Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns

Andres Gomez, Klara J. Petrzelkova, Michael B. Burns, Carl J. Yeoman, Katherine R. Amato, Klara Vlckova, David Modry, Angelique Todd, Carolyn A. Jost Robinson, Melissa J. Remis, Manolito G. Torralba, Elise Morton, Juan D. Umaña, Franck Carbonero, H. Rex Gaskins, Karen E. Nelson, Brenda A. Wilson, Rebecca M. Stumpf, Bryan A. White, Steven R. LeighRan Blekhman

Research output: Contribution to journalArticlepeer-review

144 Scopus citations


To understand how the gut microbiome is impacted by human adaptation to varying environments, we explored gut bacterial communities in the BaAka rainforest hunter-gatherers and their agriculturalist Bantu neighbors in the Central African Republic. Although the microbiome of both groups is compositionally similar, hunter-gatherers harbor increased abundance of Prevotellaceae, Treponema, and Clostridiaceae, while the Bantu gut microbiome is dominated by Firmicutes. Comparisons with US Americans reveal microbiome differences between Africans and westerners but show western-like features in the Bantu, including an increased abundance of predictive carbohydrate and xenobiotic metabolic pathways. In contrast, the hunter-gatherer gut shows increased abundance of predicted virulence, amino acid, and vitamin metabolism functions, as well as dominance of lipid and amino-acid-derived metabolites, as determined through metabolomics. Our results demonstrate gradients of traditional subsistence patterns in two neighboring African groups and highlight the adaptability of the microbiome in response to host ecology.

Original languageEnglish (US)
Pages (from-to)2142-2153
Number of pages12
JournalCell reports
Issue number9
StatePublished - Mar 8 2016

Bibliographical note

Funding Information:
We would like to thank the government of the Central African Republic, namely, the Ministre de l’Education Nationale, de l’Alphabetisation, de l’Enseignement Superieur, and de la Recherche for providing research permits to conduct our work in the Central African Republic, World Wildlife Fund and the administration of DSPA for granting research approval and for assistance with obtaining permits, and the Primate Habituation Programme for providing logistical support in the field. We thank Luis Barreiro, George (P.J.) Perry, and Laure Ségurel for important comments on previous versions of this manuscript, as well as all of our field assistants and trackers for their help in the field. This work was supported by an NSF grant (0935347), the Czech Science Foundation (number 206/09/0927), and funds from the University of Minnesota College of Biological Sciences. This publication derives from the Laboratory for Infectious Diseases Common to Humans and (non-Human) Primates from Czech Republic (HPI-Lab) and was cofinanced by the European Social Fund and the state budget of the Czech Republic (project OPVK CZ.1.07/2.3.00/20.0300). Further support came from “CEITEC”- Central European Institute of Technology (CZ.1.05/1.100/02.0068), the European Regional Development Fund, and The Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic (RVO: 68081766). This work was performed in part using computational resources at the Minnesota Supercomputing Institute.

Publisher Copyright:
© 2016 The Authors.


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