The microbiome of uncontacted Amerindians

By Jose C. Clemente, Erica C. Pehrsson, Martin J. Blaser, K. Sandhu, Zhan Gao, Bin Wang, M. Magris, G. Hidalgo, M. Contreras, Óscar Noya-Alarcón and 13 more. Science Advances, 2015

794 citations recorded by the source corpus.

Fecal, oral, and skin biomes of isolated Amerindians show higher human bacterial diversity including antibiotic resistance genes. Most studies of the human microbiome have focused on westernized people with life-style practices that decrease microbial survival and transmission, or on traditional societies that are currently in transition to westernization. We characterize the fecal, oral, and skin bacterial microbiome and resistome of members of an isolated Yanomami Amerindian village with no documented previous contact with Western people. These Yanomami harbor a microbiome with the highest diversity of bacteria and genetic functions ever reported in a human group. Despite their isolation, presumably for >11,000 years since their ancestors arrived in South America, and no known exposure to antibiotics, they harbor bacteria that carry functional antibiotic resistance (AR) genes, including those that confer resistance to synthetic antibiotics and are syntenic with mobilization elements. These results suggest that westernization significantly affects human microbiome diversity and that functional AR genes appear to be a feature of the human microbiome even in the absence of exposure to commercial antibiotics. AR genes are likely poised for mobilization and enrichment upon exposure to pharmacological levels of antibiotics. Our findings emphasize the need for extensive characterization of the function of the microbiome and resistome in remote nonwesternized populations before globalization of modern practices affects potentially beneficial bacteria harbored in the human body.

Subfields: Food Science, General Health Professions, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/1cdea680bfe164cbc2c3cfcaee6df2f94189ee82

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Citations in the corpus

Antibiotic use and its consequences for the normal microbiome (2016, background): “First, we must control those excesses, but mitigation will only stabilize the situation not reverse the deterioration that likely has progressively occurred with socioeconomic development (15).”
Gut instincts: microbiota as a key regulator of brain development, ageing and neurodegeneration (2017, background): “…from studies of remote hunter-gatherer tribes that Western guts have undergone a significant reduction in bacterial diversity and globalisation is driving this trend forward (Leach, 2013; Schnorr et al. 2014; Clemente et al. 2015; Martinez et al. 2015; Rampelli et al. 2015; Sonnenburg et al. 2016).”
Antibiotics as Major Disruptors of Gut Microbiota (2020, background): “For example, the fecal microbiota of adults from the metropolitan areas of Europe and North America is less diverse compared with adults from rural populations in Africa and South America (Clemente et al., 2015; Sonnenburg and Sonnenburg, 2019).”
Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information (2018, background): “The “Yanomami” study (26) contained 66 human samples of the same three body products from uncontacted Amerindians in Venezuela.”
The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation (2016, result): “General trends observed in follow-up studies include a decrease in microbiome diversity in developed countries compared with the diversity found in hunter-gatherers or societies with restricted access to Western medicine [63, 64].”
American Gut: an Open Platform for Citizen Science Microbiome Research (2018, positive): “A meta-analysis compared fecal samples collected from healthy individuals who were 3 years of age or older and included in the AGP data set to a previously published 16S rRNA V4 region data set that included healthy people living an industrialized, remote agrarian, or huntergatherer lifestyle (6, 11”
Impact of antibiotics on the human microbiome and consequences for host health (2022, background): “Humans are reservoirs of ARGs (J. K. Bailey et al., 2010; Clemente et al., 2015; Sommer et al., 2010) and the gut has been pinpointed as the epicenter of antibiotic resistance (Carlet, 2012).”
U.S. immigration westernizes the human gut microbiome (2018, background): “Rural indigenous populations have been found to harbor substantial biodiversity in their gut microbiomes, including novel microbial taxa not found in industrialized populations (Clemente et al., 2015; Gomez et al., 2016; Obregon-Tito et al., 2015; Schnorr et al., 2014; Smits et al., 2017; Yatsunenko”