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.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Escherichia coli | NCBITaxon:562 · TaxonMech · TraitMech |
CROSS_FEEDER
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N/A |
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| Salmonella enterica serovar Typhimurium — ontology label: Salmonella enterica subsp. enterica serovar Typhimurium | NCBITaxon:90371 · TaxonMech · TraitMech |
CROSS_FEEDER
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N/A |
|
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| Bacteroides thetaiotaomicron | NCBITaxon:818 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
CROSS_FEEDER
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N/A |
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| Bacteroides fragilis | NCBITaxon:817 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
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.
Engineered Amino Acid Cross-Feeding
CROSS_FEEDINGEngineered auxotrophy and amino acid overproduction supported consortium growth without external addition of the designated cross-fed amino acids. LC-MS production measurements and supernatant-rescue assays show unequal capacities, not complete measured all-to-all transfer. B. fragilis was not rescued by the tested overproducer supernatants although it grew in coculture. These observations support community-level nutritional dependence without identifying a dedicated transporter or proving all partner-specific fluxes. Canonical participants describe the studied four-member consortium.
Participating Taxa: Escherichia coli, Salmonella enterica serovar Typhimurium, Bacteroides thetaiotaomicron, Bacteroides fragilis
Metabolites: amino acid (CHEBI:33709 · MediaIngredientMech · CMMMech)
Biological Processes:
- cellular amino acid biosynthetic process (GO:0008652 · PathwayMech)
PARTIAL: The combined dependency/overproduction intervention introduced nutritional support and changed the in-vitro growth trajectories used to infer interaction structure. Unequal rescue and remaining negative-interaction uncertainty prevent interpreting this as a measured fully mutualistic all-to-all network.
Evidence
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doi:10.1128/mSystems.00352-19 - SUPPORT (IN_VITRO)"Each strain is auxotrophic for three amino acids and overproduces one"
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doi:10.1128/mSystems.00352-19 - SUPPORT (IN_VITRO)"Cross-feeding capabilities of each strain were assessed"
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PMID:31409662 - SUPPORT (IN_VITRO)"B. fragilis growth was not rescued by any of the strains"
Beneficial Interaction Shift
A Bayesian dynamical model fitted to in-vitro strain-specific qPCR growth trajectories inferred two positive effects from B. fragilis toward E. coli and S. Typhimurium, with weaker evidence for several negative interactions than in the WT consortium. These are model-inferred net effects under inoculum perturbations, not direct molecular exchange measurements or proof that antagonism vanished. They do not establish reciprocal benefit among every member or identify the same interaction network in vivo.
Participating Taxa: Escherichia coli, Salmonella enterica serovar Typhimurium, Bacteroides thetaiotaomicron, Bacteroides fragilis
Biological Processes:
- interspecies interaction between organisms (GO:0044419 · PathwayMech)
PARTIAL: Engineered nutritional dependencies and altered inferred net interactions are consistent with the greater evenness observed in separate in-vitro endpoint assays. The interaction-shift node was not selectively perturbed to establish mediation. Extension of this pathway to the day-10 mouse-gut endpoint is HYPOTHESIZED; in-vitro network inference does not measure in-vivo exchange.
Evidence
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doi:10.1128/mSystems.00352-19 - PARTIAL (IN_VITRO)"genetic modifications alleviated antagonistic interactions and resulted in beneficial interactions"
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PMID:31409662 - SUPPORT (COMPUTATIONAL)"although some inferred negative interactions are still present"
Cross-Feeding Increased Population Evenness
The engineered four-member consortium had higher Pielou evenness in anaerobic endpoint cultures, especially without supplemented cross-fed amino acids, despite lower overall growth in the unsupplemented in-vitro setting. In gnotobiotic mice, day-10 fecal strain-specific DNA-qPCR supported greater evenness for the engineered consortium on the low-protein diet; the standard-diet trend was not statistically significant. This is a composition endpoint, not longitudinal stability, a conventional microbiome or a host-health benefit. The assay does not directly measure amino-acid flux in the gut.
Participating Taxa: Escherichia coli, Salmonella enterica serovar Typhimurium, Bacteroides thetaiotaomicron, Bacteroides fragilis
Metabolites: amino acid (CHEBI:33709 · MediaIngredientMech · CMMMech)
Evidence
-
PMID:31409662 - SUPPORT (IN_VITRO)"Engineered cross-feeding increased population evenness"
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PMID:31409662 - SUPPORT (IN_VIVO)"low-protein diet showed significantly greater population evenness"
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PMID:31409662 - SUPPORT (IN_VIVO)"although this trend was not statistically significant"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
Engineered gut amino acid cross-feeding publication
Publication reporting engineered amino acid overproduction, auxotrophy rescue, in vitro consortium dynamics, and gnotobiotic mouse composition measurements. |
PHENOTYPE | OTHER | PMID:31409662 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which nutritional interactions mediate the diet-dependent mouse-gut evenness endpoint?
Keep unequal supernatant rescue distinct from community growth. The Bayesian model used in-vitro qPCR time series with inoculum perturbations; its net interaction edges do not identify molecular flux or prove an all-to-all mutualistic network. Higher-order effects were not supported by those data, not biologically excluded. Separate the 27-hour trajectory assays from 24-hour supplementation endpoints and day-10 fecal DNA-qPCR. Low-protein diet changes more than a single measured amino-acid flux, and the standard-diet evenness trend was nonsignificant. Do not extrapolate to longitudinal stability, conventional microbiota or clinical benefit. Canonical B. fragilis AMBIGUOUS grounding is preserved, not resolved. Non-graph cache-access wording remains #1457; cache pointer/casing issues remain #1094/#1091. No new genetic engineering procedures or pairwise mechanisms are added.
Attaches to: ecological_interactions#Engineered Amino Acid Cross-Feeding, ecological_interactions#Beneficial Interaction Shift, ecological_interactions#Cross-Feeding Increased Population Evenness
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| anaerobic modified M9 medium | Modified M9 minimal medium with starch and glucose carbon sources | N/A |
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| low-protein gnotobiotic mouse diet | 3% protein low-protein chow | N/A |
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Growth Media
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