We place the human gut microbiome into its evolutionary context across different modern populations with varying diets, lifestyles, and environmental exposures, and relate evolutionary patterns in the gut microbiome across the mammals to address several key questions. In this review, we focus on the gut microbiome, as surprisingly little comparative data are available for other body sites across human populations or other species. However, as in many other areas of biology, a true understanding of these patterns and processes requires an evolutionary perspective. Given the rush to apply knowledge of the human microbiome in fields ranging from medicine to forensics, there has been a heavy emphasis on practical applications of microbiome sequencing, largely from North American and European populations. More broadly, this wealth of additional data has drawn attention to the connections between microbes and foundational elements of organismal biology and ecology. Various aspects of the microbiome have been correlated to a surprising number of human diseases, and some microbiome-centric interventions have shown extraordinary efficacy in treatment of specific disorders like recurrent Clostridium difficile infection. Recent improvements in technology for collecting and analyzing DNA sequence data make these questions accessible for the first time.
A decade ago, very little was known of the inventory of microbes that inhabit different parts of the human body, how they assemble into communities of varying levels of complexity, and how they relate to microbiomes in other species.
We are in the midst of a revolution in our understanding of the human microbiome (Box 1).
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