BioModels record MODEL2209060002 is a community GEM combining Dolosigranulum pigrum and Staphylococcus aureus to emulate interactions in a human nasal-like environment.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Dolosigranulum pigrum | NCBITaxon:29394 · TaxonMech · TraitMech |
CROSS_FEEDER
|
N/A |
| Staphylococcus aureus | NCBITaxon:1280 · 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.
D. pigrum-S. aureus Exchange-Factor Prediction
COMPUTATIONAL - compartmentalized community FBA predicts medium- and objective-dependent exchanges for D. pigrum and S. aureus. Cysteine uptake and D-serine secretion are candidate outputs, not demonstrated antimicrobial production. Figure 4 states that S. aureus growth does not depend on the highlighted cysteine/D-serine fluxes, so they are not established mediators of inhibition.
Source Taxon: Dolosigranulum pigrum
Target Taxon: Staphylococcus aureus
Biological Processes:
- interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
-
doi:10.3389/fcimb.2022.925215 - SUPPORT (COMPUTATIONAL)"By this, we identify and characterize metabolic exchange factors involved in a specific interaction between D. pigrum and S. aureus as an in silico candidate factor for a deep insight into the associated species."
In Silico S. aureus Growth-Inhibition Hypothesis
COMPUTATIONAL - S. aureus growth varies with model formulation, medium and imposed objective weights. Equal weights generally favor S. aureus, while sufficiently high D. pigrum weight can suppress modeled S. aureus growth. These weights are not measured inoculation dynamics. The paper's competition index is not automatically reciprocal negative fitness under the local schema; poor-medium forced-growth scenarios can instead require S. aureus-to-D. pigrum support. No clinical efficacy is established.
Source Taxon: Dolosigranulum pigrum
Target Taxon: Staphylococcus aureus
Biological Processes:
- interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
-
doi:10.3389/fcimb.2022.925215 - PARTIAL (COMPUTATIONAL)"Multiple epidemiological studies identify Dolosigranulum pigrum as a likely beneficial bacterium based on its positive association with health, including negative associations with S. aureus."
-
doi:10.3389/fcimb.2022.925215 - PARTIAL (COMPUTATIONAL)"Its direct application suggests new ways to prevent disease-causing infections by inhibiting the growth of pathogens such as S. aureus through microbe–microbe interactions."
-
doi:10.3389/fcimb.2022.925215 - SUPPORT (COMPUTATIONAL)"S. aureus failed to grow"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
BioModels model file
SBML community model combining D. pigrum and S. aureus. |
OTHER | OTHER | SA_DP_community.xml |
|
Primary publication
Community GEM and use-case for nasal microbiome-relevant interaction modeling. |
OTHER | OTHER | doi:10.3389/fcimb.2022.925215 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which measured exchanges cause inhibition independently of imposed model objectives?
Assembly, SNM3 constraints and COMPM/COOPM construction are workflow context, not ecological nodes. Model growth depends on weights, media and formulation; D-serine/cysteine predictions do not prove lanthipeptide synthesis. Whole cached main paper/tables/captions read, not figures, supplemental files, source wet-lab papers or rerun models. Non-graph medium additions and generic endpoints remain in #1262.
Attaches to: ecological_interactions#D. pigrum-S. aureus Exchange-Factor Prediction, ecological_interactions#In Silico S. aureus Growth-Inhibition Hypothesis
External Resources
| Name | Repository | Resource ID |
|---|---|---|
|
BioModels entry
D. pigrum and S. aureus community model. |
BIOMODELS | MODEL2209060002 |
|
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Growth Media
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