KBase Synthetic Bacterial Community in R2A Medium

Community ID CommunityMech:000039

Ecological State ENGINEERED

Environment rhizosphere
ENVO:00005801

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	NCBITaxon:53335	PRIMARY_DEGRADER	DOMINANT
Pseudomonas sp. GM17	NCBITaxon:306	PRIMARY_DEGRADER	N/A
Variovorax sp. CF313	NCBITaxon:34072	CROSS_FEEDER	N/A

Ecological Interactions

Taxon

Cross-feeding

Mutualism

Syntrophy

Competition

Commensalism

Pantoea Metabolite Cross-Feeding to Community

CROSS_FEEDING

Source Taxon: Pantoea sp. YR343

Metabolites: organic acid (CHEBI:64709), purine (CHEBI:26401)

Evidence

PMID:33995895 - SUPPORT (COMPUTATIONAL)

"the dominant strain Pantoea sp. YR343, based on the 16S rRNA marker data, is expected to export a greater range of metabolites than it receives from the other two members of the community"
PMID:33995895 - SUPPORT (COMPUTATIONAL)

"Organic acids, purine derivatives and biogenic amines are predicted to be excreted and support the growth of the other community members."

Pseudomonas Competitive Antagonism

COMPETITION

Source Taxon: Pseudomonas sp. GM17

Target Taxon: Variovorax sp. CF313

Evidence

PMID:33995895 - SUPPORT (IN_VITRO)

"Pseudomonas sp. GM17 cells were antagonistic to the growth of the majority of the other community members"
PMID:33995895 - SUPPORT (IN_VITRO)

"although the growth of strain AP49, CF313 and CF142 were inhibited by strain GM17 in pairwise interaction screens, these strains still co-existed with strain GM17 during the 10-member community cultivation"

Variovorax Cross-Feeding on Community Metabolites

CROSS_FEEDING

Source Taxon: Variovorax sp. CF313

Metabolites: organic acid (CHEBI:64709)

Evidence

PMID:33995895 - SUPPORT (COMPUTATIONAL)

"Accessing excreted metabolites may be vital for the maintenance of those members with minor content in the community."
PMID:33995895 - SUPPORT (IN_VITRO)

"This may be attributed to intertwined metabolic interactions among these four strains, in which the beneficial effect from the metabolites in a shared extracellular environment for growth overwhelms antagonistic effects"

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