The Hitchhikers Of the Rhizosphere (THOR) is a genetically tractable three-member model microbiome assembled from Bacillus cereus, Pseudomonas koreensis, and Flavobacterium johnsoniae. The community was developed from rhizosphere-associated isolates to study microbial community assembly, competition, biofilm formation, secondary metabolism, and higher-order interactions under controlled laboratory conditions. P. koreensis produces the antibiotic koreenceine, which inhibits F. johnsoniae and drives community transcriptional responses, while B. cereus modulates antibiotic production and participates in emergent colony expansion and biofilm phenotypes.
Taxonomy
| Taxon | Ontology ID | Functional Roles | Abundance |
|---|---|---|---|
| Bacillus cereus UW85 — ontology label: Bacillus cereus | NCBITaxon:1396 · TaxonMech · TraitMech |
SYNTROPHIC_PARTNER
|
N/A |
|
|||
| Pseudomonas koreensis CI12 — ontology label: Pseudomonas koreensis | NCBITaxon:198620 · TaxonMech · TraitMech |
SYNTROPHIC_PARTNER
|
N/A |
|
|||
| Flavobacterium johnsoniae UW101 — ontology label: Flavobacterium johnsoniae | NCBITaxon:986 · TaxonMech · TraitMech |
SYNTROPHIC_PARTNER
|
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.
Koreenceine production and UW101 growth inhibition
P. koreensis CI12 produces koreenceine and inhibits F. johnsoniae UW101 in the 2022 THOR study. Deleting the koreenceine locus or reducing the initial P. koreensis inoculum increases UW101 populations. P. koreensis and B. cereus growth are not impaired by coculture under the tested conditions, so this one-sided inhibition does not establish mutual negative fitness effects. This UW101 assay must not be conflated with the founding CI04 root-exudate experiment.
Source Taxon: Pseudomonas koreensis CI12
Target Taxon: Flavobacterium johnsoniae UW101
Metabolites: koreenceine (CHEBI:22315 · MediaIngredientMech · CMMMech)
Biological Processes:
- interspecies interaction between organisms (GO:0044419 · PathwayMech)
The wild-type versus koreenceine-locus-deletion comparison supports koreenceine-dependent gene regulation in UW101 and B. cereus. PARTIAL for the direct molecular route: antibiotic exposure and indirect physiological effects can both contribute. This arrow starts from koreenceine production, not an assumption that reduced UW101 growth causes all transcriptional changes or that B. cereus growth is inhibited.
Evidence
-
PMID:35435700 - SUPPORT (IN_VITRO)"both deletion of the koreenceine locus and reduction of P. koreensis inoculum size increase F. johnsoniae populations"
-
PMID:35435700 - SUPPORT (IN_VITRO)"the growth of P. koreensis and B. cereus was not affected by coculture"
-
PMID:35435700 - SUPPORT (IN_VITRO)"Bacillus cereus UW85 (B), Flavobacterium johnsoniae UW101 (F), Pseudomonas koreensis CI12 (P)"
Koreenceine-Driven Transcriptional Regulation
At the assayed early time point, the P. koreensis koreenceine locus accounts for 85% of the greater-than-twofold pairwise response in UW101 and 22% in B. cereus. These are proportions of differentially regulated genes, not of each whole genome or of all three-member responses. Locus deletion supports dependence, while direct sensing and indirect effects of altered growth remain unresolved. B. cereus changes expression without a measured growth defect. Reducing P. koreensis initial abundance, unlike deleting the locus alone, increases its own response to UW101.
Metabolites: koreenceine (CHEBI:22315 · MediaIngredientMech · CMMMech)
Biological Processes:
- regulation of gene expression (GO:0010468 · PathwayMech)
Evidence
-
PMID:35435700 - SUPPORT (IN_VITRO)"In pairwise interactions, the koreenceine biosynthetic cluster is responsible for 85 and 22% of differentially regulated genes in F. johnsoniae and B. cereus, respectively."
-
PMID:35435700 - PARTIAL (IN_VITRO)"likely a combination of direct effects from koreenceine and indirect effects due to slower growth rate of F. johnsoniae in the presence of an antibiotic"
Bacillus protection in the UW101 THOR community
Adding B. cereus UW85 to P. koreensis CI12 and F. johnsoniae UW101 raises UW101 abundance relative to the inhibited pair in the 2022 study. This is a three-member protective effect, not facilitation of P. koreensis colonization. PARTIAL: the proposed chemical explanation draws on the earlier CI04 variant, where B. cereus reduced accumulated koreenceines A and C and its spo0H mutant lost protection. Those CI04 measurements neither quantify A/C changes in UW101 culture nor isolate reduced biosynthesis from other routes of reduced metabolite accumulation.
Participating Taxa: Bacillus cereus UW85, Pseudomonas koreensis CI12, Flavobacterium johnsoniae UW101
Metabolites: koreenceine (CHEBI:22315 · MediaIngredientMech · CMMMech)
Biological Processes:
- negative regulation of biological process (GO:0048519 · PathwayMech)
B. cereus addition reduces the population inhibition of UW101 in the three-member assay. PARTIAL for mediation by altered koreenceine accumulation: the detailed metabolite and spo0H comparisons were performed with CI04, not UW101, and do not uniquely demonstrate a biosynthesis-suppression mechanism in the UW101 community.
Evidence
-
PMID:35435700 - SUPPORT (IN_VITRO)"P. koreensis reduced growth of F. johnsoniae when they were grown as a pair, but F. johnsoniae abundance was higher when B. cereus was also present"
-
PMID:30837345 - PARTIAL (IN_VITRO)"The addition of B. cereus to cocultures of P. koreensis and F. johnsoniae severely reduced the accumulation of koreenceine A and C, with a minor effect on the level of koreenceine B"
Associated Datasets
| Dataset | Type | Repository | Accession |
|---|---|---|---|
|
THOR comparative metatranscriptomics
Comparative metatranscriptomics study of THOR pairwise and full-community interactions. |
METATRANSCRIPTOMICS | OTHER | PMID:35435700 |
Knowledge gaps & discussions (1)
KNOWLEDGE_GAP OPEN Which CI04-variant biofilm and metabolite mechanisms transfer experimentally to the UW101 THOR community?
The founding study used CI04; the 2022 Methods name UW101. In CI04 assays, both partners enhanced P. koreensis biofilm and the triple culture sustained it longer, but this does not establish the corresponding UW101 phenotype. Likewise, CI04 metabolite accumulation and spo0H tests do not resolve the UW101 protection mechanism. Strain-matched biofilm and chemical perturbations are needed before restoring that node or asserting a specific route. The UW101 locus-deletion, population and expression results remain experimental evidence.
Attaches to: ecological_interactions#Koreenceine production and UW101 growth inhibition, ecological_interactions#Koreenceine-Driven Transcriptional Regulation, ecological_interactions#Bacillus protection in the UW101 THOR community
2 evidence item(s)
Bacillus cereus UW85 (B), Flavobacterium johnsoniae UW101 (F), Pseudomonas koreensis CI12 (P)
F. johnsoniae CI04 and B. cereus UW85 each increased the maximum biofilm formed by P. koreensis CI12 at 18 h
Environmental Factors
| Factor | Value | Unit |
|---|---|---|
| Rhizosphere Origin | Field-grown soybean root/rhizosphere-associated isolates | N/A |
|
||
| Laboratory Coculture | Defined pairwise and three-member coculture | N/A |
|
||
Growth Media
Cross-Mech Suite Links
Explore related entities across the CultureBotAI X-Mech knowledge bases: