A comparative genomic analysis of Clostridium immunis

Project Summary/AbstractThe past decade has seen a resurgence of interest in understanding how the microbiota?all ofthe bacteria, viruses, fungi, and Archaea that normally live in and on every human being?impacts host physiology and susceptibility to disease. Although diseases in virtually every organsystem have been linked with changes in the microbiota, our knowledge of whether thesemicrobe?disease relationships are simply correlative or causal in nature is still in its infancy.There is a critical need to better understand the mechanistic basis of how commensalorganisms influence disease, both from the host and bacterial perspectives. There are at leasttwo critical bottlenecks to determining how bacteria impact host physiology: it is challenging toidentify specific organisms that are causally related to disease and the lack of genetic tools formanipulation of most gram-positive commensal organisms. In earlier K08-funded research, thisfirst research hurdle was addressed by developing an experimental approach that is able toidentify microbes that are causally related to a given phenotype. Use of this method coupledwith directed culture techniques led to the identification and recovery of Clostridium immunis, apreviously unknown bacterial species that is able to protect colitis-prone mice from death.Having a single microbe that is clearly causally related to disease protection affords the uniqueopportunity to discover the bacterial factor(s) that mediates this activity. This proposal seeks toperform a comparative genomic analysis of C. immunis and several closely related bacterialspecies, where genomic elements will be correlated with the disease-modulating activity of eachstrain to identify genes that are potentially related to disease protection. Moreover, genetic toolswill be developed to facilitate altering gene expression in C. immunis, thereby enablingexperimental testing of the role played by the genes identified. Ultimately, these experiments willprovide insight into the bacterial factors required for C. immunis-mediated protection from colitis.More broadly, the genetic tools developed will further mechanistic studies related to themicrobiome while simultaneously generating the preliminary data needed to develop acompetitive R01 application that further explores the host and bacterial requirements for C.immunis-mediated disease protection.