Codiversification of gut microbiota with humans

The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia and Africa, including mothers and children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes, and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes. Please note: 1) Metagenomes with the same study ID, but different “_X” appendages, where X is an integer, are technical replicates of the same biological sample (which were aggregated before using in the study). 2) The number of reads reported in the manuscript's supplement are less than that reflected in the ENA metadata; this is because the former are post-QC read counts, and the latter are raw sequencing read counts.