BioModels MODEL2405300001 Infant Gut HMO SynCom

Community ID CommunityMech:000012

Ecological State ENGINEERED

Environment laboratory environment
ENVO:01001405 · HabitatMech ↗

Modeled Environment intestine environment
ENVO:2100002 · HabitatMech ↗

BioModels record MODEL2405300001 contains genome-scale metabolic models used to study a synthetic human infant gut microbial community in the context of human milk oligosaccharides.

Taxonomy

Taxon	Ontology ID	Functional Roles	Abundance
Bifidobacterium longum subsp. infantis	NCBITaxon:1682 · TaxonMech · TraitMech	PRIMARY_DEGRADER	N/A
doi:10.1093/ismejo/wrae209 - SUPPORT (IN_VITRO) "Here, we designed BIG-Syc, a synthetic community of 13 strains from the gut of vaginally born, breastfed infants."
Bifidobacterium bifidum	NCBITaxon:1681 · TaxonMech · TraitMech	PRIMARY_DEGRADER	N/A
doi:10.1093/ismejo/wrae209 - SUPPORT (IN_VITRO) "Bifidobacterium infantis and Bifidobacterium bifidum suppressing one another"
Bifidobacterium breve	NCBITaxon:1685 · TaxonMech · TraitMech	PRIMARY_DEGRADER	N/A
Bacteroides fragilis	NCBITaxon:817 · TaxonMech · TraitMech	PRIMARY_DEGRADER	N/A
Bacteroides vulgatus — ontology label: Phocaeicola vulgatus	NCBITaxon:821 · TaxonMech · TraitMech	CROSS_FEEDER	N/A
Bacteroides ovatus	NCBITaxon:28116 · TaxonMech · TraitMech	CROSS_FEEDER	N/A
Veillonella parvula	NCBITaxon:29466 · TaxonMech · TraitMech	CROSS_FEEDER	N/A
Ruminococcus gnavus — ontology label: Mediterraneibacter gnavus	NCBITaxon:33038 · TaxonMech · TraitMech	PRIMARY_DEGRADER	N/A
Escherichia coli K-12	NCBITaxon:83333 · TaxonMech · TraitMech	CROSS_FEEDER	N/A
Lacticaseibacillus rhamnosus	NCBITaxon:47715 · TaxonMech · TraitMech	CROSS_FEEDER	N/A
Enterococcus faecalis	NCBITaxon:1351 · TaxonMech · TraitMech	CROSS_FEEDER	N/A
Streptococcus thermophilus	NCBITaxon:1308 · TaxonMech · TraitMech	CROSS_FEEDER	N/A
Blautia producta	NCBITaxon:33035 · TaxonMech · TraitMech	SECONDARY_FERMENTER	N/A

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.

Taxon

Cross-feeding

Bifidobacterium HMO Degradation and Cross-Feeding

CROSS_FEEDING

Bifidobacterial HMO use contributes to the source-reconstructed BIG-Syc resource-sharing network. B. infantis dominated four of six 4HMO replicates, whereas B. bifidum dominated 5HMO cultures. B. breve often scavenged simpler carbohydrates rather than uniformly degrading every HMO. PARTIAL - specific donor-to-recipient carbon and gas routes combine growth, metaproteomics, literature and models, not traced transfer; alternate dominance mechanisms remain hypotheses.

Participating Taxa: Bifidobacterium longum subsp. infantis, Bifidobacterium bifidum, Bifidobacterium breve

Metabolites: oligosaccharide (CHEBI:50699 · MediaIngredientMech · CMMMech), organic acid (CHEBI:64709 · MediaIngredientMech · CMMMech)

Downstream Effects:

→ Cross-Feeder Utilization of HMO Degradation Products

PARTIAL - bifidobacterial HMO processing can supply simpler substrates and fermentation products for the source-proposed recipient routes. Community depletion and proteomics support resource sharing but do not trace each donor-to-recipient flux or demonstrate identical release by all three bifidobacteria.

Evidence

doi:10.1093/ismejo/wrae209 - PARTIAL (IN_VITRO)

"BIG-Syc demonstrated teamwork as cross-feeders utilized simpler carbohydrates, organic acids, and gases released from human milk oligosaccharide degraders."
doi:10.1093/ismejo/wrae209 - SUPPORT (IN_VITRO)

"Bifidobacterium infantis and Bifidobacterium bifidum suppressing one another"

Cross-Feeder Utilization of HMO Degradation Products

CROSS_FEEDING

PARTIAL - the source reconstructs simple-sugar use by B. ovatus, B. vulgatus, L. rhamnosus, E. faecalis, S. thermophilus and E. coli, lactate use by V. parvula, and sugar/gas use by B. producta. Species assignments draw on monoculture, proteomic and model evidence. Gas production and transfer were inferred; supplied headspace CO2 prevents unique attribution to bacterial donors. Model and experimental metabolite profiles did not fully agree. The paper's S. salivarius subsp. thermophilus ATCC19258 is the taxon grounded here as S. thermophilus.

