Mucin Glycan-Degrading MDSC Synthetic Gut Community

Community ID CommunityMech:000392

Ecological State ENGINEERED

Environment anaerobic laboratory serum-bottle culture — ontology label: laboratory environment
ENVO:01001405 · HabitatMech ↗

Modeled Environment human colonic mucus layer — ontology label: intestine environment
ENVO:2100002 · HabitatMech ↗

A 14-strain in vitro synthetic community of human colonic mucus-associated mucin glycan degraders, secondary degraders, and hydrogen consumers. The MDSC was assembled from Akkermansia, Bacteroides, Phocaeicola, Ruminococcus, Lachnospiraceae, Faecalibacterium, and Desulfovibrio type strains, grown anaerobically in sequential 24 h serum-bottle batches at 37°C, and compared across porcine gastric mucin, bovine submaxillary mucin, mixed PGM/BSM, and PGM supplemented with two sialylated glycans. Mucin type drove distinct stabilized community compositions, mucin glycan degradation patterns, and metabolite profiles after four transfers.

Taxonomy

Taxon	Ontology ID	Abundance
Akkermansia muciniphila DSM 22959T — ontology label: Akkermansia muciniphila	NCBITaxon:239935 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Akkermansia muciniphila DSM 22959T"
Bacteroides caccae DSM 19024T — ontology label: Bacteroides caccae	NCBITaxon:47678 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Bacteroides caccae DSM 19024T"
Bacteroides fragilis DSM 2151T — ontology label: Bacteroides fragilis	NCBITaxon:817 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Bacteroides fragilis DSM 2151T"
Bacteroides thetaiotaomicron DSM 2079T — ontology label: Bacteroides thetaiotaomicron	NCBITaxon:818 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Bacteroides thetaiotaomicron DSM 2079T"
Phocaeicola vulgatus ATCC 8482T — ontology label: Phocaeicola vulgatus	NCBITaxon:821 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Phocaeicola vulgatus ATCC 8482T"
Ruminococcus gnavus ATCC 29149T — ontology label: Mediterraneibacter gnavus	NCBITaxon:33038 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Ruminococcus gnavus ATCC 29149T"
Ruminococcus torques ATCC 27756T — ontology label: Mediterraneibacter torques	NCBITaxon:33039 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Ruminococcus torques ATCC 27756T"
Anaerostipes caccae DSM 14662T — ontology label: Anaerostipes caccae	NCBITaxon:105841 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Anaerostipes caccae DSM 14662T"
Anaerobutyricum hallii DSM 3353T — ontology label: Anaerobutyricum hallii	NCBITaxon:39488 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Anaerobutyricum hallii DSM 3353T"
Agathobacter rectalis ATCC 33656T — ontology label: Agathobacter rectalis ATCC 33656	NCBITaxon:515619 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Agathobacter rectalis ATCC 33656T"
Faecalibacterium duncaniae DSM 17677T — ontology label: Faecalibacterium duncaniae	NCBITaxon:411483 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Faecalibacterium duncaniae DSM 17677T"
Roseburia intestinalis DSM 14610T — ontology label: Roseburia intestinalis	NCBITaxon:166486 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Roseburia intestinalis DSM 14610T"
Blautia hydrogenotrophica DSM 10507T — ontology label: Blautia hydrogenotrophica	NCBITaxon:53443 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Blautia hydrogenotrophica DSM 10507T"
Desulfovibrio piger DSM 749T — ontology label: Desulfovibrio piger	NCBITaxon:901 · TaxonMech · TraitMech	N/A
PMID:42109165 - SUPPORT (IN_VITRO) "Desulfovibrio piger DSM 749T"

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

Other

Mucin-Type-Dependent MDSC Restructuring

After four sequential transfers, the MDSC stabilized into distinct species-level compositions on PGM, PGM plus BSM, and PGM plus added sialylated glycans, with BSM alone supporting limited growth. Substrate-regime interventions establish composition responses, but taxon-specific niche partitioning or competition is an interpretation, not selectively isolated by these abundance data.

