added at day 0, Lactiplantibacillus plantarum JL-20 at day 5, Pediococcus pentosaceus PP-11 plus Tetragenococcus halophilus R44 at day 10, and Zygosaccharomyces rouxii ZQ-01 plus Candida orthopsilosis CV-13 at day 25. The best W->L->P+T->Z+C formulation raised glutamic acid, 4-ethylguaiacol, and total volatile production relative to the traditional-fermentation control under homogeneous 40-day laboratory conditions.
Soybean Chlorophyll-Selected Biofertilizer SynCom
A plant-guided soybean rhizosphere SynCom selected through iterative chlorophyll-based microbiome engineering to improve nodulation and biomass in soil.
Soybean N-Fixation Simplified SynCom
A simplified synthetic community (sfSynCom) for enhanced symbiotic nitrogen fixation in soybean, based on core-helper strain interactions. The consortium consists of Bradyrhizobium elkanii BXYD3 as the core nitrogen-fixing symbiont and two Pantoea helper strains. The helper strains produce acyl homoserine lactones (AHL) that enhance colonization and infection of soybean roots by B. elkanii through quorum sensing, significantly improving nodulation and nitrogen fixation compared to single-strain inoculation.
Soymilk Mixed-Starter Metabolic Division SynCom
A three-species lactic-acid-bacterial mixed starter culture for controlled soymilk fermentation, composed of Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, and Lactiplantibacillus plantarum. Li et al. 2026 used metatranscriptomics, non-targeted metabolomics, and single-strain dropout fermentations to resolve a cooperative succession in which S. thermophilus dominated mid-stage fermentation, L. plantarum subsequently dominated late-stage fermentation, and L. bulgaricus cross-fed the auxotrophic community.
Space Habitat Seven-Member Stress-Tolerance SynCom
A defined seven-member bacterial consortium assembled as a tractable space-habitat microbiome model from ISS-derived, spacecraft-associated, and biosafety-level-1 strains of genera commonly detected in spacecraft. The consortium contained Staphylococcus capitis K1-2-2-23, Bacillus subtilis W2-B1-K4, Pseudomonas antarctica CMS 35T, Streptococcus halotolerans HTS9T, Propionibacterium cyclohexanicum TA-12T, Micrococcus luteus W4-Al-K1, and Acinetobacter radioresistens 50V1. Equal OD-adjusted suspensions of the seven species were pooled to OD600 0.125 and used for static co-cultivation, early biofilm biomass, desiccation, X-ray irradiation, hydrogen peroxide, and pilot 16S rRNA gene sequencing assays. The study quantified stress survival of B. subtilis and S. capitis as single species and inside the full consortium; consortium context increased B. subtilis survival after 500 Gy X-ray irradiation but lowered recoverable B. subtilis CFU after 24 h co-cultivation in the full community.
Sphingobium-Nitrososphaera Phenanthrene-Carbon SynCom
A defined two-member synthetic community consisting of the PHE-degrading bacterium Sphingobium sp. RS2 and the carbon-sequestering archaeon Nitrososphaera viennensis EN76. The SynCom was added to phenanthrene-contaminated lettuce-soil pot experiments, where the accessible abstract reports 90.02% PHE removal from soil, an 81.07% reduction in PHE transferred to lettuce, and increases in soil organic carbon, microbial carbon, and total carbon.
Sphingobium-Rhodococcus Lignin-Dimer Valorization Coculture
A defined synthetic lignin-valorization coculture pairing a lignin-derived dimer-cleaving Sphingobium sp. with the aromatic-monomer-converting bacterium Rhodococcus opacus. The coculture was designed to funnel multiple low-molecular-weight lignin-derived dimers into cis,cis-muconate and gallate, addressing a key bottleneck in biological lignin conversion. The system is DOE-relevant because it targets lignin, a major underutilized component of lignocellulosic biomass, and demonstrates division of labor for microbial production of renewable chemical intermediates from lignin-derived aromatics.
SPRUCE Peatland Methane-Cycling Microbial Community
A natural peatland microbial community studied in the DOE-supported SPRUCE whole-ecosystem warming experiment at the S1 Bog in northern Minnesota. The community inhabits acidic, carbon-rich, waterlogged peat and mediates terminal anaerobic carbon turnover, including acetoclastic and hydrogenotrophic methanogenesis. Metagenome-assembled genomes and metatranscriptomes show depth-stratified microbial composition, active methanogenesis by Candidatus Methanoflorens, and temperature-sensitive methane and carbon dioxide production driven by activity changes rather than wholesale community replacement.
SPRUCE Peatland Warming Microbial Community
Microbial community from the SPRUCE (Spruce and Peatland Responses Under Changing Environments) whole-ecosystem warming experiment at Marcell Experimental Forest, Minnesota. This long-term DOE-funded experiment (ORNL) provides a unique whole-ecosystem warming gradient (+0°C to +9°C) with elevated CO2 (eCO2) treatments in a northern boreal peatland. The natural microbial community has been extensively characterized through amplicon sequencing (16S rRNA for bacteria/archaea, ITS for fungi) and metatranscriptomics, revealing climate change-driven shifts in community composition and function. Key findings include: (1) warming promotes saprophytic fungi and chemoorganoheterotrophic bacteria in root-associated environments, (2) eCO2 enhances ectomycorrhizal fungal associations with vascular plants, particularly short-distance exploration strategies targeting labile soil nitrogen, (3) vascular plant fine root traits mediate climate effects on microbial communities, serving as a critical mechanism for peatland vegetation responses to global change. The community exhibits distinct niche partitioning between aquatic (waterlogged surface peat) and terrestrial (deeper peat) zones. Viral communities (4,326 vOTUs) show strong correlations with peat depth, water content, and carbon chemistry (CH4/CO2) but not temperature during initial warming phases. This represents one of the most comprehensively studied natural microbial communities under realistic climate change scenarios, with implications for carbon cycling, methane emissions, and ecosystem feedbacks in boreal peatlands. Northern peatlands store approximately one-third of global soil carbon despite covering only 3% of land area, making their responses to warming and eCO2 critical for global carbon cycle feedbacks. The comprehensive multi-omics datasets (amplicon, metagenome, metatranscriptome, virome) make this community exceptionally well-characterized for mechanistic modeling of climate-microbe-plant-carbon interactions.
Staged Ensifer-Bacillus Cattle-Manure Wastewater SynCom
A defined two-member staged consortium, SYC, pairing the heterotrophic ammonia-oxidizing core strain Ensifer sp. S2-8-1 with an auxiliary Bacillus subtilis strain to convert cattle manure wastewater into a bioactive fermentation broth for maize growth promotion. The primary study compared an S2-8-1 monoculture, simultaneous co-culture, and the staged consortium, and reported that SYC had the best overall performance, enhanced rhizosphere nitrification, increased NO3--N availability, promoted maize growth, and increased whole-plant dry matter in a soil-maize pot experiment.
