Some gut microbes share an evolutionary history with their human hosts

Strains within dozens of bacterial species in the gut microbiota codiversified with human populations as they spread across the globe, according to a new study. The findings underscore the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease and microbiota-based therapeutics. The human gut microbiome contains hundreds of species of bacteria, and many of the most prominent species are found in people worldwide. However, within microbial species, some strains can show remarkable genetic diversity between specific human populations. Whether or not this strain-level diversity arose through a shared evolutionary history between humans and their commensal microbes isn’t fully understood. To test for codiversification, Taichi Suzuki and colleagues evaluated paired gut metagenomes and human genomes for 1225 individuals living in Europe, Asia and Africa. Suzuki et al. discovered 60 microbial strains that, between and within countries, have evolutionary histories in parallel with human phylogenies, indicating codiversification. The authors also found that the species displaying the strongest codiversification appear to have also independently evolved traits such as oxygen and temperature intolerance and reduced genomes, indicating host dependency. “[The study’s] results highlight that gut bacterial communities are not haphazard collections of bacteria but reflections of the distinct ancestries of human populations,” writes Andrew Moeller in a related Perspective. “It will be worthwhile to explore whether efforts to restore microbiota for human health can be informed by the history of codiversification uncovered by Suzuki et al.”