The bacterial chemical repertoire mediates metabolic exchange within gut microbiomes

Microbial communities in the gut have been hypothesized to play key roles in the health of the host organism. Exploring the relationship between these populations and disease states has been a focus of the human microbiome project. However, the biological roles of the compounds produced by the gut bacteria are largely unknown. We hypothesize that these compounds act as metabolic exchange factors — mediating inter-species and intra-species interactions in the microbiome. This view is supported through this review of known bacterial metabolic exchange factors and evidence for uncharacterized metabolic exchange factors in the gut. The impact of model systems and technological developments in exploring this hypothesis are also discussed. Together, these investigations are revolutionizing our understanding of the gut microbiome — presenting the possibility of identifying new strategies for treating disease in the host.

► Gut microbiome derived metabolic exchange factors have been shown to mediate biology in the gut.
► Evidence exists for the biosynthetic capability of the gut microbiome to generate active molecules.
► Key described biology may be the result of diffusible molecules produced by the gut microbiota.
► Advances in analytical technologies will develop our understanding of microbiome chemistry.