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Shapira, Michael
University of California - Berkeley
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Project Summary. Animal microbiotas are increasingly recognized as essential for host health. The gutmicrobiota is the richest, and was shown to contribute to diverse host functions. Perturbations in microbiotacomposition are associated with human disease, raising interest in manipulating the microbiota to promotehealthier living or treat pathology. However, current understanding of the factors that shape microbiotacomposition is still lacking. Studies in vertebrates characterized the effects of diet on microbiota composition,but much less is known about the role of genetic factors, due to high inter-individual variability attributed togenetic heterogeneity. As an alternative, C. elegans enables work with genetically homogenous populations,averaging-out inter-individual variation to discern gene effects. We have established C. elegans as a new modelfor studying host-microbiota interactions, identifying a reproducible gut microbiota, with commensals thatenhance host development and immunity. Our results demonstrate significant contributions of host genetics toshaping of microbiota structure and function and to preferential colonization by beneficial commensals, andidentified a role for TGFb signaling in controlling abundance of a beneficial Enterobacter commensal, preventingpathogenic dysbiosis. The goal of the proposed plan is to develop this model to expedite discovery andcharacterization of host genes that shape microbiota composition and function.Two complimentary experimental pipelines were established in the lab: one takes advantage of composted soilmicrocosms to grow worms in natural-like environments, using 16S deep sequencing to compare their gutmicrobiotas to those in their environment, and enabling isolation of environmentally-derived gut commensals;the second, uses synthetic microbiotas consisting of 30 gut isolates, offering tight control over environmentaldiversity, and interrogated using qPCR with taxa-specific primers. Combining the two approaches, the proposedplan aims to: 1) Characterize TGFb-Enterobacter interactions, determining their specificity, modulation byenvironmental factors, and the mechanisms underlying their effects on microbiota composition, using it as a casestudy for detailed investigation of gene-microbiota interactions. 2) Use worm mutants for candidate genes withdiverse functions, to characterize gene contributions to microbiota composition and function. 3) Mutagenizeworms to identify genes involved in host selectivity toward beneficial commensals; expression of two differentfluorescent proteins in two Enterbacter commensals from different Caenorhabditis species revealed preferentialcolonization of C. elegans by its own beneficial commensal when presented in a mix with a similar C. briggsaecommensal; mutants would be sought that do not show this preference.Harnessing the genetic power of C. elegans to studying host-microbiota interactions - establishing themethodologies and commensal collections, will provide essential insights about the factors that shape the gutmicrobiota. Knowledge gained will form the basis for rational engineering of these communities.
Funding Source
Nat'l. Inst. of Health
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Project number
Sanitation and Quality Standards
Bacterial Pathogens
Microbiological Standards and Guidelines