The Industrialized Gut Microbiome: In Need of Repair

The links between our gut microbiome and our health, combined with the malleability of this community, suggests that if we learn the rules for how to manipulate our gut microbes, we may be able to treat and prevent disease. Recent data from our lab and others focused on humans living different lifestyles ranging from hunter-gatherer to industrialized suggest that the gut microbiome is profoundly influenced by lifestyle. Those of us in the industrialized world are harboring a community of microbes that diverges from ancestral states. Loss of species and functions that inhabited humans over much of our evolution, and replacement with new taxa, may result in incompatibilities between the industrialized microbiome and human biology. Diet has emerged as one of the most powerful levers available to shape the composition and function of microbes within the gut. We are addressing whether diet, when combined with bacterial genetic engineering, can be used to engraft desirable microbes into the gut community. Molecular mechanisms of host-microbial interaction are pursued using an array of technologies and experimental approaches including gnotobiotic and conventional mouse models, quantitative imaging, and a metabolomics pipeline focused on defining microbiota-dependent metabolites.