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Sci Adv. 2015 Apr 3;1(3). pii: e1500183.

The microbiome of uncontacted Amerindians.

Author information

1
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA ; Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
2
Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
3
Laboratory Service, VA Medical Center, New York, NY 10010, USA ; New York University School of Medicine, New York, NY 10016, USA.
4
New York University School of Medicine, New York, NY 10016, USA.
5
Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela.
6
Venezuelan Institute for Scientific Research, Caracas 1020-A, Venezuela.
7
Sección de Ecología Parasitaria, Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas 1051, Venezuela.
8
Anaerobe Systems, Morgan Hill, CA 95037, USA.
9
Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA.
10
Department of Biology, University of Puerto Rico, Rio Piedras 00931, Puerto Rico.
11
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
12
Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
13
Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA ; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA.
14
Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA ; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
15
New York University School of Medicine, New York, NY 10016, USA ; Venezuelan Institute for Scientific Research, Caracas 1020-A, Venezuela ; Department of Biology, University of Puerto Rico, Rio Piedras 00931, Puerto Rico.

Abstract

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.

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