We apply experimental, comparative and computational approaches to investigate the factors contributing to the evolution of bacterial genomes and microbial communities. Some of our current projects investigate: 1. The role of adaptive and non-adaptive processes in bacterial genome evolution 2. The causes and consequences of genome reduction in bacterial pathogens 3. The origins of new genes and functional complexity 4.The microbial community diversity residing in Great Ape hosts
Despite the current large body of work concerning the human microbiome and its role in human health, there is relatively little information about how the microbiome evolves or the factors causing differentiation among species. Analysis of the gut microbiomes of great ape species, including humans, revealed that the phylogeny based on microbiome compositions was congruent with the known relationships of the hosts. Our investigations of the microbiomes of great apes have informed several other features of the human microbiome. For example, the gut microbial communities of humans assort into enterotypes, i.e., groups having discrete species compositions, and there is on-going debate about the cause, function, and even the existence of enterotypes. We found that wild chimpanzees and gorillas also possess gut enterotypes, and, interestingly, they are compositionally similar to those in humans. Thus, stratification of microbial communities into enterotypes preceded the divergence of great ape species and did not originate in humans as a result of modern diets, as has been speculated. Furthermore, by comparing the gut microbiomes of great ape species in a phylogenetic context, we reconstructed how the human microbiome evolved during great ape diversification. We found that human gut microbiomes have been diverging at a greatly accelerated rate since our split from other great apes due to the loss of microbial diversity at every taxonomic level.