Worlds within worlds: evolution of the vertebrate gut microbiota

Ley, Gordon and colleagues have analysed and compared published sequences of bacterial communities from humans with both free-living communities and those that are associated with diverse animals. They conclude that gut-associated microbiotas are profoundly different from other free-living microbiotas, and call for widespread sampling of the human gut microbiota to study how different cultures, lifestyles and technologies are impacting on the biodiversity within these fascinating communities. In this Analysis we use published 16S ribosomal RNA gene sequences to compare the bacterial assemblages that are associated with humans and other mammals, metazoa and free-living microbial communities that span a range of environments. The composition of the vertebrate gut microbiota is influenced by diet, host morphology and phylogeny, and in this respect the human gut bacterial community is typical of an omnivorous primate. However, the vertebrate gut microbiota is different from free-living communities that are not associated with animal body habitats. We propose that the recently initiated international Human Microbiome Project should strive to include a broad representation of humans, as well as other mammalian and environmental samples, as comparative analyses of microbiotas and their microbiomes are a powerful way to explore the evolutionary history of the biosphere.