Public KBase narrative for community modeling and flux balance analysis of a synthetic bacterial community in R2A medium. The workflow applies gapfilling, merged community model construction, and FBA for a Populus-associated SynCom context.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Pantoea sp. YR343 — ontology label: Pantoea | NCBITaxon:53335 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
|
DOMINANT |
| Pseudomonas sp. GM17 — ontology label: Pseudomonas sp. | NCBITaxon:306 · TaxonMech · TraitMech |
PRIMARY_DEGRADER
|
N/A |
| Variovorax sp. CF313 — ontology label: Variovorax | NCBITaxon:34072 · 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.
Predicted R2A Community Metabolite Exchange
PARTIAL - the R2A community FBA model predicts that Pantoea sp. YR343 exports organic acids, purine derivatives and biogenic amines to other modeled members, and predicts a higher Pantoea growth rate in the community than in its individual model. The actual three-member model comprises YR343, Pseudomonas sp. GM17 and Sphingobium sp. AP49, not Variovorax CF313. The listed canonical participants are only the two correctly represented model members; AP49 membership and strain grounding remain unresolved in record metadata (#1533). Models were gapfilled, combined using final-passage 16S ratios and constrained by carbon uptake calibrated to experimental growth rates. These are conditional predictions, not measurements of exchange flux or reciprocal fitness benefit. Metaproteomics detects relevant enzymes but does not confirm metabolite transfer. Pantoea dominance is based on 16S data; protein-based abundance estimates differ.
Participating Taxa: Pantoea sp. YR343, Pseudomonas sp. GM17
Metabolites: organic acid (CHEBI:64709 · MediaIngredientMech · CMMMech), purines (CHEBI:26401 · MediaIngredientMech · CMMMech)
Evidence
-
PMID:33995895 - PARTIAL (COMPUTATIONAL)"Organic acids, purine derivatives and biogenic amines are predicted to be excreted"
-
PMID:33995895 - SUPPORT (IN_VITRO)"The less abundant strains in R2A medium are Pseudomonas sp. GM17 and Sphingobium sp. AP49."
Pseudomonas Competitive Antagonism
COMPETITIONPseudomonas sp. GM17 inhibited Variovorax sp. CF313 in a pairwise R2A-agar lawn/spot screen: 5 microliters of overnight culture was spotted onto a lawn of the other strain and incubated at 25 degrees C for 48 hours. Preserve this experimentally observed antagonism as an assay-specific pair, not as membership of CF313 in the three-member R2A FBA model. The source reports coexistence during ten-member liquid cultivation despite agar inhibition. HYPOTHESIZED - beneficial shared metabolites could compensate for antagonism, but liquid-versus-static-agar conditions are an explicit alternative explanation. No selective metabolite rescue, inhibitory molecule or causal link from antagonism to cross-feeding was established.
Source Taxon: Pseudomonas sp. GM17
Target Taxon: Variovorax sp. CF313
Biological Processes:
- biological process involved in interspecies interaction between organisms (GO:0044419 · PathwayMech)
Evidence
-
PMID:33995895 - SUPPORT (IN_VITRO)"although the growth of strain AP49, CF313 and CF142 were inhibited by strain GM17 in pairwise interaction screens"
-
PMID:33995895 - PARTIAL (IN_VITRO)"Alternatively, different experimental conditions may account for the unexpected result."
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
Populus PD10 amplicon profiling
16S profiling dataset used in the original PD10 SynCom study. |
AMPLICON_16S | NCBI_BIOPROJECT | PRJNA658537 |
|
Primary publication
Publication for Populus PD10 synthetic community assembly and modeling. |
OTHER | OTHER | PMID:33995895 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which R2A exchanges occur in culture, and what explains coexistence despite agar antagonism?
The three-member R2A model contains YR343, GM17 and AP49; CF313 belongs to the four-member MOPS model. The CF313 cross-feeding node and both arrows were removed because they transplant medium-specific predictions and a proposed compensation mechanism into R2A. Preserve the measured GM17-to-CF313 agar assay separately. Model fluxes and enzyme representation do not trace exchange; liquid-versus-agar conditions offer an alternative to metabolic rescue. Canonical membership, AP49 grounding, CF313 role and ten-isolate assembly metadata remain unresolved under #1533 and were not altered or certified here. Full primary extracted main text/Methods/Tables1-2/main captions read; no original figure pixels, supplements, raw data or executed KBase narrative. No new causal structure or Edison spend for this repair.
Attaches to: ecological_interactions#Predicted R2A Community Metabolite Exchange, ecological_interactions#Pseudomonas Competitive Antagonism
External Resources
| Name | Repository | Resource ID |
|---|---|---|
|
KBase narrative
Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium. |
KBASE | ws.73221.obj.117 |
|
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Growth Media
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