Small-molecule-mediated interactions in complex microbial communities
Much like human beings, microbes often live in diverse communities interacting with both collaborators and competitors. Small molecule natural products mediate a significant portion of these interactions. As expected, the more complex a microbial community is, the richer its small molecule chemical arsenal becomes. This phenomenon has been observed in the complex microbiomes of marine invertebrates, terrestrial soils, human gut, and the plant rhizosphere, among others. Our research interests are mainly to study the chemical and biological interactions within complex microbial communities (microbe-microbe interactions) and between microbial communities and their multicellular hosts (microbe-host interactions). In respect to the human body and its microbial inhabitants (the human microbiome), these interactions can define the difference between commensals and pathogens, and thus between health and disease states. In the case of marine invertebrates (e.g., sponges and ascidians) and their symbionts, these interactions can provide the host with indispensible means of chemical defense, allowing it to survive in a predator-rich environment. In the soil or seawater, these interactions can dictate the microbial community’s composition, fitness and stability over time. Our ongoing efforts towards understanding these interactions will not only explain fundamentals of basic biology in these systems, but will also supply a suite of biologically active small molecules that can be developed as therapeutic agents.
In addition, the Donia lab has a special interest in the uncultivable microbial components of complex communities, which have eluded research attempts for decades despite their abundance and clear importance. Recent advances in the fields of metagenomics and single-cell genomics have allowed access to the genetic information of some of these unculturable microbes, while functional studies remain challenging. Our goal is to develop the necessary computational and experimental tools to functionally study the interactions mediated by uncultivable members of complex microbiomes, using an integrated multi “omics” approach, including metagenomics, metabolomics and metatranscriptomics. The Donia lab functions at the intersection between multiple disciplines: microbiology, molecular biology, biochemistry, small molecule chemistry and biosynthesis, metagenomics and bioinformatics, aiming to answer basic biological questions and to develop new therapeutics.