Browsing by Author "Carbonero, Franck"

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Gut Microbiome of Coexisting BaAka Pygmies and Bantu Reflects Gradients of Traditional Subsistence Patterns
(2016-03) Gomez, Andres; Petrzelkova, Klara J.; Burns, Michael B.; Yeoman, Carl J.; Amato, Katherine R.; Vlckova, Klara; Modry, David; Todd, Angelique F.; Jost Robinson, Carolyn A.; Remis, Melissa J.; Torralba, Manolito G.; Morton, Elise; Umaña, Juan D.; Carbonero, Franck; Gaskins, H. Rex; Nelson, Karen E.; Wilson, Brenda A.; Stumpf, Rebecca M.; White, Bryan A.; Leigh, Steven R.; Blekhman, Ran
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.
Plasticity in the Human Gut Microbiome Defies Evolutionary Constraints
(2019-07-19) Gomez, Andres; Sharma, Ashok Kumar; Mallott, Elizabeth K.; Petrzelkova, Klara J.; Jost Robinson, Carolyn A.; Yeoman, Carl J.; Carbonero, Franck; Pafco, Barbora; Rothman, Jessica M.; Ulanov, Alexander; Vlckova, Klara; Amato, Katherine R.; Schnorr, Stephanie L.; Dominy, Nathaniel J.; Modry, David; Todd, Angelique F.; Torralba, Manolito; Nelson, Karen E.; Burns, Michael B.; Blekhman, Ran; Remis, Melissa; Stumpf, Rebecca M.; Wilson, Brenda A.; Gaskins, H. Rex; Garber, Paul A.; White, Bryan A.; Leigh, Steven R.
The gut microbiome of primates, including humans, is reported to closely follow host evolutionary history, with gut microbiome composition being specific to the genetic background of its primate host. However, the comparative models used to date have mainly included a limited set of closely related primates. To further understand the forces that shape the primate gut microbiome, with reference to human populations, we expanded the comparative analysis of variation among gut microbiome compositions and their primate hosts, including 9 different primate species and 4 human groups characterized by a diverse set of subsistence patterns (n = 448 samples). The results show that the taxonomic composition of the human gut microbiome, at the genus level, exhibits increased compositional plasticity. Specifically, we show unexpected similarities between African Old World monkeys that rely on eclectic foraging and human populations engaging in nonindustrial subsistence patterns; these similarities transcend host phylogenetic constraints. Thus, instead of following evolutionary trends that would make their microbiomes more similar to that of conspecifics or more phylogenetically similar apes, gut microbiome composition in humans from nonindustrial populations resembles that of generalist cercopithecine monkeys. We also document that wild cercopithecine monkeys with eclectic diets and humans following nonindustrial subsistence patterns harbor high gut microbiome diversity that is not only higher than that seen in humans engaging in industrialized lifestyles but also higher compared to wild primates that typically consume fiber-rich diets.