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Bacteroides-Eubacterium Gnotobiotic Gut Model

Community ID CommunityMech:000158
Ecological State ENGINEERED
Environment gnotobiotic mouse gut environment — ontology label: intestine environment
ENVO:2100002 · HabitatMech ↗

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.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Bacteroides thetaiotaomicron VPI-5482 NCBITaxon:226186 · TaxonMech · TraitMech
PRIMARY_DEGRADER CROSS_FEEDER
N/A
  • PMID:19321416 - SUPPORT (IN_VIVO)
    "Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron"
  • PMID:19321416 - SUPPORT (COMPUTATIONAL)
    "The finished genome sequences of B. thetaiotaomicron VPI-5482"
Eubacterium rectale ATCC 33656 — ontology label: Agathobacter rectalis ATCC 33656 NCBITaxon:515619 · TaxonMech · TraitMech
SECONDARY_FERMENTER CROSS_FEEDER
N/A
  • PMID:19321416 - SUPPORT (IN_VIVO)
    "Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron"
  • PMID:19321416 - SUPPORT (COMPUTATIONAL)
    "the human gut-derived E. rectale strain ATCC 33656"

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.

Ecological interaction network for Bacteroides-Eubacterium Gnotobiotic Gut Model Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding, niche partitioning. Rare or untyped interactions share the Other symbol; exact curated types remain in the interaction details.
Taxon
Cross-feeding
Niche partitioning
Other

Bacteroides Polysaccharide Niche Expansion

NICHE_PARTITIONING

B. thetaiotaomicron responds to E. rectale by increasing expression of polysaccharide utilization loci and broadening glycan foraging, including host-derived mucin glycans that E. rectale cannot use.

Source Taxon: Eubacterium rectale ATCC 33656

Target Taxon: Bacteroides thetaiotaomicron VPI-5482

Biological Processes:

Downstream Effects:
→ Cecal Short-Chain Fatty Acid Remodeling

PARTIAL - the source proposes that Bacteroides dietary-glycan processing supplies substrates for E. rectale metabolism, contributing to the measured SCFA pools. Increased host-mucin foraging is a distinct niche response, not direct evidence that host glycans feed E. rectale; donor-specific transfer was not traced in the inspected main paper.

Evidence

  • PMID:19321416 - SUPPORT (IN_VIVO)
    "B. thetaiotaomicron adapts to the presence of E. rectale by up-regulating a variety of loci specific for host-derived mucin glycans that E. rectale is unable to use"

Eubacterium Transport and Butyrate Shift

CROSS_FEEDING

E. rectale decreases glycan-degrading enzyme expression and increases selected transport functions during biassociation. PARTIAL - combined acetate, redox, enzyme-expression and host Mct1 observations support the source's proposed acetate-to-butyrate cross-feeding model; they do not directly measure donor-resolved flux or increased production/uptake rates.

Source Taxon: Bacteroides thetaiotaomicron VPI-5482

Target Taxon: Eubacterium rectale ATCC 33656

Metabolites: acetate (CHEBI:30089 · MediaIngredientMech · CMMMech), butyrate (CHEBI:17968 · MediaIngredientMech · CMMMech)

Biological Processes:

Downstream Effects:
→ Cecal Short-Chain Fatty Acid Remodeling

PARTIAL - inferred acetate use in E. rectale butyrate metabolism could contribute to lower acetate and maintained standing butyrate concentrations. Similar butyrate pools plus higher host Mct1 expression do not directly quantify increased production or epithelial uptake.

Evidence

  • PMID:19321416 - SUPPORT (IN_VIVO)
    "E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters"
  • PMID:19321416 - PARTIAL (IN_VIVO)
    "generation of butyrate from acetate"

Cecal Short-Chain Fatty Acid Remodeling

Biassociation lowered cecal acetate relative to B. thetaiotaomicron monoassociation, while cecal butyrate concentration was similar to E. rectale monoassociation. These comparator-specific standing pools are not production or uptake rates. Both organisms had similar colonization levels under mono- and biassociation on polysaccharide-rich chow.

Participating Taxa: Bacteroides thetaiotaomicron VPI-5482, Eubacterium rectale ATCC 33656

Metabolites: acetate (CHEBI:30089 · MediaIngredientMech · CMMMech), butyrate (CHEBI:17968 · MediaIngredientMech · CMMMech)

Biological Processes:

Evidence

  • PMID:19321416 - SUPPORT (IN_VIVO)
    "cecal acetate levels are significantly lower in cocolonized mice compared with B. thetaiotaomicron monoassociated animals"
  • PMID:19321416 - SUPPORT (IN_VIVO)
    "cecal butyrate levels are similar in E. rectale mono- and biassociated animals"

Associated Datasets

Dataset Type Repository Accession
Exact-composition publication - Bacteroides thetaiotaomicron VPI-5482 and Eubacterium rectale ATCC 33656
Primary publication reporting the exact two-member gnotobiotic mouse model, with microbial transcriptomics, proteomics, metabolite assays, and host-response measurements. 		PHENOTYPE OTHER PMID:19321416
Bacteroides-Eubacterium gnotobiotic mouse GEO datasets
GEO accessions deposited with the PNAS study for transcriptional profiling data from the gnotobiotic model. 		METATRANSCRIPTOMICS OTHER GSE14686; GSE14709; GSE14737
Eubacterium rectale ATCC 33656 complete genome project
NCBI BioProject for the E. rectale ATCC 33656 genome sequenced in the same study. 		GENOMICS NCBI_BIOPROJECT PRJNA29071

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN What donor-specific carbon flux and epithelial uptake mediate the biassociation SCFA response?

Main-paper expression, pools and diet perturbation support a metabolic model but do not isolate acetate transfer, host uptake rates or pathway necessity. Diet restriction tests substrate dependence, not molecule-specific exchange. SI Methods/Results, supplementary figures/tables and underlying data were not inspected. Non-graph ingredient flux wording remains a separate follow-up.

Attaches to: ecological_interactions#Bacteroides Polysaccharide Niche Expansion, ecological_interactions#Eubacterium Transport and Butyrate Shift, ecological_interactions#Cecal Short-Chain Fatty Acid Remodeling

Environmental Factors

Factor Value Unit
germ-free mouse host Germ-free mice colonized with one or both human gut-derived strains. N/A
  • PMID:19321416 - SUPPORT (IN_VIVO)
    "Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron"
dietary perturbation three dietary conditions N/A
  • PMID:19321416 - SUPPORT (IN_VIVO)
    "in combination under 3 dietary conditions"

Growth Media

gnotobiotic mouse gut (standard chow diet rich in complex plant polysaccharides)

Preparation notes: Germ-free mice were colonized by gavage with single strains (monoassociation) or both strains (biassociation) and fed a standard chow diet rich in complex plant polysaccharides; ceca were sampled 10 to 14 days after inoculation, when both species had colonized to high levels. Detailed in-vitro bacterial culture conditions are reported only in the paper's SI Methods.

Evidence

PMID:19321416

"Ten to fourteen days after inoculation by gavage, both species colonized the ceca of recipient mice, fed a standard chow diet rich in complex plant polysaccharides, to high levels"

Cross-Mech Suite Links

Explore related entities across the CultureBotAI X-Mech knowledge bases:

HabitatMech: gnotobiotic mouse gut environment ↗ TaxonMech: Bacteroides thetaiotaomicron VPI-5482 ↗ TraitMech: Bacteroides thetaiotaomicron VPI-5482 ↗ TaxonMech: Eubacterium rectale ATCC 33656 ↗ TraitMech: Eubacterium rectale ATCC 33656 ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