Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny

Katherine R. Amato, Elizabeth K. Mallott, Daniel McDonald, Nathaniel J. Dominy, Tony Goldberg, Joanna E. Lambert, Larissa Swedell, Jessica L. Metcalf, Andres Gomez, Gillian A.O. Britton, Rebecca M. Stumpf, Steven R. Leigh, Rob Knight

Research output: Contribution to journalArticle

Abstract

Background: Comparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. Here, in an effort to improve our understanding of the human microbiome, we compare gut microbiome composition and functional potential in 14 populations of humans from ten nations and 18 species of wild, non-human primates. Results: Contrary to expectations from host phylogenetics, we find that human gut microbiome composition and functional potential are more similar to those of cercopithecines, a subfamily of Old World monkey, particularly baboons, than to those of African apes. Additionally, our data reveal more inter-individual variation in gut microbiome functional potential within the human species than across other primate species, suggesting that the human gut microbiome may exhibit more plasticity in response to environmental variation compared to that of other primates. Conclusions: Given similarities of ancestral human habitats and dietary strategies to those of baboons, these findings suggest that convergent ecologies shaped the gut microbiomes of both humans and cercopithecines, perhaps through environmental exposure to microbes, diet, and/or associated physiological adaptations. Increased inter-individual variation in the human microbiome may be associated with human dietary diversity or the ability of humans to inhabit novel environments. Overall, these findings show that diet, ecology, and physiological adaptations are more important than host-microbe co-diversification in shaping the human microbiome, providing a key foundation for comparative analyses of the role of the microbiome in human biology and health.

Original languageEnglish (US)
Article number201
JournalGenome biology
Volume20
Issue number1
DOIs
StatePublished - Oct 8 2019

Fingerprint

Cercopithecidae
Microbiota
Phylogeny
Ecology
primate
phylogeny
digestive system
Primates
individual variation
Physiological Adaptation
Papio
diet
ecology
plasticity
Diet
Gastrointestinal Microbiome
microbiome
human ecology
Hominidae
Environmental Exposure

Keywords

  • Cercopithecine
  • Human evolution
  • Human gut microbiome
  • Primate gut microbiome

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Amato, K. R., Mallott, E. K., McDonald, D., Dominy, N. J., Goldberg, T., Lambert, J. E., ... Knight, R. (2019). Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny. Genome biology, 20(1), [201]. https://doi.org/10.1186/s13059-019-1807-z

Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny. / Amato, Katherine R.; Mallott, Elizabeth K.; McDonald, Daniel; Dominy, Nathaniel J.; Goldberg, Tony; Lambert, Joanna E.; Swedell, Larissa; Metcalf, Jessica L.; Gomez, Andres; Britton, Gillian A.O.; Stumpf, Rebecca M.; Leigh, Steven R.; Knight, Rob.

In: Genome biology, Vol. 20, No. 1, 201, 08.10.2019.

Research output: Contribution to journalArticle

Amato, KR, Mallott, EK, McDonald, D, Dominy, NJ, Goldberg, T, Lambert, JE, Swedell, L, Metcalf, JL, Gomez, A, Britton, GAO, Stumpf, RM, Leigh, SR & Knight, R 2019, 'Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny', Genome biology, vol. 20, no. 1, 201. https://doi.org/10.1186/s13059-019-1807-z
Amato, Katherine R. ; Mallott, Elizabeth K. ; McDonald, Daniel ; Dominy, Nathaniel J. ; Goldberg, Tony ; Lambert, Joanna E. ; Swedell, Larissa ; Metcalf, Jessica L. ; Gomez, Andres ; Britton, Gillian A.O. ; Stumpf, Rebecca M. ; Leigh, Steven R. ; Knight, Rob. / Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny. In: Genome biology. 2019 ; Vol. 20, No. 1.
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