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 — ontology label: Anaerostipes caccae | NCBITaxon:105841 · TaxonMech · TraitMech |
SECONDARY_FERMENTER
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N/A |
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| Bacteroides thetaiotaomicron DSMZ 2079 — ontology label: Bacteroides thetaiotaomicron | NCBITaxon:818 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
|
N/A |
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| Bifidobacterium longum NCC 2705 — ontology label: Bifidobacterium longum | NCBITaxon:216816 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
|
N/A |
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| Blautia producta DSMZ 2950 — ontology label: Blautia producta | NCBITaxon:33035 · TaxonMech · TraitMech |
SECONDARY_FERMENTER
|
N/A |
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| Clostridium butyricum DSMZ 10702 — ontology label: Clostridium butyricum | NCBITaxon:1492 · TaxonMech · TraitMech |
SECONDARY_FERMENTER
|
N/A |
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| Clostridium ramosum DSMZ 1402 — ontology label: Thomasclavelia ramosa | NCBITaxon:1547 · TaxonMech · TraitMech |
SECONDARY_FERMENTER
|
N/A |
|
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| Escherichia coli K-12 MG1655 — ontology label: Escherichia coli str. K-12 substr. MG1655 | NCBITaxon:511145 · TaxonMech · TraitMech |
CROSS_FEEDER
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N/A |
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| Lactobacillus plantarum DSMZ 20174 — ontology label: Lactiplantibacillus plantarum | NCBITaxon:1590 · TaxonMech · TraitMech |
CROSS_FEEDER
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N/A |
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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.
Anaerobic Fermentation and Short-Chain Fatty Acid Output
SIHUMIx bioreactor studies measured community short-chain fatty acid output. The transit-time study reports lower butyrate and selected other acids at shorter transit time; total SCFA, acetate and propionate did not change significantly with transit time. These bulk endpoints do not identify donor-recipient exchange or establish BP5 mediation.
Metabolites: acetate (CHEBI:30089 · MediaIngredientMech · CMMMech), propionate (CHEBI:17272 · MediaIngredientMech · CMMMech), butyrate (CHEBI:17968 · MediaIngredientMech · CMMMech)
Biological Processes:
- fermentation (GO:0006113 · PathwayMech)
Evidence
-
doi:10.3390/microorganisms7120641 - SUPPORT (IN_VITRO)"a reduction in butyrate, methyl butyrate, isobutyrate, valerate, and isovalerate concentrations"
Community-Specific Small Protein Expression
Six novel small proteins were detected only in the community comparison. This is positive expression evidence, but single-strain and community cultivation conditions differed, so community-specific regulation is not isolated. Antimicrobial predictions and the limited positive synthetic-CR2 assay do not establish colonization facilitation or a native BP5-mediated exchange mechanism.
Biological Processes:
- gene expression (GO:0010467 · PathwayMech)
- interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
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PMID:33622394 - SUPPORT (IN_VITRO)"six of these sProteins were only identified in the SIHUMIx community"
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PMID:33622394 - PARTIAL (COMPUTATIONAL)"Two of these novel sProteins have a potential antimicrobial function"
Predicted Blautia Exchange After BP5-Neighbor Reaction Knockout
CROSS_FEEDINGCOMPUTATIONAL: constraint-based modelling predicted altered B. producta exchanges after in silico removal of rxn15467, a valine-biosynthesis reaction encoded near BP5. The predictions included reduced acetate production and increased choline uptake/betaine production. This was not a BP5 knockout; genomic proximity and community-only detection leave BP5 mediation HYPOTHESIZED. Predicted exchange is not measured transfer or an established cause of SCFA outcomes in the separate transit-time study.
Metabolites: acetate (CHEBI:30089 · MediaIngredientMech · CMMMech), choline (CHEBI:15354 · MediaIngredientMech · CMMMech)
Biological Processes:
- interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
-
PMID:33622394 - PARTIAL (COMPUTATIONAL)"An in silico knockout of (R)-2,3-dihydroxy-3-methylbutanoate hydrolyase which is in close genomic neighborhood to BP5 and catalyzes the second-to-last step in valine biosynthesis, led to a reduced metabolite production and concurrently increased metabolite consumption by B. producta for the SIHUMIx community members."
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
SIHUMIx metaproteomics and metatranscriptomics study
Multi-omics study identifying community-relevant small proteins in SIHUMIx. |
METAPROTEOMICS | OTHER | PMID:33622394 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Does native BP5 regulate community metabolite exchange?
Selected primary cultivation, modelling, results and discussion sections were read. BP5 adjacency does not demonstrate regulation of the neighboring enzyme, and the authors explicitly call its mediation hypothetical. Different single/community growth conditions confound the expression comparison. The primary main text also reports a positive synthetic-CR2 effect on C. butyricum lag and cell size; this limited assay is not evidence of colonization facilitation or proof of native peptide action within the whole consortium. No new CR2 node or mechanism is added without the required extension workflow. The separate transit-time study measures community outputs, not BP5-dependent flux; its discussion contains inconsistent BCFA direction wording, so the graph follows the explicit Results and abstract. Non-graph modelling-source labels and culture-temperature scope remain issue1770.
Attaches to: ecological_interactions#Anaerobic Fermentation and Short-Chain Fatty Acid Output, ecological_interactions#Community-Specific Small Protein Expression, ecological_interactions#Predicted Blautia Exchange After BP5-Neighbor Reaction Knockout
3 evidence item(s)
growth and cultivation conditions differ between individual cultures and communities
The source explicitly identifies this confounder.
BP5 may serve as potential mediator or modulator
The authors label BP5 mediation a hypothesis.
we observed a significant reduction in cell size after treatment of C. butyricum with CR2
Positive synthetic-peptide assay evidence is acknowledged without claiming native community mediation.
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Anaerobic Atmosphere | Nitrogen-gassed anaerobic bioreactor | N/A |
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| Temperature | 37 | degrees Celsius |
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| Transit Time Perturbation | 12 h, 24 h, and 48 h transit-time simulations | N/A |
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Growth Media
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