Distinct N and C cross-feeding networks in a synthetic mouse gut consortium

Abstract

The complex interactions between gut microbiome and host or pathogen colonization resistance cannot solely be understood from community composition. Missing are causal relationships such as metabolic interactions among species to better understand what shapes the microbiome. Here, we focused on metabolic niches generated and occupied by the Oligo-Mouse-Microbiota consortium, a synthetic community composed of 12 members that is increasingly used as a model for the mouse gut microbiome. Combining mono-cultures and spent medium experiments with untargeted metabolomics uncovered broad metabolic diversity in the consortium, constituting a dense cross-feeding network with more than 100 pairwise interactions. Quantitative analysis of the cross-feeding network revealed distinct C and N food webs that highlight the two Bacteroidetes consortium members B. caecimuris and M. intestinale as primary suppliers of carbon, and a more diverse group as nitrogen providers. Cross-fed metabolites were mainly carboxylic acids, amino acids, and the so far not reported nucleobases. In particular the dicarboxylic acids malate and fumarate provided a strong physiological benefit to consumers, presumably as anaerobic electron acceptors. Isotopic tracer experiments validated the fate of a subset of cross-fed metabolites, in particular the conversion of the most abundant cross-fed compound succinate to butyrate. Thus, we show that this consortium is tailored to produce the anti-inflammatory metabolite butyrate. Overall, we provide evidence for metabolic niches generated and occupied by OMM members that lays a metabolic foundation to facilitate understanding of the more complex in vivo behavior of this consortium in the mouse gut. ImportanceThis article maps out the cross-feeding network amongst 10 members of a synthetic consortium that is increasingly used as the model mouse gut microbiota. Combining metabolomics with in vitro cultivations, two dense networks of carbon and nitrogen exchange are described. The vast majority of the about 100 interactions are synergistic in nature, in several cases providing distinct physiological benefits to the recipient species. These networks lay the ground work towards understanding gut community dynamics and host-gut microbe interactions.