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.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Akkermansia muciniphila DSM 22959 — ontology label: Akkermansia muciniphila | NCBITaxon:239935 · TaxonMech · TraitMech | N/A | |
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| Bacteroides ovatus DSM 1896 — ontology label: Bacteroides ovatus | NCBITaxon:28116 · TaxonMech · TraitMech | N/A | |
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| Bacteroides thetaiotaomicron DSM 2079 — ontology label: Bacteroides thetaiotaomicron | NCBITaxon:818 · TaxonMech · TraitMech | N/A | |
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| Bifidobacterium adolescentis DSM 20083 — ontology label: Bifidobacterium adolescentis | NCBITaxon:1680 · TaxonMech · TraitMech | N/A | |
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| Blautia obeum DSM 25238 — ontology label: Blautia obeum | NCBITaxon:40520 · TaxonMech · TraitMech | N/A | |
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| Escherichia coli DSM 18039 — ontology label: Escherichia coli | NCBITaxon:562 · TaxonMech · TraitMech | N/A | |
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| Faecalibacterium prausnitzii DSM 107838 — ontology label: Faecalibacterium prausnitzii | NCBITaxon:853 · TaxonMech · TraitMech | N/A | |
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| Lachnospiraceae bacterium DSM 24404 — ontology label: Lachnospiraceae bacterium | NCBITaxon:1898203 · TaxonMech · TraitMech | N/A | |
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| Lactobacillus johnsonii DSM 10533 — ontology label: Lactobacillus johnsonii | NCBITaxon:33959 · TaxonMech · TraitMech | N/A | |
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| Roseburia intestinalis DSM 14610 — ontology label: Roseburia intestinalis | NCBITaxon:166486 · 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.
Negative Conditioned-Medium Interactions
Cell-free stationary-phase spent YCFA medium from each species was mixed with fresh YCFA and used to grow every other species. Final-density effects were mostly negative, consistent with soluble resource depletion or inhibitory products dominating the tested donor-acceptor interaction matrix.
Biological Processes:
- biological process involved in interspecies interaction (GO:0044419 · PathwayMech)
Evidence
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PMID:41960919 - SUPPORT (IN_VITRO)"negative interactions, which could be caused by e.g., resource competition or toxin production, dominate between the tested species"
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PMID:41960919 - SUPPORT (IN_VITRO)"We then prepared conditioned medium by mixing 60% fresh YCFA medium with 40% of spent medium."
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
Amsterdam gut SynCom data and code repository
Paper-linked repository containing conditioned-medium growth, co-culture, and invasion assay data and analysis code for the ten-species gut SynCom. |
OTHER | OTHER | github:WortelLab/SynCom |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which depleted nutrients or inhibitory compounds explain the negative conditioned-medium effects?
PMID:41960919 measures recipient final density in fresh/spent YCFA mixtures. The source explicitly states that conditioned media do not reveal molecular mechanisms. Reciprocal negative responses were not enriched; competition, inhibitory products and their combinations remain unresolved.
Attaches to: ecological_interactions#Negative Conditioned-Medium Interactions
External Resources
| Name | Repository | Resource ID |
|---|---|---|
|
Amsterdam gut SynCom mSystems article
DOI landing page for the article reporting environmentally mediated interaction assays, generalized Lotka-Volterra co-culture predictions, and invasion validation in the ten-species gut SynCom. |
OTHER | doi:10.1128/msystems.00113-26 |
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Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| 40 percent spent YCFA conditioned medium | 60% fresh YCFA medium plus 40% spent medium | N/A |
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Growth Media
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