Staphylococcus-Candida Context-Dependent Biofilm Coculture
A defined interkingdom biofilm composed of Staphylococcus aureus and Candida albicans. Primary studies of this exact species composition report outcomes ranging from contact-dependent antagonism to hypha-supported colonization and copper-mediated mutualism, demonstrating strong dependence on strains, nutrients, surfaces, growth state, and colonization order.
Stordalen Mire Methylotrophic Methanogenesis Community
Natural thaw-gradient peat microbial communities from Stordalen Mire in Arctic Sweden, curated around genome-resolved multi-omics evidence for direct and indirect methylotrophic routes to methane production. The study expanded genomic representation of native methanogens, identified methanogenic MAGs with methylotrophic potential and transcriptional activity, detected broad bacterial anaerobic methylotrophic potential, and observed active methylotrophy across palsa, bog, and fen stages of permafrost thaw. The community is DOE-relevant through USDOE Office of Science BER, PNNL EMSL, and JGI involvement and links permafrost thaw, wetland carbon cycling, and methane emissions.
Streptococcus mutans - Candida albicans ECC Biofilm Model
A defined cross-kingdom dual-species plaque biofilm model capturing the synergistic virulence of Streptococcus mutans and Candida albicans in early childhood caries. Coinfection produces an EPS-rich biofilm with higher biomass, larger microcolonies, and more severe carious lesions than either species alone.
Streptococcus mutans - Selenomonas sputigena ECC Pathobiont Model
A defined dual-species oral biofilm model derived from early childhood caries discovery-validation work. Selenomonas sputigena becomes trapped within Streptococcus mutans exoglucans, builds a honeycomb-like multicellular superstructure, enhances acidogenesis, and increases enamel lesion severity in vivo.
Streptococcus mutans - Veillonella parvula Adult Severe Caries Model
A defined dual-species oral biofilm model for adult severe caries pairing Streptococcus mutans with the ASC-associated pathobiont Veillonella parvula. The coculture increases mature biofilm formation, acid resistance, oxidative stress tolerance, and rodent caries severity relative to Streptococcus mutans alone.
Streptomyces A2-A5-A11-M7 Pesticide-Bioremediation Consortium
A repeatedly studied defined consortium of four Argentine Streptomyces soil and sediment isolates: A2, A5, A11, and M7. The unchanged composition has been evaluated across liquid cultures, immobilized cultures, soil slurries, microcosms, and mesocosms for lindane and other chlorinated pesticides, and most recently for atrazine removal and detoxification.
Subsurface Carboxydocella CO-Oxidation Aquifer Community
A deep subsurface (1.4 km) aquifer microbial community perturbed by injection of 150 tons of supercritical CO2 (scCO2) in a geosequestration experiment. Detailed genome-resolved metagenomics resolved the native carboxydotrophic Carboxydocella, a thermophilic CO-utilizing anaerobe whose relative abundance decreased post-scCO2 injection. Analysis of its carbon monoxide dehydrogenase (CODH) gene before and after the experiment documented a switch in CO-oxidation potential by Carboxydocella, with implications for subsurface flow of carbon and electrons from oxidation of the metabolic intermediate CO.
Suillus clintonianus-Bacillus altitudinis Thiamine Cross-Feeding SynCom
A cross-domain synthetic community in which the ectomycorrhizal fungus Suillus clintonianus, which cannot effectively obtain or synthesize the thiamine (vitamin B1) it needs for growth, recruits the hyphae-associated bacterium Bacillus altitudinis B4 to its mycelial surface. The fungus first secretes ureidosuccinic acid and pregnenolone to recruit the bacterium; the secreted ureidosuccinic acid then stimulates B. altitudinis B4 to increase biomass and upregulate thiamine biosynthesis genes, enhancing thiamine production. The fungus absorbs the bacterially produced thiamine, which promotes fungal growth and increases the ectomycorrhizal colonization rate of the host pine Pinus massoniana. The mechanism, resolved by nontargeted metabolomics and whole-genome sequencing, illustrates a vitamin-mediated tripartite symbiosis in which a prototrophic bacterial partner fulfills a fungal thiamine auxotrophy to support host-fungal mutualism.
Sulfide Spring Autotrophic CPR-Hosting Biofilm
An autotrophic biofilm community in sulfide-rich springs sustained by deeply sourced groundwater. Genome-resolved metagenomics combined with bulk geochemistry and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K reveals biofilms dominated by chemolithotrophic sulfur-oxidizing bacteria including Thiothrix and Beggiatoa, with diverse Candidate Phyla Radiation (CPR) bacteria (Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, Parcubacteria). STXM imaging shows ultra-small cells adhered near filamentous bacteria, suggesting CPR episymbiosis. Carbon K and sulfur L2,3 edge NEXAFS spectroscopy indicates that filamentous bacteria contain protein-encapsulated elemental sulfur granules consistent with Thiothrix-like sulfur oxidation, and Berkelbacteria and Moranbacteria are predicted to encode a novel electron bifurcation system.
SynCom + Chlorella sorokiniana Biogas-slurry Coupling System
A sequential synthetic microbial community (SynCom)-microalga coupling system engineered to treat livestock biogas slurry. An autochthonous microalga, Chlorella sorokiniana, isolated from the slurry is coupled with a SynCom pretreatment stage. The system operated stably for 60 days, achieving 94.41% nitrate-nitrogen removal, 81.84% total-phosphorus removal, and 6.31% chemical oxygen demand removal. SynCom pretreatment increased the biomass and soluble protein content of C. sorokiniana (by 27.15% and 488.10% vs the BG11 control), upregulating Rubisco and glutamine synthetase, providing a strategy for simultaneous pollutant abatement and resource recovery.
SynCom ARC Peanut Aflatoxin-Control and Nodulation-Coupling Community
A four-strain rhizosphere synthetic community — three Bacillus isolates (Bl13-2C11, Ba13-20E05, Bm14-5G09) and one Enterobacter isolate (El17-4B09) — assembled to couple two functions that are normally pursued separately in peanut: suppression of the aflatoxin-producing fungus Aspergillus flavus, and induction of rhizobia-legume nodulation. Candidate genera were chosen from cross-regional rhizosphere surveys as taxa negatively correlated with Aspergillus abundance but not with Bradyrhizobium, so that antifungal activity would not come at the cost of the nitrogen- fixing symbiont; strains that inhibited Bradyrhizobium in coculture were screened out on exactly that criterion. The resulting community, SynCom ARC, reduced peanut aflatoxin by 85.6% across four years of field trials and enhanced nodulation and nitrogenase activity while retaining active nodules at harvest. The record captures the community as a deliberately compatibility- constrained consortium: its design problem is not maximal antifungal potency but antagonism of the pathogen that spares a mutualist.
