The 88th Annual Meeting of the American Association of Physical Anthropologists (2019)


High variability and decoupling from phylogenetic effects characterize the human microbiome

STEVEN R. LEIGH1,2, DANIEL MCDONALD3, NATHANIEL J. DOMINY4, TONY L. GOLDBERG5, JOANNA LAMBERT6, JESSICA L. METCALF7, ANDRES GOMEZ8, GILLIAN AO. BRITTON4, REBECCA M. STUMPF2,9, ROB KNIGHT10,11,12,3, ELIZABETH K. MALLOTT13 and KATHERING R. AMATO13.

1Anthropology, University of Colorado, Boulder, CO, 2Carl Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 3Pediatrics, University of California San Diego, San Diego, CA, 4Anthropology, Dartmouth College, Hanover, NH, 5Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, 6Environmental Studies Program, University of Colorado, Boulder, CO, 7Animal Sciences, Colorado State University, Fort Collins, CO, 8Animal Sciences, University of Minnesota, Minneapolis, MN, 9Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL, 10Computer Science and Engineering, University of California San Diego, San Diego, CA, 11Bioengineering, University of California San Diego, San Diego, CA, 12Center for Microbiome Innovation, University of California San Diego, San Diego, CA, 13Anthropology, Northwestern University, Evanston, IL

March 28, 2019 5:15, CC Room 26 C Add to calendar

The community of microbes residing in the human colon influences host nutritional status, immune function, and even behavior, making an understanding of host-microbe interactions critical to human biology. Increasingly, data from non-human primates are being used to provide evolutionary context. Hominoids have thus far been assumed to be the best comparative system, given their close phylogenetic relationship to humans.

We compare 16S rRNA sequence and Metacyc pathway data from 18 species of wild, nonhuman primates to 14 literature-reported human populations. Human samples include both “industrialized” and “nonindustrialized” populations. Results reveal substantially more variability in gut microbiome composition and function within and among human populations than within and among other primate species. Moreover, the composition and function of the human gut microbiome is more similar to that of Old World monkeys (Family Cercopithecinae), particularly baboons, than to other hominoids, including great apes. Unlike previous comparisons among nonhuman primate species that reveal close phylogenetic clustering, the human microbiome differs substantially from closely related hominoids.

These findings indicate that apes are insufficient for placing the human microbiome in an evolutionary context, and underscore that host physiology and environment can be as or more important in shaping the primate gut microbiome than host-microbe co-diversification. Compared to that of other primates, the human gut microbiome has followed a unique evolutionary trajectory, which may provide insight into humans’ marked dietary plasticity and widespread geographical distribution. Comparative studies of the human gut microbiome should further examine the functional convergence between humans and cercopithecines and its evolutionary implications.

Supported by NSF 0935347