? CORE C A major need in host-microbiome research is the development of tractable model systems that provide a path to understand the mechanistic contributions of gut microbes to various diseases in which they participate. Germfree mice implanted with ?synthetic communities? of cultured microorganisms, provide such a path as the resulting ?gnotobiotic mouse? only contains microbes of known identity and often genome sequence. However, even when cultured and fully sequenced microbes are used, a major limitation is understanding the metabolic potential of the microbes involved. High-throughput metabolic phenotyping of cultured microbes helps to address the knowledge gap associated with the latter point. The main goals of the Microbial Phenotyping and Gnotobiotic Model Core will be to 1. Provide the resources for culturing and combining existing microbes associated with resistant starch degradation, butyrate production, H2 consumption and bile salt hydrolysis; 2. Perform targeted and deep culture on patient samples that vary in their responses to resistant starch consumption with the goal of modeling these variations in gnotobiotic mice colonized with the isolated species; and 3. Perform metabolic phenotyping combined with genome sequencing on isolated microbes so that their causal roles in determining the outcomes of resistant starch consumption on GVHD and bile acid modification on Enterococcus infection can be investigated through the lens of defined functions. In the latter case, such functions will include phenotypes believed to be directly involved the outcomes of the proposed disease models (degradation of resistant starch, butyrate production and bile salt hydrolases activity). However, we also anticipate extending our phenotypic measurements to define other metabolic facets, such as microbial interactions with dietary nutrients beyond resistant starch, so that we can better understand their contributions to community behavior, butyrate production, etc. The Martens Lab has extensive experience assaying cultured human gut bacteria in custom phenotypic growth arrays (e.g., for broadly measuring polysaccharide-degrading abilities), building synthetic communities from groups of microbes with defined phenotypes and driving differences in host disease progression through exogenous forces on the microbiota, such as diet. This core will be foundational to the execution of experiments in several of the proposed projects and will also establish the resources for building complex gnotobiotic systems that still preserve an experimental path towards defining mechanisms.