SynCom BsBv Cigar Tobacco Leaf Fermentation
Two-species synthetic microbial community (the BsBv SynCom) of Bacillus safensis and Bacillus velezensis, screened for high extracellular cellulase, amylase and protease activities and applied to cigar tobacco leaves (cultivar QX204) during a 42-day fermentation. The consortium accelerated degradation of cellulose, protein, and starch, shifted the leaf bacterial community toward Firmicutes/Bacillus, and modulated the volatile flavor metabolite profile (e.g. phenylacetic acid, phytol, farnesol) to enhance honey, floral, and baked aromas while reducing irritancy, thereby directionally improving cigar tobacco leaf quality.
SynCom MetG2 Rhizobacteria Sugarcane Stress Resilience
A rhizobacteria synthetic community (SynCom) named MetG2 inoculated onto sugarcane in a greenhouse experiment to enhance stress resilience through targeted modulation of plant-microbe interactions. Shotgun metagenome and metatranscriptome sequencing revealed temporal shifts in the rhizosphere microbial community, with up-regulation of genes for flagellar assembly, chemotaxis, quorum sensing, and biofilm formation (particularly within Proteobacteria), indicating active microbial movement toward root surfaces, alongside enrichment of genes for nutrient acquisition, hormone synthesis, siderophore production, and VOC synthesis. Sugarcane responded with up-regulation of hormone-related and nutrient-transporter genes and induction of stress-resistance genes, supporting MetG2 as a sustainable strategy to enhance crop productivity and resilience.
SynCom Y Agrobacterium-Bacillus Biofilm Biocontrol Co-culture
Two-species synthetic bacterial community (SynCom Y) of Agrobacterium deltaense LSQ16 and Bacillus velezensis WB, simplified from a larger biocontrol SynCom Q by stepwise strain omission. Co-cultivation synergistically enhances multispecies biofilm formation, extracellular polysaccharide production, and metabolic activity, improving suppression of watermelon Fusarium wilt. Genome-scale modeling predicts interspecies metabolite exchange (amino acids, purines, phosphates); exogenous L-ornithine and guanine enhance B. velezensis biofilm formation, consistent with cross-feeding-supported cooperation.
SynComBac10 Chicken Intestinal SynCom
A 10-member synthetic chicken intestinal community that promotes gut homeostasis and anti-Salmonella immunity through segmented filamentous bacteria establishment.
Synechococcus-Azotobacter Photoproduction Mutualism
A designed two-member light-driven microbial mutualism pairing sucrose-exporting cscB Synechococcus elongatus PCC 7942 with the diazotroph Azotobacter vinelandii AV3. The engineered cyanobacterium fixes carbon under illumination and exports sucrose, while A. vinelandii fixes nitrogen and can produce industrially relevant biopolymers such as polyhydroxybutyrate and alginate. The coculture was engineered to grow without added fixed carbon or fixed nitrogen and is relevant to DOE interests in photosynthetic bioproduction, carbon utilization, and nitrogen self-sufficient synthetic consortia.
Synechococcus-Bacillus Synthetic Photosynthetic Consortium
A synthetic, light-driven consortium pairing the cyanobacterium Synechococcus elongatus PCC 7942 (engineered to secrete sucrose via the cscB+ transporter) with Bacillus subtilis 168. The cyanobacterium fixes CO2 and exports sucrose, which supports heterotrophic growth of B. subtilis. This modular platform demonstrates a stable photosynthetic co-culture for sustainable carbon cycling.
Synechococcus-E.coli Synthetic Photosynthetic Consortium
A synthetic, light-driven consortium pairing the cyanobacterium Synechococcus elongatus PCC 7942 (engineered to secrete sucrose via the cscB+ transporter) with Escherichia coli. The cyanobacterium fixes CO2 and exports up to 85% of fixed carbon as sucrose, which supports heterotrophic growth of E. coli. This modular platform enables stable, long-term photosynthetic co-culture for biofuel precursor production and demonstrates a synthetic cross-feeding interaction that persists over days to months.
Synechococcus-Halomonas Light-Driven PHB Coculture
A synthetic, light-driven two-member phototroph-heterotroph consortium pairing sucrose-exporting Synechococcus elongatus PCC 7942 cscB with the halotolerant polyhydroxybutyrate producer Halomonas boliviensis LC1. The cyanobacterium fixes carbon dioxide under illumination and exports sucrose, while H. boliviensis consumes the cyanobacterial sucrose and accumulates the bioplastic precursor polyhydroxybutyrate. The system is relevant to DOE carbon utilization and bioproduct goals because it couples photosynthetic carbon fixation to heterotrophic biopolymer production in a modular synthetic coculture.
Synechococcus-Pseudomonas Phototrophic PHA and DNT Coculture
A synthetic, light-driven two-species coculture pairing engineered Synechococcus elongatus PCC 7942 cscB with engineered Pseudomonas putida strains that consume cyanobacterial sucrose. The cyanobacterium fixes CO2 and exports sucrose under salt/IPTG induction, while P. putida converts the transferred carbon into polyhydroxyalkanoates (PHA) and, in a related engineered implementation, transforms the industrial pollutant 2,4-dinitrotoluene. This platform is relevant to DOE carbon utilization, bioproduct formation, and contaminant bioremediation because it couples photosynthetic CO2 fixation to heterotrophic biocatalysis in a controlled laboratory community.
Synechococcus-Saccharomyces Synthetic Photosynthetic Consortium
A synthetic, light-driven consortium pairing the cyanobacterium Synechococcus elongatus PCC 7942 (engineered to secrete sucrose via the cscB+ transporter) with the budding yeast Saccharomyces cerevisiae W303Clump. The cyanobacterium fixes CO2 and exports sucrose, which supports heterotrophic growth of the yeast. Wild-type W303 did not grow in co-culture; W303Clump, an evolved derivative carrying mutations that enhance fitness in dilute sucrose, did, and maintained viability in continuous co-culture for more than two months.
Synechococcus-Shewanella D-Lactate Biophotovoltaic Consortium
A two-species engineered biophotovoltaic consortium pairing engineered Synechococcus elongatus UTEX 2973 with engineered Shewanella oneidensis MR-1. The cyanobacterium converts light and carbon dioxide into D-lactate, and the exoelectrogenic Shewanella partner oxidizes D-lactate and transfers electrons to an anode. The system is relevant to DOE bioenergy and bioelectrochemical research because it demonstrates division of labor for renewable electricity production from photosynthesis, metabolite transfer, and extracellular electron transfer.
