Systems Biology of a Complete, Defined Gut Microbiome

The composition and abundance of microbial species in various physiological niches in and on the human body have been causally associated with a multitude of diseases. The metabolic activity of these communities is of interest because of the apparent influence of microbial metabolism on host energy balance and immune and neural functions. The intestinal microbiota is difficult to study because most gut microbes are unculturable using standard microbiological techniques; furthermore, existing DNA-based approaches such as metagenomic or 16S sequencing are not well-equipped to identify the causal agent in host-microbe interactions. To overcome these issues and study the metabolic interactions between physiologically relevant microbes, we have developed an in vitro pipeline for culturing and studying the Altered Schaedler Flora (ASF). Mice colonized with the ASF develop a relatively normal immune system and as a defined group of 8 bacterial species it is feasible to study individual members alongside community function.. We present the first characterization of colony and cellular morphology of ASF species and a comparative analysis between the ASF and all gut-derived reference species in the Human Microbiome Project to demonstrate the metabolic potential of this small community compared to a larger consortium. We have characterized the growth of ASF members individually and in coculture on defined media through the use of optical density-based and species-specific qPCR-based methods. To isolate metabolic interactions between species, we performed spent media growth experiments, in which a single species is grown in the filter-sterilized media that another species grew in. Metabolomics data has been collected for all media before and after inoculation in spent media experiments to determine compounds being consumed and produced, thereby revealing potential symbiosis or competition. We have developed genome-scale metabolic models (GEMs) for all 8 ASF species using a metabolic network reconstruction method that leverages the phylogenetic relationship between species. GEMs are being used alongside metabolomics data from spent media experiments to help characterize interactions between species. Together, our integrated computational and experimental pipeline provides an in vitro parallel for in vivo mouse-ASF studies as well as a well-characterized, controlled testing ground for the development of community modeling methods.