This paper introduces THOR (The Hitchhikers Of the Rhizosphere), a defined and genetically tractable model microbiome designed for the genetic dissection of community behavior. Developed to address the difficulty in manipulating complex microbiomes, THOR comprises three representatives from dominant rhizosphere taxa: Bacillus cereus (Firmicutes), Pseudomonas koreensis (Proteobacteria), and Flavobacterium johnsoniae (Bacteroidetes). The community exhibits several complex emergent properties, including the induction of dendritic colony expansion in B. cereus by the other members and the formation of more robust collective biofilms compared to individual isolates. Furthermore, the community displays intricate biochemical interactions: P. koreensis produces a novel family of alkaloid antibiotics inhibitory to F. johnsoniae, the production of which is inhibited by B. cereus. THOR provides a foundational tool set—including genetic, genomic, and biochemical resources—to achieve a deeper mechanistic understanding of microbial community dynamics for applications in health, agriculture, and environmental sustainability.
Introducing THOR: A Model Microbiome for Dissecting Community Behavior
Objective: To develop a genetically tractable model community to dissect complex microbial community interactions and emergent properties, advancing strategies for manipulating microbiomes.
Model Community (THOR): Named "The Hitchhikers Of the Rhizosphere," THOR consists of three key organisms representing dominant rhizosphere taxa:
Bacillus cereus (Firmicutes)
Pseudomonas koreensis (Proteobacteria, selected from the high tier of a competition network)
Flavobacterium johnsoniae (Bacteroidetes, selected from the bottom tier of a competition network)
Emergent Property 1 (Colony Morphology): The presence of either P. koreensis or F. johnsoniae induces dendritic (branching) expansion of B. cereus colonies.
Emergent Property 2 (Biofilm Robustness): The three members together produce significantly more robust biofilms than when they are cultured individually.
Biochemical Interaction 1 (Inhibition):P. koreensis produces a novel family of alkaloid antibiotics that specifically inhibit the growth of F. johnsoniae.
Biochemical Interaction 2 (Regulation): The production of these inhibitory alkaloids by P. koreensis is, in turn, inhibited by the presence of B. cereus.
Key Takeaway: THOR provides an essential model system, complete with available genetic, genomic, and biochemical tools, for understanding complex, community-level microbial behavior, which is crucial for future manipulation and engineering of microbiomes in human, environmental, and agricultural contexts.