Synechocystis-Pseudomonas Acetate-Butanol Coculture
A two-member photosynthetic synthetic consortium pairing acetate-secreting Synechocystis sp. PCC 6803 WT_PKPa_RBS_BsPta_Δacs with a Pseudomonas taiwanensis VLB120 derivative engineered with the TPC4 1-butanol pathway under the Pem7 promoter. The coculture was grown for 42 days in illuminated CoBG11 with repeated medium replacement, added bicarbonate, and pH adjustment. The system tests whether Synechocystis can route light- and CO2-derived carbon through extracellular acetate toward heterotrophic production of the bulk chemical 1-butanol.
Synthetic Lichen Synechococcus-Rhodotorula Coculture
A synthetic lichen-inspired phototroph-heterotroph coculture pairing engineered sucrose-secreting Synechococcus elongatus PCC 7942 with the oleaginous yeast Rhodotorula glutinis. The cyanobacterium fixes carbon dioxide under illumination and exports sucrose, while R. glutinis consumes the cyanobacterial photosynthate, increases coculture biomass and lipid yield, and alleviates reactive oxygen stress that limits low-density cyanobacterial axenic growth.
Synthetic Periphyton Freshwater Biofilm
A 26-member phototrophic synthetic periphyton biofilm used as a reproducible freshwater model system for species dynamics and stressor response.
Syntrophobacter-Methanobacterium Syntrophic Consortium
A syntrophic, obligate two-member anaerobic consortium consisting of Syntrophobacter fumaroxidans, which oxidizes propionate to acetate, and Methanobacterium formicicum, a hydrogen and formate-utilizing methanogen. S. fumaroxidans degrades propionate via the methylmalonyl-CoA pathway only in coculture with H2/formate-using archaea, as it uses protons as the electron acceptor with H2 and formate as electron sink products. The removal of H2 and formate by M. formicicum is thermodynamically essential for continued propionate oxidation by S. fumaroxidans. This syntrophic relationship is fundamental to understanding methane production from propionate in anaerobic environments such as digesters, sediments, and wastewater treatment systems, playing a critical role in biogeochemical cycling.
Syntrophobacter-Methanospirillum Syntrophic Consortium
A syntrophic, obligate two-member anaerobic consortium consisting of Syntrophobacter fumaroxidans, which oxidizes propionate to acetate, and Methanospirillum hungatei, a hydrogen and formate-utilizing methanogen. S. fumaroxidans degrades propionate via the methylmalonyl-CoA pathway only in coculture with H2/formate-using archaea, as it uses protons as the electron acceptor with H2 and formate as electron sink products. The removal of H2 and formate by M. hungatei is thermodynamically essential for continued propionate oxidation by S. fumaroxidans. This syntrophic relationship is fundamental to understanding methane production from propionate in anaerobic environments such as digesters, sediments, and wastewater treatment systems, playing a critical role in biogeochemical cycling.
Syntrophomonas-Methanococcus Butyrate Growth Coordination Coculture
A defined mesophilic anaerobic coculture pairing the butyrate-oxidizing syntroph Syntrophomonas wolfei with the hydrogenotrophic methanogen Methanococcus maripaludis. The system is used to study how a fatty acid-oxidizing bacterium and a methanogen synchronize growth, form syntrophic aggregates, and maintain cell-to-cell attraction during methanogenic butyrate conversion. It is relevant to DOE interests in anaerobic carbon cycling, methane production, syntrophic energy sharing, and engineered bioreactor microbiology.
Syntrophomonas-Methanospirillum Syntrophic Consortium
A syntrophic, obligate two-member anaerobic consortium consisting of Syntrophomonas wolfei, which β-oxidizes saturated fatty acids (butyrate through octanoate) to acetate, and Methanospirillum hungatei, a hydrogen-utilizing methanogen. S. wolfei degrades butyrate only in coculture with H2-using bacteria, as it uses protons as the electron acceptor with H2 as the electron sink product. The removal of H2 by M. hungatei is thermodynamically essential for continued fatty acid oxidation by S. wolfei. This classic syntrophic relationship is fundamental to understanding methane production from fatty acids in anaerobic environments such as digesters, sediments, and the rumen.
Syntrophus Benzoate Degrader
A two-member anaerobic syntrophic coculture consisting of Syntrophus aciditrophicus SB, which metabolizes benzoate and alicyclic intermediates in coculture with hydrogen-using partners, and Methanospirillum hungatei, a hydrogenotrophic methanogen. S. aciditrophicus-M. hungatei cocultures convert benzoate to acetate and methane while keeping hydrogen low enough for syntrophic benzoate degradation to proceed under methanogenic, strictly anaerobic conditions.
Syntrophus-Methanospirillum Gentianae Benzoate Coculture
A defined anaerobic syntrophic coculture in which Syntrophus gentianae degrades benzoate in association with the methanogen Methanospirillum hungatei. The system is relevant to DOE anaerobic carbon cycling, wastewater digestion, and aromatic-compound bioconversion because it links methanogenic benzoate degradation, thermodynamic thresholds, acetate inhibition, and methane formation in a tractable two-member community.
TCP Non-Dehalogenimonas Groundwater Consortium
A long-term domesticated non-Dehalogenimonas synergistic consortium optimized for bioremediation of 1,2,3-trichloropropane (TCP) in groundwater. The PubMed abstract reports complete TCP removal within 3.5 days after co-metabolic substrate stimulation, links the transformation to a Fusibacter, Desulfovibrio, Nitratidesulfovibrio, and Parabacteroides alliance, and describes a coupled metabolic module involving hydrogen production, cofactor synthesis, and reductive dechlorination.
Teosinte-Derived Maize Biofertilizer SynCom7
A seven-strain teosinte-derived bacterial SynCom tested as a maize biofertilizer under conventional and precision fertilization strategies.
Thalassiosira-Marinobacter Marine Snow Coculture
A defined marine diatom-bacterium coculture pairing the centric diatom Thalassiosira weissflogii, currently represented in NCBI Taxonomy as Conticribra weissflogii, with the diatom-attaching heterotrophic bacterium Marinobacter adhaerens HP15. The system is used to study phycosphere attachment, transparent exopolymer particle formation, aggregate formation, and sinking-particle processes relevant to the marine biological carbon pump. Multiple publications use the same exact diatom-bacterium model, including studies of aggregation requirements, chemotaxis-mediated attachment, and temperature/pCO2 perturbations.