Participating Taxa: Bacteroides ovatus, Bacteroides vulgatus, Veillonella parvula, Escherichia coli K-12, Lacticaseibacillus rhamnosus, Enterococcus faecalis, Streptococcus thermophilus, Blautia producta

Metabolites: monosaccharide (CHEBI:35381 · MediaIngredientMech · CMMMech), organic acid (CHEBI:64709 · MediaIngredientMech · CMMMech)

Evidence

doi:10.1093/ismejo/wrae209 - PARTIAL (IN_VITRO)

"BIG-Syc demonstrated teamwork as cross-feeders utilized simpler carbohydrates, organic acids, and gases released from human milk oligosaccharide degraders."
doi:10.1093/ismejo/wrae209 - SUPPORT (IN_VITRO)

"B. ovatus, B. vulgatus, L. rhamnosus, S. salivarius, E. faecalis, and E. coli proliferated via cross-feeding of simple sugars"
doi:10.1093/ismejo/wrae209 - PARTIAL (IN_VITRO)

"human milk oligosaccharides prompt resource-sharing for their complete degradation while leading to a different compositional and functional profile in the community"

Non-Bifidobacterial HMO Degradation

CROSS_FEEDING

PARTIAL - B. fragilis and R. gnavus contribute non-bifidobacterial HMO-degrading capacity. Growth and enzyme observations, interpreted with prior strain literature, motivate release of simpler substrates to the community. These are reconstructed routes, not measured flux from every named donor; exact extracellular activity and R. gnavus fucose/lactose release depend partly on cited external studies.

Participating Taxa: Bacteroides fragilis, Ruminococcus gnavus

Metabolites: oligosaccharide (CHEBI:50699 · MediaIngredientMech · CMMMech)

Downstream Effects:

→ Cross-Feeder Utilization of HMO Degradation Products

PARTIAL - the authors propose that extracellular HMO processing by B. fragilis and R. gnavus supplies simpler substrates to recipients. The main study supports a resource-sharing model rather than donor-resolved tracer transfer or necessity of every participating strain.

Evidence

doi:10.1093/ismejo/wrae209 - PARTIAL (IN_VITRO)

"The HMO degraders, namely B. infantis, B. bifidum, B. breve, B. fragilis, and R. gnavus were able to fully degrade the HMOs present"

Associated Datasets

Dataset	Type	Repository	Accession
BioModels model archive Zipped genome-scale model files submitted with MODEL2405300001.	OTHER	OTHER	Gap-filled_Curated_HMO_GEMs.zip
Primary publication Publication associated with the submitted synthetic infant gut community GEMs.	OTHER	OTHER	doi:10.1093/ismejo/wrae209

Knowledge gaps & discussions (1)

KNOWLEDGE_GAP OPEN Which strain-specific transfer routes and dependencies explain HMO depletion?

Community LC-MS showed greater than 90% depletion with a 6-SL exception at t119C in 4HMO 1; this is not proof of every transfer or member necessity. The mixes differ in relative HMO proportions as well as LNT presence. Gas predictions and model/in-vitro disagreement require validation. Full main paper/Table 1/captions read, not images, supplements, raw data or rerun models. Preserve B. ovatus NCBITaxon:28116 and the two existing donor-to-recipient arrows. Non-graph medium/environment wording remains #1262.

Attaches to: ecological_interactions#Bifidobacterium HMO Degradation and Cross-Feeding, ecological_interactions#Cross-Feeder Utilization of HMO Degradation Products, ecological_interactions#Non-Bifidobacterial HMO Degradation

External Resources

Name	Repository	Resource ID
BioModels entry Synthetic Human Infant Gut Microbial Community with Human Milk Oligosaccharides.	BIOMODELS	MODEL2405300001
doi:10.1093/ismejo/wrae209 - SUPPORT (COMPUTATIONAL) "Here, we designed BIG-Syc, a synthetic community of 13 strains from the gut of vaginally born, breastfed infants."

Growth Media

anoxic minimal medium with human milk oligosaccharides as sole carbon source

pH 6

Temperature 37 °C

Atmosphere ANAEROBIC

Preparation notes: Minimal/basal medium (1 g/L yeast extract, Na2S excluded) with 0.4% w/v four- or five-HMO mix as sole carbon source; anoxic (redox constantly below -300 mV); 80% N2:20% CO2 sparged at 6 sl/h; each strain inoculated at 1% v/v of an OD:1-normalized culture; batch start then switched to continuous feed at 12.5 mL/h.

Evidence

doi:10.1093/ismejo/wrae209

"The working volume was 300 ml and the temperature was set to 37°C. The pH was monitored and maintained at 6"

doi:10.1093/ismejo/wrae209

"A mixed gas of 80% N2: 20% CO2 was introduced at a 6 sl/h rate."

doi:10.1093/ismejo/wrae209

"Anoxic conditions were monitored based on the redox potential that was constantly below −300 mV."

Cross-Mech Suite Links

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

HabitatMech: laboratory environment ↗ TaxonMech: Bifidobacterium longum subsp. infantis ↗ TraitMech: Bifidobacterium longum subsp. infantis ↗ TaxonMech: Bifidobacterium bifidum ↗ TraitMech: Bifidobacterium bifidum ↗ TaxonMech: Bifidobacterium breve ↗ TraitMech: Bifidobacterium breve ↗ TaxonMech: Bacteroides fragilis ↗ TraitMech: Bacteroides fragilis ↗ TaxonMech: Bacteroides vulgatus ↗ TraitMech: Bacteroides vulgatus ↗ TaxonMech: Bacteroides ovatus ↗ TraitMech: Bacteroides ovatus ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