Fig. 1.

The human gut microbiome within the context of populations and deeper evolutionary landscapes. a The microbiomes of different human populations are distinct from each other, especially between industrialized populations such as in the USA and remote, non-industrialized populations such as Malawians or the Guahibo and Yanomami people of the Amazon [14, 17]. b Within the context of the greater primates lineage, these differences between human populations become smaller and a connection between humans and captive populations of non-human primates can be seen. c Zooming out to include other vertebrate lineages further diminishes those differences, as the effects of deep evolutionary splits between host species and lifestyle characteristics on the gut microbiome become evident. Methods: All data were drawn from publically available studies in Qiita (https://qiita.ucsd.edu/; studies 850, 894, 940, 963, 1056, 1696, 1734, 1736, 1747, 1773, 2182, 2259, 2300, 10052, 10171, 10315, 10376, 10407, 10522). Sequence data for all samples were generated using the same protocol [134] and sequenced on an Illumina MiSeq or HiSeq platform. Sequence data were trimmed to 100 nucleotides and OTUs were picked using the deblur method [135]. Up to five samples per species were randomly selected, rarefied to 10,000 sequences per sample, and unweighted UniFrac [136] distances between samples were computed using Qiime 1.9.1 [137]. The non-metric multidimensional scaling ordination technique was employed in R 3.3.3 [138] to visualize these distances. Silhouettes of the running woman, primate, bird, and bat in c are designed by Vexels.com and reproduced with permission