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Clostridial isoDCA Mini Consortium

Community ID CommunityMech:000396
Ecological State ENGINEERED
Environment anaerobic laboratory bile-acid culture — ontology label: laboratory environment
ENVO:01001405 · HabitatMech ↗
Modeled Environment antibiotic-treated mouse gut — ontology label: intestine environment
ENVO:2100002 · HabitatMech ↗

A two-member engineered Clostridia consortium pairing Peptacetobacter hiranonis with Ruminococcus gnavus VPI C7-9 WT so the community converts host-derived taurocholic acid through cholic acid and deoxycholic acid to isodeoxycholic acid. Ionescu et al. also built a matched P. hiranonis plus R. gnavus KO consortium with rumgna_00694 disrupted as an isoDCA-negative control, enabling in vitro bile-acid conversion assays and antibiotic-treated mouse engraftment experiments that isolate the host effects of isoDCA.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Peptacetobacter hiranonis NCBITaxon:89152 · TaxonMech · TraitMech
CROSS_FEEDER
N/A
Ruminococcus gnavus VPI C7-9 WT — ontology label: Mediterraneibacter gnavus NCBITaxon:33038 · TaxonMech · TraitMech
CROSS_FEEDER
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.

Ecological interaction network for Clostridial isoDCA Mini Consortium Bipartite graph where circles represent taxa and non-circular symbols represent interactions, with distinct shapes and colours for cross-feeding.
Taxon
Cross-feeding

P. hiranonis and R. gnavus WT isoDCA production

CROSS_FEEDING

Peptacetobacter hiranonis first converts taurocholic acid through cholic acid to deoxycholic acid; R. gnavus WT then converts the P. hiranonis-derived bile-acid products to isoDCA, yielding an isoDCA-positive paired consortium.

Source Taxon: Peptacetobacter hiranonis

Target Taxon: Ruminococcus gnavus VPI C7-9 WT

Evidence

Knowledge gaps & discussions (1)

CURATION_TODO OPEN Which Peptacetobacter hiranonis strain was used in the isoDCA-positive mini-consortium?

The inspected preprint methods name the R. gnavus parent as VPI C7-9 from ATCC 29149, but only identify the consortium's P. hiranonis member at species level.

Attaches to: taxonomy#Peptacetobacter hiranonis

External Resources

Name Repository Resource ID
Primary bioRxiv preprint - engineered Clostridial isoDCA mini consortium
bioRxiv preprint reporting the two-member P. hiranonis and R. gnavus WT isoDCA+ consortium. 		OTHER doi:10.64898/2026.08.11.743107

Growth Media

BHI-S supplemented brain heart infusion medium

Temperature 37 degrees Celsius
Atmosphere ANAEROBIC

Composition

Component Concentration Unit CHEBI
brain heart infusion powder · MediaIngredientMech 37 g/L N/A
yeast extract · MediaIngredientMech 5 g/L N/A
L-cysteine · MediaIngredientMech 1 % v/v of 10% w/v stock N/A

Preparation notes: Used for liquid culturing and OD600-normalized glycerol-stock preparation of both isoDCA+ consortium members.

Evidence

doi:10.64898/2026.08.11.743107

"were cultured at 37 °C in an incubator inside a flexible vinyl anaerobic chamber"

doi:10.64898/2026.08.11.743107

"flexible vinyl anaerobic chamber with concentrations of H2 = 2.5-3.0% and O2 < 50 ppm"

doi:10.64898/2026.08.11.743107

"supplemented brain heart infusion (BHI-S) medium consisting of 37 g/L of brain heart infusion powder (BD Difco), 5 g/L yeast extract (BD Bacto), and 1% (v/v) of 10% (w/v) L-cysteine (Sigma)"

doi:10.64898/2026.08.11.743107

"secondary cultures in BHI-S medium that were grown at 37 °C for 12-16 hours to OD 600 ≈ 0.800"

YCFAC medium for bile-acid metabolism

Temperature 37 degrees Celsius
Atmosphere ANAEROBIC

Preparation notes: Used for in vitro bile-acid conversion assays because the source avoided BHI-S sterol compounds during those assays.

Evidence

doi:10.64898/2026.08.11.743107

"yeast casitone fatty acids broth with carbohydrates (YCFAC) medium"

doi:10.64898/2026.08.11.743107

"avoid sterol compounds found in BHI-S medium"

doi:10.64898/2026.08.11.743107

"secondary YCFAC cultures were spiked with 8 μL of 100 mM bile acids prior to reduction in the anaerobic chamber"

doi:10.64898/2026.08.11.743107

"Secondary cultures spiked with bile acids were inoculated with 50 μL of P. hiranonis, R. gnavus WT, or R. gnavus KO turbid primary cultures and grown at 37 °C overnight"

Cross-Mech Suite Links

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

HabitatMech: anaerobic laboratory bile-acid culture ↗ TaxonMech: Peptacetobacter hiranonis ↗ TraitMech: Peptacetobacter hiranonis ↗ TaxonMech: Ruminococcus gnavus VPI C7-9 WT ↗ TraitMech: Ruminococcus gnavus VPI C7-9 WT ↗ CultureMech Growth Media ↗ PathwayMech Pathways ↗