title: Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns.
abstract: 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.
authors.affiliation: Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA. Electronic address: agomez@jcvi.org.
authors.forename: Andres
authors.initials: A
authors.lastname: Gomez
authors.affiliation: Institute of Vertebrate Biology, Academy of Sciences of the Czech Republic, Brno 603 65, Czech Republic; Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice 370 05, Czech Republic; Liberec Zoo, Liberec 460 01, Czech Republic.
authors.forename: Klara J
authors.initials: KJ
authors.lastname: Petrzelkova
authors.affiliation: Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA.
authors.forename: Michael B
authors.initials: MB
authors.lastname: Burns
authors.affiliation: Department of Animal and Range Sciences, Montana State University, Bozeman, MT 59717, USA.
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Yeoman
authors.affiliation: Department of Anthropology, Northwestern University, Evanston, IL 60208, USA.
authors.forename: Katherine R
authors.initials: KR
authors.lastname: Amato
authors.affiliation: Faculty of Veterinary Medicine, Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic.
authors.forename: Klara
authors.initials: K
authors.lastname: Vlckova
authors.affiliation: Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice 370 05, Czech Republic; Faculty of Veterinary Medicine, Department of Pathology and Parasitology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic; CEITEC, Central European Institute for Technology, University of Veterinary and Pharmaceutical Sciences, Brno 612 42, Czech Republic.
authors.forename: David
authors.initials: D
authors.lastname: Modry
authors.affiliation: Dzanga-Sangha Protected Areas, World Wildlife Fund, Bayanga, Central African Republic.
authors.forename: Angelique
authors.initials: A
authors.lastname: Todd
authors.affiliation: Department of Anthropology, University of North Carolina, Wilmington, NC 28403, USA.
authors.forename: Carolyn A
authors.initials: CA
authors.lastname: Jost Robinson
authors.affiliation: Department of Anthropology, Purdue University, West Lafayette, IN 47907, USA.
authors.forename: Melissa J
authors.initials: MJ
authors.lastname: Remis
authors.affiliation: The J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Manolito G
authors.initials: MG
authors.lastname: Torralba
authors.affiliation: Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA.
authors.forename: Elise
authors.initials: E
authors.lastname: Morton
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Juan D
authors.initials: JD
authors.lastname: Umaña
authors.affiliation: Department of Food Science, University of Arkansas, Fayetteville, AK 72704, USA.
authors.forename: Franck
authors.initials: F
authors.lastname: Carbonero
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: H Rex
authors.initials: HR
authors.lastname: Gaskins
authors.affiliation: The J. Craig Venter Institute, La Jolla, CA 92037, USA.
authors.forename: Karen E
authors.initials: KE
authors.lastname: Nelson
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Brenda A
authors.initials: BA
authors.lastname: Wilson
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Rebecca M
authors.initials: RM
authors.lastname: Stumpf
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
authors.forename: Bryan A
authors.initials: BA
authors.lastname: White
authors.affiliation: Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Anthropology, University of Colorado, Boulder, CO 80309, USA. Electronic address: steven.leigh@colorado.edu.
authors.forename: Steven R
authors.initials: SR
authors.lastname: Leigh
authors.affiliation: Department of Genetics, Cell Biology, and Development, University of Minnesota, Twin Cities, MN 55108, USA; Department of Ecology, Evolution, and Behavior, University of Minnesota, Twin Cities, MN 55108, USA. Electronic address: blekhman@umn.edu.
authors.forename: Ran
authors.initials: R
authors.lastname: Blekhman
mesh_terms: D041963:Bacteroidetes / Q000235:genetics; D044383:Black People; D002488:Central African Republic; D066046:Diet, Paleolithic; D066273:Diet, Western; D005260:Female; D000068536:Bacillota / Q000235:genetics; D000069196:Gastrointestinal Microbiome / Q000235:genetics*; D053263:Gene Regulatory Networks; D005798:Genes, Bacterial; D006801:Humans; D008297:Male; D058889:Molecular Typing; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017423:Sequence Analysis, RNA; D014481:United States; D001741:Black or African American
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S