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.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Pseudomonas putida HAMBI 6 — ontology label: Pseudomonas putida | NCBITaxon:303 · TaxonMech · TraitMech | N/A | |
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| Agrobacterium tumefaciens HAMBI 105 — ontology label: Agrobacterium tumefaciens | NCBITaxon:358 · TaxonMech · TraitMech | N/A | |
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| Comamonas testosteroni HAMBI 403 — ontology label: Comamonas testosteroni | NCBITaxon:285 · TaxonMech · TraitMech | N/A | |
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| Citrobacter koseri HAMBI 1287 — ontology label: Citrobacter koseri | NCBITaxon:545 · TaxonMech · TraitMech | N/A | |
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| Morganella morganii HAMBI 1292 — ontology label: Morganella morganii | NCBITaxon:582 · TaxonMech · TraitMech | N/A | |
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| Kluyvera intermedia HAMBI 1299 — ontology label: Kluyvera intermedia | NCBITaxon:61648 · TaxonMech · TraitMech | N/A | |
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| Sphingobium yanoikuyae HAMBI 1842 — ontology label: Sphingobium yanoikuyae | NCBITaxon:13690 · TaxonMech · TraitMech | N/A | |
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| Sphingobacterium spiritivorum HAMBI 1896 — ontology label: Sphingobacterium spiritivorum | NCBITaxon:258 · TaxonMech · TraitMech | N/A | |
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| Aeromonas caviae HAMBI 1972 — ontology label: Aeromonas caviae | NCBITaxon:648 · TaxonMech · TraitMech | N/A | |
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| Pseudomonas chlororaphis HAMBI 1977 — ontology label: Pseudomonas chlororaphis | NCBITaxon:587753 · TaxonMech · TraitMech | N/A | |
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| Bordetella avium HAMBI 2160 — ontology label: Bordetella avium | NCBITaxon:521 · TaxonMech · TraitMech | N/A | |
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| Cupriavidus oxalaticus HAMBI 2164 — ontology label: Cupriavidus oxalaticus | NCBITaxon:96344 · TaxonMech · TraitMech | N/A | |
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| Paracoccus denitrificans HAMBI 2443 — ontology label: Paracoccus denitrificans | NCBITaxon:266 · TaxonMech · TraitMech | N/A | |
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| Stenotrophomonas maltophilia HAMBI 2659 — ontology label: Stenotrophomonas maltophilia | NCBITaxon:40324 · TaxonMech · TraitMech | N/A | |
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| Niabella yanshanensis HAMBI 3031 — ontology label: Paraniabella yanshanensis | NCBITaxon:577386 · TaxonMech · TraitMech | N/A | |
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| Microvirga lotononidis HAMBI 3237 — ontology label: Microvirga lotononidis | NCBITaxon:864069 · TaxonMech · TraitMech | 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.
Total-carbon-driven community state shifts
Controlled glucose/R2A carbon gradients produced repeatable community-composition shifts: A. caviae dominated low carbon, P. chlororaphis co-dominated with A. caviae at intermediate carbon, and C. koseri dominated high carbon. R2A-derived complexity modulated this pattern within the tested media. Relative 16S profiles and the authors' OD-scaled abundance analysis support the result, but are not direct viable-cell counts or proof of extinction. The authors interpret dominance as competitive sorting; ancestral monoculture lag and growth traits predict patterns but do not selectively establish competition, lag time or pH as the mediator. Clusters across different resource conditions do not demonstrate alternative stable states within one condition.
Participating Taxa: Pseudomonas putida HAMBI 6, Agrobacterium tumefaciens HAMBI 105, Comamonas testosteroni HAMBI 403, Citrobacter koseri HAMBI 1287, Morganella morganii HAMBI 1292, Kluyvera intermedia HAMBI 1299, Sphingobium yanoikuyae HAMBI 1842, Sphingobacterium spiritivorum HAMBI 1896, Aeromonas caviae HAMBI 1972, Pseudomonas chlororaphis HAMBI 1977, Bordetella avium HAMBI 2160, Cupriavidus oxalaticus HAMBI 2164, Paracoccus denitrificans HAMBI 2443, Stenotrophomonas maltophilia HAMBI 2659, Niabella yanshanensis HAMBI 3031, Microvirga lotononidis HAMBI 3237
Biological Processes:
- interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:42367191 - SUPPORT (IN_VITRO)"we observed a repeatable state shift pattern in the serially transferred multispecies synthetic community"
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PMID:42367191 - SUPPORT (IN_VITRO)"total carbon availability was the principal driver of community-level state transitions"
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which member interactions and traits mediate the carbon-dependent state shifts?
Preserve the positive controlled carbon response and the authors' competitive-sorting interpretation. Monoculture trait prediction, endpoint pH associations and OD-scaled abundance are informative but not selective mediator perturbations or viable-cell enumeration. Partner removal, trait manipulation and pH control would test the proposed mechanisms. R2A is a proxy for resource complexity with uncertain effective availability, not an exhaustive complexity experiment; no within-condition hysteresis or alternative-attractor demonstration is established by clustering. All 16 canonical strains denote the input community, not proven persistence at every endpoint. Non-graph metadata is preserved, not recertified.
Attaches to: ecological_interactions#Total-carbon-driven community state shifts
External Resources
| Name | Repository | Resource ID |
|---|---|---|
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PubMed - HAMBI Carbon-Gradient 16-species SynCom
PubMed record for the ISME Communications paper on HAMBI 16-species SynCom community state shifts along total-carbon and R2A-complexity gradients. |
OTHER | PMID:42367191 |
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Publication DOI - HAMBI Carbon-Gradient 16-species SynCom
DOI for the primary ISME Communications publication. |
OTHER | doi:10.1093/ismeco/ycag149 |
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PMC full text - HAMBI Carbon-Gradient 16-species SynCom
Open-access PMC full text for the primary ISME Communications publication. |
OTHER | PMC:PMC13298641 |
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Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| total carbon concentration | 0.031 to 4 g C/L | N/A |
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| R2A-derived carbon fraction | 0 to 100% of total carbon | N/A |
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Growth Media
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