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.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Ruminiclostridium cellulolyticum H10 — ontology label: Ruminiclostridium cellulolyticum | NCBITaxon:1521 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
CROSS_FEEDER
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N/A |
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| Methanospirillum hungatei JF-1 | NCBITaxon:323259 · TaxonMech · TraitMech |
SYNTROPHIC_PARTNER
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N/A |
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| Methanosaeta concilii GP6 — ontology label: Methanothrix soehngenii | NCBITaxon:2223 · TaxonMech · TraitMech |
SYNTROPHIC_PARTNER
|
N/A |
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| Desulfovibrio vulgaris Hildenborough — ontology label: Nitratidesulfovibrio vulgaris str. Hildenborough | NCBITaxon:882 · TaxonMech · TraitMech |
SYNTROPHIC_PARTNER
CROSS_FEEDER
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N/A |
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Ecological Interactions
The graph shows only explicitly linked interaction participants. Community members without an asserted participant link are omitted; membership alone does not imply an interaction.
Combinatorial cellulose-fed interaction rewiring
COMPUTATIONAL - composition changes altered SMETANA MIP/MRO scores in this bounded cellulose-fed panel. These are exchange-potential and shared-import proxies, not measured reciprocal fitness. Resource overlap includes auxiliary imports; one four-member configuration cannot establish a general richness rule.
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:40937471 - SUPPORT (IN_VITRO)"Different combinations of R. cellulolyticum, M. hungatei, M. concilii, and D. vulgaris, including one mono-culture, three bi-cultures, three tri-cultures, and one quad-culture, were co-cultured in a medium with cellulose as the sole carbon source "
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PMID:40937471 - SUPPORT (COMPUTATIONAL)"These results suggest that tri-cultures enhance cooperation and reduce competition"
Acetoclastic methanogenesis as dominant methane route
CROSS_FEEDINGCOMPUTATIONAL - the fitted stoichiometric model attributes acetate transfer from R. cellulolyticum to M. concilii and identifies acetoclastic methanogenesis as an important methane route in assemblies containing that methanogen. This is not directly traced transfer or a route available in every panel member.
Source Taxon: Ruminiclostridium cellulolyticum H10
Target Taxon: Methanosaeta concilii GP6
Metabolites: acetate (CHEBI:30089 · MediaIngredientMech · CMMMech)
Biological Processes:
- acetoclastic methanogenesis (GO:0019385 · PathwayMech)
Evidence
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PMID:40937471 - SUPPORT (COMPUTATIONAL)"Flux analysis identified acetoclastic methanogenesis as the primary CH₄ and CO₂ source, especially in multi-species cultures "
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PMID:40937471 - SUPPORT (COMPUTATIONAL)"This was followed by the acetate exchange flux between R. cellulolyticum and M. concilii "
D. vulgaris hydrogen turnover supports methanogenesis
SYNTROPHYPARTIAL - the source proposes D. vulgaris lactate oxidation and hydrogen supply coupled to methanogen consumption under sulfate limitation. H2 accumulation and fitted fluxes do not directly resolve turnover or partner dependence. Low H2 can favor donor lactate oxidation; it is not itself evidence that hydrogenotrophic methanogenesis is more energetically favorable.
Source Taxon: Desulfovibrio vulgaris Hildenborough
Target Taxon: Methanospirillum hungatei JF-1
Metabolites: lactate (CHEBI:24996 · MediaIngredientMech · CMMMech), dihydrogen (CHEBI:18276 · MediaIngredientMech · CMMMech)
Biological Processes:
- hydrogenotrophic methanogenesis (GO:0019386 · PathwayMech)
Evidence
-
PMID:40937471 - PARTIAL (COMPUTATIONAL)"Desulfovibrio vulgaris likely promotes hydrogen turnover, maintaining low partial pressures that favor this pathway "
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PMID:40937471 - PARTIAL (COMPUTATIONAL)"Desulfovibrio vulgaris oxidizes lactate to acetate, CO2, and H2 in the absence of sulfate"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which isotope- or perturbation-resolved exchanges validate the modeled composition-specific mechanisms?
PMID:40937471 combines CarveMe/SMETANA predictions with a separate stoichiometric fit using protein and ATP assumptions. Results report reduced acetate exchange in the Rc/Mc/Dv tri-culture, limiting the discussion claim of consistent Dv enhancement. Narrative and table thermodynamic values differ; no new numerical energy claims are asserted. Prior acetate/lactate evidence and the removal of summary arrows are preserved.
Attaches to: ecological_interactions#Combinatorial cellulose-fed interaction rewiring, ecological_interactions#Acetoclastic methanogenesis as dominant methane route, ecological_interactions#D. vulgaris hydrogen turnover supports methanogenesis
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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Primary publication - cellulose-to-methane combinatorial SynCom panel
Open-access ISME Communications paper reporting proteogenomics and metabolic modeling across the R. cellulolyticum-centered cellulose-to-methane combinatorial panel. |
OTHER | doi:10.1093/ismeco/ycaf142 |
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Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| fully combinatorial species composition | one R. cellulolyticum mono-culture, three bi-cultures, three tri-cultures, and one quad-culture | N/A |
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| cellulose as the sole carbon source | 10 g/L cellulose | N/A |
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Growth Media
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