. 2019 Oct 8;20(1):201.

doi: 10.1186/s13059-019-1807-z.

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

Katherine R Amato¹, Elizabeth K Mallott², Daniel McDonald^{3

4}, Nathaniel J Dominy⁵, Tony Goldberg⁶, Joanna E Lambert⁷, Larissa Swedell⁸, Jessica L Metcalf⁹, Andres Gomez¹⁰, Gillian A O Britton⁵, Rebecca M Stumpf¹¹, Steven R Leigh¹², Rob Knight^{3

4

13

14}

Affiliations

¹ Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL, 60208, USA. katherine.amato@northwestern.edu.
² Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL, 60208, USA.
³ Department of Pediatrics, University of California San Diego, San Diego, 92093, USA.
⁴ Center for Microbiome Innovation, University of California San Diego, San Diego, 92093, USA.
⁵ Department of Anthropology, Dartmouth College, Hanover, 03755, USA.
⁶ Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, 53706, USA.
⁷ Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, 80302, USA.
⁸ Department of Anthropology, City University of New York - Queens College, New York, 11367, USA.
⁹ Department of Animal Sciences, Colorado State University, Fort Collins, 80521, USA.
¹⁰ Department of Animal Sciences, University of Minnesota, Minneapolis, 55108, USA.
¹¹ Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, 61801, USA.
¹² Department of Anthropology, University of Colorado Boulder, Boulder, 80302, USA.
¹³ Department of Computer Science and Engineering, University of California San Diego, San Diego, 92093, USA.
¹⁴ Department of Bioengineering, University of California San Diego, San Diego, 92093, USA.

PMID: 31590679
PMCID: PMC6781418
DOI: 10.1186/s13059-019-1807-z

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

Katherine R Amato et al. Genome Biol. 2019.

. 2019 Oct 8;20(1):201.

doi: 10.1186/s13059-019-1807-z.

Authors

Affiliations

¹ Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL, 60208, USA. katherine.amato@northwestern.edu.
² Department of Anthropology, Northwestern University, 1810 Hinman Ave, Evanston, IL, 60208, USA.
³ Department of Pediatrics, University of California San Diego, San Diego, 92093, USA.
⁴ Center for Microbiome Innovation, University of California San Diego, San Diego, 92093, USA.
⁵ Department of Anthropology, Dartmouth College, Hanover, 03755, USA.
⁶ Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, 53706, USA.
⁷ Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, 80302, USA.
⁸ Department of Anthropology, City University of New York - Queens College, New York, 11367, USA.
⁹ Department of Animal Sciences, Colorado State University, Fort Collins, 80521, USA.
¹⁰ Department of Animal Sciences, University of Minnesota, Minneapolis, 55108, USA.
¹¹ Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, 61801, USA.
¹² Department of Anthropology, University of Colorado Boulder, Boulder, 80302, USA.
¹³ Department of Computer Science and Engineering, University of California San Diego, San Diego, 92093, USA.
¹⁴ Department of Bioengineering, University of California San Diego, San Diego, 92093, USA.

PMID: 31590679
PMCID: PMC6781418
DOI: 10.1186/s13059-019-1807-z

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.

Keywords: Cercopithecine; Human evolution; Human gut microbiome; Primate gut microbiome.

PubMed Disclaimer

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

**Fig. 1**
Similarity of gut microbiome composition among humans, apes, and cercopithecines. a Principal coordinates analysis (PCoA) plot of 16S rRNA gene amplicon data based on unweighted UniFrac distances. b PCoA plot of 16S rRNA gene amplicon data based on weighted UniFrac distances. c Consensus unweighted pair group method with arithmetic mean (UPGMA) tree of 16S rRNA gene amplicon data based on unweighted UniFrac distances. d Consensus unweighted pair group method with arithmetic mean (UPGMA) tree of 16S rRNA gene amplicon data based on weighted UniFrac distances

**Fig. 2**
Similarity of gut microbiome functional potential among non-industrialized humans, apes, and cercopithecines. a Principal coordinates analysis (PCoA) plot of shotgun metagenomic sequencing data based on Bray-Curtis distances. b Consensus unweighted pair group method with arithmetic mean (UPGMA) tree of shotgun metagenomic sequencing data based on unweighted UniFrac distances

See this image and copyright information in PMC

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

Affiliations

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

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Substances

LinkOut - more resources

Full Text Sources