Thalassiosira-Ruegeria Phycosphere Coculture
A defined two-member marine phytoplankton-bacterium model community composed of the diatom Thalassiosira pseudonana CCMP1335 and the heterotrophic roseobacter Ruegeria pomeroyi DSS-3. The coculture is used to study bacterial recognition by a diatom, phytoplankton-derived metabolite transfer, and bacterial use of recent photosynthate in a controlled marine algal medium.
Thermacetogenium-Methanothermobacter Acetate Oxidation Coculture
A defined thermophilic anaerobic two-member syntrophic coculture in which Thermacetogenium phaeum strain PB oxidizes acetate using the reversible Wood-Ljungdahl/CO dehydrogenase-acetyl-CoA pathway, while Methanothermobacter thermautotrophicus strain TM consumes reduced products through hydrogenotrophic methanogenesis. This model system is relevant to anaerobic digestion and methane cycling because acetate oxidation is coupled to methane formation under low hydrogen partial pressure.
Thermoleptolyngbya-Chelatococcus Arsenic Detoxification Coculture
A defined light-driven coculture pairing the hot-spring cyanobacterium "Thermoleptolyngbya sichuanensis" XZ-Cy5 with the mat-derived heterotroph Chelatococcus sp. XZ-Ab1. Qing et al. 2026 used pure-culture and coculture comparisons, arsenite oxidation assays, 13CO2 NanoSIMS tracing, and genome analyses to show that XZ-Cy5 supplied photoautotroph-derived organic carbon to Chelatococcus sp. XZ-Ab1, while Chelatococcus detoxified arsenite to arsenate and thereby promoted XZ-Cy5 growth under arsenic stress.
Thermophilic Ex-Situ Biomethanation Mixed Culture
An engineered mixed microbial culture for ex-situ thermophilic biomethanation that was enriched from autoclaved anaerobic digested sewage sludge in a 0.4 L working-volume continuously stirred tank reactor. The proof-of-concept reactor was conditioned with intermittent washouts and reached sustained H2/CO2 4:1 throughput of 500 L/L/d at 50 C in the final phase, where Euryarchaeota, Firmicutes, and Coprothermobacterota dominated the 16S phylum profile and Methanobacteria, Methanosarcina, and Methanosaeta were tracked by qPCR as methane content rose to 86% by day 69.
Thermophilic Lignocellulose-degrading Composting SynCom
A five-member thermophilic lignocellulose-degrading synthetic microbial community (SynCom) designed for manure composting, comprising the bacteria Bacillus cereus, Achromobacter sp., and Pseudomonas sp. together with the fungi Cladosporium sp. and Trichoderma harzianum. Inoculation drives a metabolic reprogramming from a biofilm-dependent defense-survival mode toward an active motility-metabolism mode (depleted lipopolysaccharide biosynthesis, enriched flagellar assembly), which restricts horizontal gene transfer opportunities. By intensifying thermophilic fermentation, lowering the carbon/nitrogen ratio, and enhancing humification, the SynCom attenuates antibiotic resistance genes and virulence factors, collapses high-risk ARG-mobilome interactomes, and achieves deep bio-sanitization by eliminating high-risk pathogens such as Pseudomonas aeruginosa.
Thermophilic Pyrite Quorum Sensing Consortium
A moderately thermophilic three-species bioleaching consortium used to study the effects of quorum sensing (QS) signaling on pyrite and chalcopyrite dissolution. This acidophilic community consists of Leptospirillum ferriphilum DSM 14647, Acidithiobacillus caldus DSM 8584, and Sulfobacillus thermosulfidooxidans DSM 9293, operating at pH 2.0-2.5 and 40°C. The consortium demonstrates coordinated microbial behavior mediated by diffusible signal factor (DSF) and N-acyl-homoserine lactone (AHL) quorum sensing systems. Treatment with DSF-family compounds (DSF and BDSF at 2 μM each) reduced pyrite and chalcopyrite dissolution via inhibitory effects on iron oxidation and mineral colonization. DSF compounds induced A. caldus motility and dispersion from pyrite with concomitant expansion of L. ferriphilum on mineral surfaces, while AHL-mediated signaling (C12-AHL, C14-AHL, 3-OH-C12-AHL, 3-OH-C14-AHL at 5 μM each) repressed L. ferriphilum motility. The consortium was subjected to RNA-seq transcriptomics (12 samples, 271 Gbases) to elucidate gene expression changes in response to QS molecules (NCBI BioProject PRJNA1259591). This system represents the first comprehensive study of quorum sensing regulation in moderately thermophilic biomining bacteria, revealing that QS molecules change planktonic/mineral subpopulation distributions and modulate leaching efficiency through control of cell attachment and iron oxidation rates.
Thermotoga-Methanocaldococcus Hyperthermophilic Syntrophy
A defined hyperthermophilic bacterial-archaeal coculture in which Thermotoga maritima MSB8 ferments organic substrates and transfers hydrogen to the hydrogenotrophic methanogen historically reported as Methanococcus jannaschii, now represented by NCBI as Methanocaldococcus jannaschii DSM 2661. The coculture is relevant to DOE bioenergy and subsurface biogeochemistry because it links high-temperature fermentation, interspecies hydrogen transfer, cell aggregation, and methane formation in an experimentally tractable system.
Thiocyanate-Degrading Afipia and Thiobacillus Bioreactor Community
A laboratory bioreactor microbial community derived from consortia used to treat thiocyanate-contaminated water, perturbed by systematically increased SCN- input loading and the presence or absence of molasses as organic carbon. Five experiments over 790 days with genome-resolved metagenomics showed that a single Thiobacillus strain proliferated in all reactors at high SCN- loading, while a single Afipia variant dominated the molasses- free reactor at moderate loadings. The Afipia variant is predicted to degrade SCN- via a novel thiocyanate desulfurase, oxidize the resulting reduced sulfur, degrade the cyanate product to ammonia and CO2 via cyanate hydratase, and fix CO2 via the Calvin-Benson-Bassham cycle. Removal of molasses reproducibly selects for this autotrophic strain, although molasses-free reactors did not sustain high-loading SCN- degradation, possibly due to loss of biofilm-associated niche diversity.
THOR Rhizosphere Model Community
The Hitchhikers Of the Rhizosphere (THOR) is a genetically tractable three-member model microbiome assembled from Bacillus cereus, Pseudomonas koreensis, and Flavobacterium johnsoniae. The community was developed from rhizosphere-associated isolates to study microbial community assembly, competition, biofilm formation, secondary metabolism, and higher-order interactions under controlled laboratory conditions. P. koreensis produces the antibiotic koreenceine, which inhibits F. johnsoniae and drives community transcriptional responses, while B. cereus modulates antibiotic production and participates in emergent colony expansion and biofilm phenotypes.