Biological Processes:

biological process involved in interspecies interaction (GO:0044419 · PathwayMech)

Downstream Effects:

→ Substrate-Dependent Mucin Glycan Degradation

PARTIAL - Substrate-selected community composition can change the available glycan-degrading enzyme repertoire and thereby influence degradation. The paper reports coordinated composition and glycan changes, including convergence of added-glycan degradation rates, but changes mucin substrate rather than holding substrate fixed while selectively changing composition. Direct substrate accessibility and composition-mediated effects are therefore not separated.

Evidence

PMID:42109165 - SUPPORT (IN_VITRO)

"After four transfers, the composition of the community differed as a result of mucin type condition"

Substrate-Dependent Mucin Glycan Degradation

The MDSC rapidly degrades PGM and mixed PGM/BSM O-glycans and degrades added sialylated glycans. BSM alone supports little growth and only minimal O-glycan degradation, while its low-abundance identified N-glycans are completely degraded. Added sialylated structures show different early rates and some remain detectable at120 h. These community substrate-processing outcomes do not identify the donor-recipient fluxes implied by a pairwise cross-feeding mechanism.

Biological Processes:

carbohydrate metabolic process (GO:0005975 · PathwayMech)

Evidence

PMID:42109165 - SUPPORT (IN_VITRO)

"Furthermore, glycan degradation and metabolite production were also affected by mucin type"

Mucin-Type-Dependent Fermentation Profile

HPLC measurements showed that PGM, BSM, PGM/BSM, and PGM plus sialylated glycans yielded distinct extracellular metabolite profiles, including condition-dependent changes in acetate, propionate, formate, and ethanol after community stabilization. These are extracellular pool profiles, not measured transfer between particular members. Low metabolite output on BSM may include yeast-extract fermentation; an increase in metabolite concentration is not proof of production exclusively from mucin.

Metabolites: acetate (CHEBI:30089 · MediaIngredientMech · CMMMech), propionate (CHEBI:17272 · MediaIngredientMech · CMMMech), formate (CHEBI:15740 · MediaIngredientMech · CMMMech), ethanol (CHEBI:16236 · MediaIngredientMech · CMMMech)

Biological Processes:

fermentation (GO:0006113 · PathwayMech)

Evidence

PMID:42109165 - SUPPORT (IN_VITRO)

"Incubation of the MDSC with different mucin types resulted in distinct metabolite profiles"

Associated Datasets

Dataset	Type	Repository	Accession
MDSC 16S rRNA amplicon sequencing ENA project ENA project for 16S rRNA gene amplicon sequencing from the MDSC mucin-type experiment.	AMPLICON_16S	ENA	PRJEB83805
MDSC mucin glycan Yoda dataset Yoda raw and processed glycan dataset generated in the MDSC mucin-type experiment.	OTHER	OTHER	doi:10.17887/WUR01-8PT7T6

Knowledge gaps & discussions (2)

KNOWLEDGE_GAP OPEN Which exact MDSC members acted as primary mucin glycan degraders, secondary degraders, and hydrogen consumers in each mucin condition?

The 2026 MDSC paper states that the community design included primary mucin degraders, secondary degraders, and hydrogen consumers and measured condition-level community composition, glycan degradation, and metabolite production. Pairwise member-to-member carbon or gas fluxes in the exact 14-strain MDSC were not resolved from this paper alone, so this record captures only community-level mucin responses.

Attaches to: ecological_interactions

KNOWLEDGE_GAP OPEN Which selective mechanisms explain the measured community responses?

Preserve the experimentally altered mucin regimes and positive composition, glycan and metabolite responses. The retained composition-to-degradation mechanism is PARTIAL because composition and substrate accessibility change together. Do not confuse failure to degrade most BSM O-glycans with failure to degrade its N-glycans, or A.muciniphila abundance with demonstrated sialic-acid utilization. Monoculture BSM plus threonine did not restore A.muciniphila growth. Existing unresolved pairwise-flux discussion and prior957/958/959 repairs remain intact.

