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. Leigh,
Ran Blekhman
Affiliations
Andres Gomez
Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA
Klara J. Petrzelkova
Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno 603 65, Czech Republic
Michael B. Burns
Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA
Carl J. Yeoman
Department of Animal and Range Sciences, Montana State University, Bozeman, MT 59717, USA
Katherine R. Amato
Department of Anthropology, Northwestern University, Evanston, IL 60208, USA
Klara Vlckova
Faculty of Veterinary Medicine, Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic
David Modry
Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice 370 05, Czech Republic
Angelique Todd
Dzanga-Sangha Protected Areas, World Wildlife Fund, Bayanga, Central African Republic
Carolyn A. Jost Robinson
Department of Anthropology, University of North Carolina, Wilmington, NC 28403, USA
Melissa J. Remis
Department of Anthropology, Purdue University, West Lafayette, IN 47907, USA
Manolito G. Torralba
The J. Craig Venter Institute, La Jolla, CA 92037, USA
Elise Morton
Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA
Juan D. Umaña
Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Franck Carbonero
Department of Food Science, University of Arkansas, Fayetteville, AK 72704, USA
H. Rex Gaskins
Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Karen E. Nelson
The J. Craig Venter Institute, La Jolla, CA 92037, USA
Brenda A. Wilson
Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Rebecca M. Stumpf
Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Bryan A. White
Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Steven R. Leigh
Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
Ran Blekhman
Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA
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.