Tinto River Iron Cycling Community
A natural acidic iron-cycling microbial community from the Rio Tinto River in southwestern Spain, distinguished by exceptional eukaryotic diversity (>65% of total biomass) in an extremely acidic environment (mean pH 2.2). While prokaryotic diversity is low with 80% of bacteria belonging to three iron-cycling genera (Leptospirillum, Acidithiobacillus, Acidiphilium), eukaryotic diversity is remarkably high including algae (diatoms, Chlorophyta, Euglenozoa, Rhodophyta), fungi (Hortaea, Acidomyces), and diverse protists (ciliates, amoebae, heliozoans, cercomonads, stramenopiles). The river has constant acidic pH (mean 2.2, range 1.0-2.5) and high metal concentrations (Fe 2.3 g/L, Cu 0.11 g/L, Zn 0.22 g/L) throughout its 100 km length, driven by natural oxidation of massive sulfide deposits in the Iberian Pyrite Belt. The prokaryotic community drives iron cycling through Fe²⁺ oxidation (Leptospirillum, Acidithiobacillus) and heterotrophic carbon cycling (Acidiphilium), creating stromatolite-like iron oxide precipitates. Eukaryotes contribute primary production (photosynthetic algae), heterotrophic consumption (protists, fungi), and trophic structure (ciliate predators, heliozoan top predators). The ecosystem represents a natural analog for early Earth conditions and extraterrestrial iron-rich acidic environments, supporting astrobiology research. Rio Tinto demonstrates that complex food webs with eukaryotic dominance can thrive in extreme acid-metal conditions, challenging assumptions about habitability limits.
Tobacco Chemotactic Biocontrol SynCom
A chemotactic three-member SynCom in bioorganic fertilizer for suppressing Ralstonia solanacearum in tobacco fields.
Tomato Oxylipin-Protective SynCom3
A three-species simplified tomato rhizosphere SynCom that steers oxylipin pathways and protects against Botrytis cinerea.
Tribromophenol Anaerobic Bioremediation SynCom
A synthetic anaerobic community with Clostridium, Dehalobacter, and Desulfatiglans functions for 2,4,6-tribromophenol mineralization.
Trichococcus-Syntrophomonas-Methanospirillum Butyrate Coculture
A defined anaerobic three-member coculture in which fermentative Trichococcus flocculiformis strain ES5 stimulates the syntrophic butyrate-oxidizing partnership between Syntrophomonas wolfei and Methanospirillum hungatei. The system extends the classic two-member fatty-acid syntrophy model by adding a fermentative bacterium that increases butyrate consumption and methane production and aggregates with the syntrophic partners. It is relevant to DOE anaerobic carbon cycling, wastewater treatment bioreactors, and engineered methanogenic consortia.
Trichoderma Lactate Platform for SCFA Production
A heterogeneous 3-member consortium for direct conversion of lignocellulose to short-chain fatty acids (SCFAs), specifically butyric acid. The platform consists of Trichoderma reesei Rut-C30 (aerobic fungus producing cellulases), Lactobacillus pentosus (facultative anaerobic lactic acid bacterium), and Clostridium tyrobutyricum (obligate anaerobic butyrate producer). Sequential inoculation creates an oxygen gradient allowing coexistence of all members. T. reesei degrades cellulose to sugars, LAB converts sugars to lactate and creates anaerobic conditions, and C. tyrobutyricum ferments lactate to butyrate, achieving 196 kg butyric acid per metric ton of beechwood.
Trichoderma lentiforme and Burkholderia Cross-Feeding Atrazine-Degrading Consortium
Cross-kingdom fungal-bacterial synthetic consortium pairing the atrazine-degrading fungus Trichoderma lentiforme HN154 with rhizosphere Burkholderia isolates (strains Bur-4, Bur-5, and Bur-14) to remediate atrazine-contaminated corn-soybean rotation soil and protect soybean (Glycine max) from residual phytotoxicity. Trichoderma lentiforme HN154 transforms atrazine into hydroxyatrazine and biuret intermediates that stimulate Burkholderia chemotaxis, swarming, and swimming motility; cross-feeding on these intermediates harnesses bacterial atzB, atzC, atzE, and atzF catabolic enzymes to achieve 86.3% atrazine degradation within 168 h while boosting soybean SOD, POD, and CAT antioxidant defenses.
Trichoderma-E. coli Cellulosic Isobutanol Coculture
A synthetic fungal-bacterial consortium designed for direct conversion of cellulosic biomass to isobutanol. The community divides labor between Trichoderma reesei, which secretes cellulases that hydrolyze lignocellulosic biomass into soluble saccharides, and Escherichia coli, which metabolizes those saccharides into the target biofuel product. The study demonstrated conversion of microcrystalline cellulose and pretreated corn stover to isobutanol, making the system relevant to DOE lignocellulosic biofuel and consolidated bioprocessing goals.
Trichoderma-Streptomyces Filamentous Cellulose Coculture
A synthetic filamentous coculture pairing the cellulolytic fungus Trichoderma reesei RUT-C30 with the noncellulolytic bacterium Streptomyces coelicolor A3(2). The coculture was designed to use cellulose as the carbon source, making S. coelicolor dependent on hydrolysate sugars released by T. reesei cellulases. The system is DOE-relevant as a controllable model for lignocellulose-oriented coculture bioprocessing, where population dynamics, cellulase formation, and secondary-metabolite/pigment production can be tuned through inoculation ratio and abiotic process parameters.
Trichodesmium-Alteromonas Marine Consortium
A marine cyanobacterial colony consortium centered on the nitrogen-fixing photoautotroph Trichodesmium erythraeum IMS101 and conserved heterotrophic partners, especially Alteromonas macleodii. Multi-omics studies support recurring Trichodesmium-associated bacterial consortia in cultures and natural colonies, with potential interactions involving iron and phosphorus acquisition, vitamin B12 exchange, small-carbon compound catabolism, reactive oxygen detoxification, and coordinated diel resource cycling.