Attaches to: ecological_interactions#Mucin-Type-Dependent MDSC Restructuring, ecological_interactions#Substrate-Dependent Mucin Glycan Degradation, ecological_interactions#Mucin-Type-Dependent Fermentation Profile

External Resources

Name	Repository	Resource ID
Primary publication - MDSC mucin glycan SynCom Environmental Microbiology article reporting the 14-member MDSC and mucin-type sequential-batch experiment.	OTHER	PMID:42109165
PMID:42109165 - SUPPORT (OTHER) "Mucin Type Drives Composition and Mucin Glycan Degradation of an In Vitro Synthetic Microbial Community"
Primary publication DOI - MDSC mucin glycan SynCom DOI landing page for the Environmental Microbiology MDSC primary publication.	OTHER	doi:10.1111/1462-2920.70288
PMID:42109165 - SUPPORT (OTHER) "10.1111/1462-2920.70288"

Environmental Factors

Factor	Value	Unit
Porcine gastric mucin	0.5	% w/v
PMID:42109165 - SUPPORT (IN_VITRO) "porcine gastric mucin type III (PGM, purified powder, 0.5% w/v"
Bovine submaxillary mucin	0.5	% w/v
PMID:42109165 - SUPPORT (IN_VITRO) "bovine submaxillary mucin type I-S (BSM, 0.5% w/v"
Mixed PGM plus BSM	2 x 0.25	% w/v
PMID:42109165 - SUPPORT (IN_VITRO) "a combination of both (PGM + BSM, 2 × 0.25% w/v)"
Added sialylated glycans	0.05 then 0.03	% w/v combined
PMID:42109165 - SUPPORT (IN_VITRO) "As additive sialylated glycans (SG), 3′‐sialylgalacto‐N‐biose (sodium salt, Neu5Acα2‐3Galβ1‐3GlcNAc) (0.025% w/v) and 6′‐α‐sialyl‐N‐acetyllactosamine (sodium salt, Neu5Acα2‐6Galβ1‐4GlcNAc) (0.025% w/v) were used" PMID:42109165 - SUPPORT (IN_VITRO) "For the PGM + SG condition, the sialylated glycans were added at a combined concentration of 0.05% (w/v) in the first three bottles, whereas the last two contained the sialylated glycans at a concentration of 0.03% (w/v)"

Growth Media

Anoxic bicarbonate buffered mucin medium

Temperature 37 C

Atmosphere ANAEROBIC

Composition

Component	Concentration	Unit	CHEBI
yeast extract · MediaIngredientMech	1	g/L	N/A

Preparation notes: The anoxic bicarbonate buffered medium was reduced with cysteine-HCl and supplied with PGM, BSM, equal PGM/BSM, or PGM plus sialylated glycans as the carbon source. The 5% v/v mixed inoculum was prepared from individual precultures combined in a 1:1 ratio based on OD600.

Evidence

PMID:42109165

"The medium was an anoxic bicarbonate buffered medium prepared as described previously"

PMID:42109165

"Serum bottles were incubated without shaking at 37°C for 24 h"

Cross-Mech Suite Links

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

HabitatMech: anaerobic laboratory serum-bottle culture ↗ TaxonMech: Akkermansia muciniphila DSM 22959T ↗ TraitMech: Akkermansia muciniphila DSM 22959T ↗ TaxonMech: Bacteroides caccae DSM 19024T ↗ TraitMech: Bacteroides caccae DSM 19024T ↗ TaxonMech: Bacteroides fragilis DSM 2151T ↗ TraitMech: Bacteroides fragilis DSM 2151T ↗ TaxonMech: Bacteroides thetaiotaomicron DSM 2079T ↗ TraitMech: Bacteroides thetaiotaomicron DSM 2079T ↗ TaxonMech: Phocaeicola vulgatus ATCC 8482T ↗ TraitMech: Phocaeicola vulgatus ATCC 8482T ↗ TaxonMech: Ruminococcus gnavus ATCC 29149T ↗ TraitMech: Ruminococcus gnavus ATCC 29149T ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