title: The microbiome of uncontacted Amerindians.
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.
authors.affiliation: 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.
authors.forename: Jose C
authors.initials: JC
authors.lastname: Clemente
authors.affiliation: Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Erica C
authors.initials: EC
authors.lastname: Pehrsson
authors.affiliation: Laboratory Service, VA Medical Center, New York, NY 10010, USA ; New York University School of Medicine, New York, NY 10016, USA.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Blaser
authors.affiliation: New York University School of Medicine, New York, NY 10016, USA.
authors.forename: Kuldip
authors.initials: K
authors.lastname: Sandhu
authors.affiliation: New York University School of Medicine, New York, NY 10016, USA.
authors.forename: Zhan
authors.initials: Z
authors.lastname: Gao
authors.affiliation: Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.affiliation: Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela.
authors.forename: Magda
authors.initials: M
authors.lastname: Magris
authors.affiliation: Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela.
authors.forename: Glida
authors.initials: G
authors.lastname: Hidalgo
authors.affiliation: Venezuelan Institute for Scientific Research, Caracas 1020-A, Venezuela.
authors.forename: Monica
authors.initials: M
authors.lastname: Contreras
authors.affiliation: Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela.
authors.forename: Óscar
authors.initials: Ó
authors.lastname: Noya-Alarcón
authors.affiliation: Sección de Ecología Parasitaria, Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas 1051, Venezuela.
authors.forename: Orlana
authors.initials: O
authors.lastname: Lander
authors.affiliation: Anaerobe Systems, Morgan Hill, CA 95037, USA.
authors.forename: Jeremy
authors.initials: J
authors.lastname: McDonald
authors.affiliation: Anaerobe Systems, Morgan Hill, CA 95037, USA.
authors.forename: Mike
authors.initials: M
authors.lastname: Cox
authors.affiliation: Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA.
authors.forename: Jens
authors.initials: J
authors.lastname: Walter
authors.affiliation: Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA.
authors.forename: Phaik Lyn
authors.initials: PL
authors.lastname: Oh
authors.affiliation: Department of Biology, University of Puerto Rico, Rio Piedras 00931, Puerto Rico.
authors.forename: Jean F
authors.initials: JF
authors.lastname: Ruiz
authors.affiliation: Department of Biology, University of Puerto Rico, Rio Piedras 00931, Puerto Rico.
authors.forename: Selena
authors.initials: S
authors.lastname: Rodriguez
authors.affiliation: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
authors.forename: Nan
authors.initials: N
authors.lastname: Shen
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
authors.forename: Se Jin
authors.initials: SJ
authors.lastname: Song
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.
authors.forename: Jessica
authors.initials: J
authors.lastname: Metcalf
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA ; Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA.
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
authors.affiliation: 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.
authors.forename: Gautam
authors.initials: G
authors.lastname: Dantas
authors.affiliation: 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.
authors.forename: M Gloria
authors.initials: MG
authors.lastname: Dominguez-Bello