Tropidoatractus magnetotacticus Magnetotactic Ciliate Tripartite Syntrophy
A natural tripartite anaerobic symbiosis inside a single ciliate cell, found in freshwater rainforest stream sediment near Libreville, Gabon. The host, Tropidoatractus magnetotacticus sp. nov., produces H2 in hydrogenosomal mitochondrion-related organelles. Two intracellular prokaryotic partners consume it: a magnetotactic sulfate-reducing bacterial population in the Thermodesulfobacteriota that encodes and expresses a magnetosome gene cluster, and an endosymbiotic hydrogenotrophic methanogen affiliated with Methanoregula. The bacterial partner biomineralizes chains of ferrimagnetic magnetite nanoparticles inside the host, so the eukaryote's magnetotaxis is a trait acquired from a symbiont rather than one it encodes itself. "Tripartite" names three functional guilds, not three genomes. The sulfate reducer bin splits by GC content into a magnetosome-bearing and a magnetosome-free population, and refined binning yielded six MAGs for the former, two for the methanogen, and four sub-bins for the ciliate. The whole syntrophic network is built from gene presence and transcript expression. No metabolite concentration or flux was measured, no FISH confirmation succeeded, and the source microcosm died after two years, so nothing here rests on a cultivated or re-samplable system.
TYQ1 Nematode Biocontrol SynCom
An 8-member synthetic community centered on keystone species Rhizobium pusense TYQ1, which is enriched during root-knot nematode (Meloidogyne incognita) infection of cucumber (Cucumis sativus cv. Zhongnong 26). TYQ1 recruits 7 biomarker species that enhance biofilm formation and metabolic cross-feeding, creating a tightly interconnected network for synergistic nematode suppression. The community was identified through stress-induced enrichment analysis and validated across 12 soil types, demonstrating that keystone species recruitment can guide functional microbial community assembly to synergistically enhance plant health.
Urine Nitrification Synthetic Microbial Community
A five-member synthetic microbial community containing nitrifiers and ureolytic heterotrophs for urine nitrification.
Variovorax-Cryptococcus Vitamin Cross-Feeding Microcosm
A two-member vitamin cross-feeding microcosm derived from mine tailings laboratory microbial consortia, in which a Variovorax species produces thiamine (vitamin B1) as a community hub for correlated thiamine auxotrophs and a Cryptococcus yeast supplies pantothenate (vitamin B5) required by Variovorax. Co-culture of the two members yielded a 90-130 fold fitness increase for both organisms, supporting the bidirectional vitamin-dependent mutualism predicted from metagenome-informed abundance correlation networks of mine-tailings-derived consortia grown under dozens of conditions.
Viili Fungus-Bacterium EPS SynCom
A top-down three-strain synthetic microbial consortium from Viili fermented milk, composed of Lactococcus lactis V9, Lacticaseibacillus paracasei V21, and Geotrichum candidum Y1. Hu et al. 2026 used monoculture, co-culture, supernatant-supplementation, metabolomics, amino-acid depletion, amino-acid supplementation, and AI-2 perturbation assays to show that G. candidum supplies lactic-acid bacteria with nitrogen sources including valine, increases AI-2/luxS quorum-sensing activity, and gives the three-member community the highest measured exopolysaccharide concentration among the tested microbial combinations.
Waste-Sludge Electro-Fermentation Biofilm-Suspension Community
An engineered waste-activated-sludge electro-fermentation community with spatially differentiated electrode-biofilm and planktonic fractions. The source reports biofilm-associated reductive debromination of 4-bromophenol and suspension-associated acidogenesis for volatile-fatty-acid recovery. The five genera recorded here are enriched functional examples, not an exhaustive inventory of the sludge community.
Watermelon Rhizosphere Fusarium-Protective SynCom8
A simplified eight-member watermelon rhizosphere SynCom derived from an initial 16-member grafted-watermelon core community.
Wetland Lindane-Degrading Organochlorine Bacterial Consortium
Functional anaerobic organochlorine-degrading bacterial consortia (top-down consortium M and bottom-up consortium Y13) constructed around generalist non-obligate organochlorine-degrading Enterococcus strains (Enterococcus casseliflavus PseS3, R1, R3, R12) alongside organohalide-respiring and fermentative partners (Sulfurospirillum multivorans, Trichlorobacter lovleyi, Dehalococcoides mccartyi, and Petrimonas sulfuriphila) for gamma-hexachlorocyclohexane (lindane) bioremediation in coastal wetland sediment microcosms while suppressing CO2-reduction methanogenesis.
Wetland Oxygen-Sulfate Greenhouse Gas Microcosm Community
Freshwater wetland soil microbial microcosms incubated under anoxic non-sulfate, anoxic sulfate-addition, oxic non-sulfate, and oxic sulfate-addition conditions to resolve how climate-linked oxygen and sulfate exposures alter methane and carbon dioxide emissions. The study integrated geochemical measurements, proteogenomics, metaproteomics, and stoichiometric modeling to identify altered microbial guilds and metabolic processes driving CH4 and CO2 emissions. Sulfate exposure reduced methane production, oxygen shifted greenhouse gas emissions from CH4 toward CO2, and the combined exposure resembled oxygen exposure alone.
Wheat Crown-Rot Six-Strain Cross-Kingdom SMC
A six-strain cross-kingdom wheat-rhizosphere synthetic microbial community that combined Trichoderma harzianum T19, Bacillus subtilis BS-Z15, Bacillus spizizenii PM9, Bacillus rugosus PM16, Bacillus rugosus S32, and Bacillus halotolerans S8 for nonsterile-soil wheat pot assays against Fusarium pseudograminearum Fusarium crown rot. Zhou et al. 2026 assembled the SMC from antagonistic, growth-promoting, and auxiliary wheat-rhizosphere isolates and compared sterile-water, Fusarium-only, SMC-only, and SMC-plus-Fusarium treatments for plant growth, disease severity, resident rhizosphere amplicon profiles, co-occurrence networks, and rhizosphere metabolomics.
Wheat Crown-Rot TB Cross-Kingdom SynCom
A minimal two-member cross-kingdom wheat-rhizosphere SynCom, named TB by Zhou et al. 2026, that mixed Trichoderma harzianum T19 with Bacillus rugosus PM16 and was soil-drenched onto Fusarium-pseudograminearum-challenged Triticum aestivum cv. Hechun 213 seedlings. The controlled tissue-culture-chamber pot experiment tested sterile-water, Fusarium-only, SynCom-only, and Fusarium-plus-SynCom treatments in non-sterile topsoil; after 45 days the authors scored wheat crown rot, profiled rhizosphere 16S/ITS communities, and measured rhizosphere metabolites.
Wheat DT Rhizosphere SynCom
A defined sixteen-strain drought-tolerant bacterial synthetic community assembled from wheat-rhizosphere isolates collected at the Global Change Experimental Facility in Bad Lauchstadt. Rigerte et al. selected isolates with overlapping 16S rDNA sequences to drought- or future-climate-associated amplicon sequence variants, cultured the wheat isolate set on YME agar, combined equal proportions of the sixteen single-strain suspensions, and applied the Wheat DT-SynCom to barley seedlings before Blumeria graminis f. sp. hordei challenge and pre-challenge rhizosphere multi-omics assays.
