Relatives have more similar gut microbiomes than nonrelatives, but the degree to which this similarity results from shared genotypes versus shared environments has been controversial. Here, we leveraged 16,234 gut microbiome profiles, collected over 14 years from 585 wild baboons, to reveal that host genetic effects on the gut microbiome are nearly universal. Controlling for diet, age, and socioecological variation, 97% of microbiome phenotypes were significantly heritable, including several reported as heritable in humans. Heritability was typically low (mean = 0.068) but was systematically greater in the dry season, with low diet diversity, and in older hosts. We show that longitudinal profiles and large sample sizes are crucial to quantifying microbiome heritability, and indicate scope for selection on microbiome characteristics as a host phenotype.
Bibliographical noteFunding Information:
This work was directly supported by NSF DEB 1840223 (E.A.A., J.A.G.), NIH R21 AG055777 (E.A.A., R.B.), NIH R01 AG053330 (E.A.A.), and NIGMS R35 GM128716 (R.B.). We also acknowledge support from the University of Minnesota Grand Challenges in Biology Postdoctoral Fellowship (to L.G.), the Duke University Population Research Institute P2C-HD065563 (pilot award to J.T.), and Notre Dame’s Eck Institute for Global Health (E.A.A.) and Environmental Change Initiative (E.A.A.). Since 2000, ABRP has been supported by NSF and NIH, including IOS 1456832 (S.C.A.), IOS 1053461 (E.A.A.), DEB 1405308 (J.T.), IOS 0919200 (S.C.A.), DEB 0846286 (S.C.A.), DEB 0846532 (S.C.A.), IBN 0322781 (S.C.A.), IBN 0322613 (S.C.A.), BCS 0323553 (S.C.A.), BCS 0323596 (S.C.A.), P01AG031719 (S.C.A.), R21AG049936 (J.T., S.C.A.), R03AG045459 (J.T., S.C.A.), R01AG034513 (S.C.A.), R01HD088558 (J.T.), and P30AG024361 (S.C.A.). We also thank Princeton University, the Chicago Zoological Society, the Max Planck Institute for Demographic Research, the L.S.B. Leakey Foundation, and the National Geographic Society.
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