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SIHUMIx Human Intestinal Model Community

Community ID CommunityMech:000080
Ecological State ENGINEERED
Environment human gut environment
ENVO:0001998

SIHUMIx is an extended simplified human intestinal microbiota consisting of eight bacterial strains used as a reduced-complexity in vitro model of the human gut microbiome. The community includes common intestinal anaerobes and facultative bacteria spanning major gut-associated lineages, and it is maintained under anaerobic bioreactor conditions in complex intestinal medium. SIHUMIx supports controlled metaproteomic, metabolomic, metatranscriptomic, and community stability studies, including analysis of short-chain fatty acid output and community-specific small proteins.

Taxonomy

Taxon Ontology ID Functional Roles Abundance
Anaerostipes caccae DSMZ 14662 NCBITaxon:105841
SECONDARY_FERMENTER
N/A
  • PMID:33622394 - SUPPORT (IN_VITRO)
    "The SIHUMIx community is composed of eight individual bacterial species"
Bacteroides thetaiotaomicron DSMZ 2079 NCBITaxon:818
PRIMARY_DEGRADER
N/A
  • PMID:33622394 - SUPPORT (IN_VITRO)
    "Bacteroides thetaiotaomicron (DSMZ 2079)"
Bifidobacterium longum NCC 2705 NCBITaxon:216816
PRIMARY_DEGRADER
N/A
  • PMID:33622394 - SUPPORT (IN_VITRO)
    "Bifidobacterium longum (NCC 2705)"
Blautia producta DSMZ 2950 NCBITaxon:33035
SECONDARY_FERMENTER
N/A
  • PMID:33622394 - SUPPORT (IN_VITRO)
    "Blautia producta (DSMZ 2950)"
Clostridium butyricum DSMZ 10702 NCBITaxon:1492
SECONDARY_FERMENTER
N/A
  • PMID:33622394 - SUPPORT (IN_VITRO)
    "Clostridium butyricum (DSMZ 10702)"
Clostridium ramosum DSMZ 1402 NCBITaxon:1547
SECONDARY_FERMENTER
N/A
  • PMID:33622394 - SUPPORT (IN_VITRO)
    "Clostridium ramosum (DSMZ 1402)"
Escherichia coli K-12 MG1655 NCBITaxon:511145
CROSS_FEEDER
N/A
  • PMID:33622394 - SUPPORT (IN_VITRO)
    "Escherichia coli K-12 (MG1655)"
Lactobacillus plantarum DSMZ 20174 NCBITaxon:1590
CROSS_FEEDER
N/A
  • PMID:33622394 - SUPPORT (IN_VITRO)
    "Lactobacillus plantarum (DSMZ 20174)"

Ecological Interactions

Ecological interaction network for SIHUMIx Human Intestinal Model Community Bipartite graph where circle nodes represent taxa and colored rectangles represent ecological interactions (cross-feeding, mutualism, syntrophy, competition, commensalism).
Taxon
Cross-feeding
Mutualism
Syntrophy
Competition
Commensalism
Niche partitioning
Colonization facilitation
Strain competition
Predation

Anaerobic Fermentation and Short-Chain Fatty Acid Output

CROSS_FEEDING

Metabolites: acetate (CHEBI:30089), propionate (CHEBI:17272), butyrate (CHEBI:17968)

Biological Processes:

Evidence

  • doi:10.3390/microorganisms7120641 - SUPPORT (IN_VITRO)
    "a reduction in butyrate, methyl butyrate, isobutyrate, valerate, and isovalerate concentrations"
  • PMID:33622394 - SUPPORT (IN_VITRO)
    "The reduced complexity compared to the intestinal microbiome allows researchers to use the in vitro model system"

Community-Specific Small Protein Expression

COLONIZATION_FACILITATION

Biological Processes:

Evidence

  • PMID:33622394 - SUPPORT (IN_VITRO)
    "six of these sProteins were only identified in the SIHUMIx community"
  • PMID:33622394 - SUPPORT (IN_VITRO)
    "Two of these novel sProteins have a potential antimicrobial function"

Associated Datasets

Dataset Type Repository Accession
SIHUMIx metaproteomics and metatranscriptomics study
Multi-omics study identifying community-relevant small proteins in SIHUMIx. 		METAPROTEOME OTHER PMID:33622394

Environmental Factors

Factor Value Unit
Anaerobic Atmosphere Nitrogen-gassed anaerobic bioreactor N/A
  • PMID:33622394 - SUPPORT (IN_VITRO)
    "maintained under anaerobic conditions by continuously gassing the bioreactor vessels with nitrogen"
Temperature 37 degrees Celsius
  • PMID:33622394 - SUPPORT (IN_VITRO)
    "under anaerobic conditions at 37 °C"
Transit Time Perturbation 12 h, 24 h, and 48 h transit-time simulations N/A

Growth Media

Complex intestinal medium for SIHUMIx bioreactor cultivation

Temperature 37 degrees Celsius
Atmosphere ANAEROBIC

Preparation notes: The eight strains are grown individually before inoculation and the mixed community is maintained anaerobically in complex intestinal medium.

Evidence

PMID:33622394

"continuously cultivated in complex intestinal medium"

PMID:33622394

"the eight bacterial species were cultivated individually for 72 h before inoculation"