Wheat Straw Biogas Pretreatment SynCom
A four-member bacterial-fungal synthetic microbial community that produces enzymes for wheat straw pretreatment and enhanced biogas production.
Wheat SynCom-SASW01 Drought-Resistance Inoculant
A five-strain bacterial synthetic community composed of Enterobacter hormaechei FN0603, Enterobacter cloacae FWP0601, Enterobacter ludwigii FWP1205, Pseudomonas putida FWP0405, and Stenotrophomonas maltophilia HLPD6. Yu et al. activated each stored strain on R2A agar, verified species identity by 16S rRNA V5-V7 sequencing, normalized the strains to OD600 1.0, and mixed the suspensions at an equal 1:1:1:1:1 ratio to assemble SynCom-SASW01. The study applied the consortium alone or as a biochar-based wheat seed coating under drought stress, then measured wheat growth, rhizosphere nutrients, root-associated microbiomes, antioxidant physiology, and dual-site field yield.
Wheat Synthetic Consortium C1
A four-member wheat-rhizosphere synthetic consortium (SynCom 1/C1) composed of Pseudomonas sp. B5, Pseudomonas sp. B11, Pseudomonas sp. B12, and Pseudomonas sp. P25. Yin et al. reported that C1 inhibited Rhizoctonia solani AG8 radial growth in dual culture and significantly reduced wheat root rot while increasing wheat fresh root weight under AG8 challenge.
Wheat Synthetic Consortium C6
A four-member mixed-genus wheat-rhizosphere synthetic consortium (SynCom 6/C6) composed of Streptomyces sp. B6, Chryseobacterium sp. B7, Pseudomonas sp. B12, and Sphingomonas sp. B17. Yin et al. reported that C6 inhibited Rhizoctonia solani AG8 radial growth in dual culture and produced auxin in vitro as a whole consortium.
Wine Yeast Five-Species Strain-Substitution Consortium
A defined five-species wine yeast consortium assembled from Saccharomyces cerevisiae, Lachancea thermotolerans, Hanseniaspora uvarum, Starmerella bacillaris, and Torulaspora delbrueckii. Wang et al. 2026 represented each species with two phenotypically diverging strains and systematically perturbed the consortium by species drop-out and strain substitution to quantify fermentation kinetics, sugar utilization, population dynamics, primary metabolites, and major volatile compounds. Species drop-out and strain substitution both shifted population, growth, and metabolic outputs, with non-Saccharomyces substitutions affecting metabolic output more broadly than S. cerevisiae strain choice.
Wine Yeast Three-Species Contact Consortium
A defined three-member wine yeast consortium built from fluorescently labeled Saccharomyces cerevisiae VIN13, Lachancea thermotolerans IWBT Y1240, and Torulaspora delbrueckii LO544 to compare direct cell-cell contact against metabolic-only contact in a multi-membrane bioreactor. Asmus et al. 2026 cultured the yeasts in yeast nitrogen base with glucose and ammonium sulfate, either together in the same 700 mL vessel or separated by 0.1 um membranes with continuous medium exchange, and measured 12 h growth, extracellular glucose, ammonia and amino acids, and S. cerevisiae RNA-seq at 5 and 9 h.
Wolffia Mankai Endosphere Cobamide Guild
A host-filtered bacterial endosphere community from the edible aquatic plant Wolffia globosa Mankai, sampled from industrial rotating raceway cultivation. Amplicon and shotgun metagenomic analyses showed that Mankai medium, phyllosphere, and surface-sterilized internal-tissue fractions formed distinct communities; downstream MAG analysis of the endosphere found a low-diversity Proteobacteria/Pseudomonadota-dominated consortium in which Alphaproteobacterial members encoded near-complete cobamide biosynthesis pathways, while many Gammaproteobacteria and Bacteroidota lineages carried incomplete pathways enriched for cobamide salvage and remodeling. A MAG-derived functional-complementarity network placed Hyphomicrobium zavarzinii, Methylobacterium, Devosia, Labrys, and Ferrovibrionaceae among the inferred producer-side taxa, supporting a producer-salvager model for cobamide metabolism in the plant-associated niche.
Wollastonite Ramichloridium-Talaromyces Fungal Consortium
A defined two-fungus mixed culture of Ramichloridium apiculatum CMS-1 and Talaromyces pseudofuniculosus hzt-3′ grown with wollastonite in modified Czapek liquid medium. The source study varied the CMS-1:hzt-3′ inoculation ratio and found that 20% CMS-1 plus 80% hzt-3′ gave the strongest Ca2+ and Si4+ leaching, with CMS-1-derived extracellular polysaccharides and proteins cross-feeding hzt-3′ organic-acid and amino-acid production.
Yarrowia lipolytica Division-of-Labor Lipid Consortium
A defined two-strain Yarrowia lipolytica consortium engineered to convert lignocellulose-derived oligosaccharides into lipids through metabolic division of labor. The system partitions hydrolysis and assimilation between a cellobiose-specialized YBGL3/YBGL1 lineage and a xylooligosaccharide-specialized YBXT-XR lineage, then benchmarks the consortium against a single multifunctional YBXT-XR-BGL3 strain. In mixed glucose, cellobiose, and xylooligosaccharide coculture, the division-of-labor consortium raised lipid accumulation above the monoculture benchmark and shifted toward the YBXT-XR partner after cellobiose depletion.
Yogurt Two-Species Starter Culture
A defined thermophilic dairy fermentation community composed of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus. The two lactic-acid bacteria form the canonical yogurt starter association, where metabolite exchange accelerates milk acidification: S. thermophilus provides formate, carbon dioxide, and urease-dependent ammonia/carbon dioxide effects that stimulate the lactobacillus, while proteolytic activity of L. delbrueckii subsp. bulgaricus releases peptides and amino acids that support the more weakly proteolytic streptococcus.
Zymomonas-E. coli Exometabolomics-Designed Obligate Mutualism
A defined synthetic obligate mutualism pairing auxotrophic Zymomonas mobilis with auxotrophic Escherichia coli. Exometabolomics of Z. mobilis spent medium identified amino acid exometabolites used to select E. coli proA, pheA, and ilvA auxotroph partners, while mutant fitness profiling selected a Z. mobilis ZMO0748 auxotroph whose rescue was linked to glutathione-related metabolites in E. coli spent medium. The system is DOE-relevant because it was developed by LBNL and Sandia researchers with DOE BER support as a synthetic microbial ecology platform for more resilient biotechnology processes.