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Ward TL, Dominguez-Bello MG, Heisel T, Al-Ghalith G, Knights D, Gale CA. Development of the Human Mycobiome over the First Month of Life and across Body Sites. mSystems 2018; 3:e00140-17. [PMID: 29546248 PMCID: PMC5840654 DOI: 10.1128/msystems.00140-17] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 02/13/2018] [Indexed: 12/24/2022] Open
Abstract
With the advent of next-generation sequencing and microbial community characterization, we are beginning to understand the key factors that shape early-life microbial colonization and associated health outcomes. Studies characterizing infant microbial colonization have focused mostly on bacteria in the microbiome and have largely neglected fungi (the mycobiome), despite their relevance to mucosal infections in healthy infants. In this pilot study, we characterized the skin, oral, and anal mycobiomes of infants over the first month of life (n = 17) and the anal and vaginal mycobiomes of mothers (n = 16) by internal transcribed spacer 2 (ITS2) amplicon sequencing. We found that infant mycobiomes differed by body site, with the infant mycobiomes at the anal sites being different from those at the skin and oral sites. The relative abundances of body site-specific taxa differed by birth mode, with significantly more Candida albicans fungi present on the skin of vaginally born infants on day 30 and significantly more Candida orthopsilosis fungi present in the oral cavity of caesarean section-born infants throughout the first month of life. We found the mycobiomes within individual infants to be variable over the first month of life, and vaginal birth did not result in infant mycobiomes that were more similar to the mother's vaginal mycobiome. Therefore, although vertical transmission of specific fungal isolates from mother to infant has been reported, it is likely that other sources (environment, other caregivers) also contribute to early-life mycobiome establishment. Thus, future longitudinal studies of mycobiome and bacterial microbiome codevelopment, with dense sampling from birth to beyond the first month of life, are warranted. IMPORTANCE Humans are colonized by diverse fungi (mycobiome), which have received much less study to date than colonizing bacteria. We know very little about the succession of fungal colonization in early life and whether it may relate to long-term health. To better understand fungal colonization and its sources, we studied the skin, oral, and anal mycobiomes of healthy term infants and the vaginal and anal mycobiomes of their mothers. Generally, infants were colonized by few fungal taxa, and fungal alpha diversity did not increase over the first month of life. There was no clear community maturation over the first month of life, regardless of body site. Key body-site-specific taxa, but not overall fungal community structures, were impacted by birth mode. Thus, additional studies to characterize mycobiome acquisition and succession throughout early life are needed to form a foundation for research into the relationship between mycobiome development and human disease.
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Affiliation(s)
- Tonya L. Ward
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
| | - Maria Gloria Dominguez-Bello
- Departments of Biochemistry and Microbiology and Anthropology, Rutgers University, New Brunswick, New Jersey, USA
| | - Tim Heisel
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Gabriel Al-Ghalith
- Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Dan Knights
- BioTechnology Institute, University of Minnesota, St. Paul, Minnesota, USA
- Department of Computer Science and Engineering, University of Minnesota, Minneapolis, Minnesota, USA
| | - Cheryl A. Gale
- Department of Pediatrics, University of Minnesota, Minneapolis, Minnesota, USA
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Martinez KA, Devlin JC, Lacher CR, Yin Y, Cai Y, Wang J, Dominguez-Bello MG. Increased weight gain by C-section: Functional significance of the primordial microbiome. Sci Adv 2017; 3:eaao1874. [PMID: 29026883 PMCID: PMC5636202 DOI: 10.1126/sciadv.aao1874] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 09/19/2017] [Indexed: 05/03/2023]
Abstract
Epidemiological evidence supports a direct association between early microbiota impact-including C-section-and obesity. We performed antibiotic-free, fostered C-sections and determined the impact on the early microbiota and body weight during development. Mice in the C-section group gained more body mass after weaning, with a stronger phenotype in females. C-section-born mice lacked the dynamic developmental gut microbiota changes observed in control mice. The results demonstrate a causal relationship between C-section and increased body weight, supporting the involvement of maternal vaginal bacteria in normal metabolic development.
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Affiliation(s)
- Keith A. Martinez
- Division of Translational Medicine, Department of Medicine, New York University, School of Medicine, New York, NY 10016, USA
- Sackler Institute of Graduate Biomedical Sciences, Department of Microbiology, New York University, School of Medicine, New York, NY 10016, USA
| | - Joseph C. Devlin
- Division of Translational Medicine, Department of Medicine, New York University, School of Medicine, New York, NY 10016, USA
| | - Corey R. Lacher
- Division of Translational Medicine, Department of Medicine, New York University, School of Medicine, New York, NY 10016, USA
| | - Yue Yin
- Division of Translational Medicine, Department of Medicine, New York University, School of Medicine, New York, NY 10016, USA
| | - Yi Cai
- Division of Translational Medicine, Department of Medicine, New York University, School of Medicine, New York, NY 10016, USA
| | - Jincheng Wang
- Division of Translational Medicine, Department of Medicine, New York University, School of Medicine, New York, NY 10016, USA
| | - Maria G. Dominguez-Bello
- Division of Translational Medicine, Department of Medicine, New York University, School of Medicine, New York, NY 10016, USA
- Sackler Institute of Graduate Biomedical Sciences, Department of Microbiology, New York University, School of Medicine, New York, NY 10016, USA
- Corresponding author.
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Clemente JC, Pehrsson EC, Blaser MJ, Sandhu K, Gao Z, Wang B, Magris M, Hidalgo G, Contreras M, Noya-Alarcón Ó, Lander O, McDonald J, Cox M, Walter J, Oh PL, Ruiz JF, Rodriguez S, Shen N, Song SJ, Metcalf J, Knight R, Dantas G, Dominguez-Bello MG. The microbiome of uncontacted Amerindians. Sci Adv 2015; 1:e1500183. [PMID: 26229982 PMCID: PMC4517851 DOI: 10.1126/sciadv.1500183] [Citation(s) in RCA: 502] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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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Affiliation(s)
- Jose C. Clemente
- 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
| | - Erica C. Pehrsson
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Martin J. Blaser
- Laboratory Service, VA Medical Center, New York, NY 10010, USA
- New York University School of Medicine, New York, NY 10016, USA
| | - Kuldip Sandhu
- New York University School of Medicine, New York, NY 10016, USA
| | - Zhan Gao
- New York University School of Medicine, New York, NY 10016, USA
| | - Bin Wang
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Magda Magris
- Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela
| | - Glida Hidalgo
- Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela
| | - Monica Contreras
- Venezuelan Institute for Scientific Research, Caracas 1020-A, Venezuela
| | - Óscar Noya-Alarcón
- Amazonic Center for Research and Control of Tropical Diseases (CAICET), Puerto Ayacucho 7101, Venezuela
| | - Orlana Lander
- Sección de Ecología Parasitaria, Instituto de Medicina Tropical, Universidad Central de Venezuela, Caracas 1051, Venezuela
| | | | - Mike Cox
- Anaerobe Systems, Morgan Hill, CA 95037, USA
| | - Jens Walter
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA
| | - Phaik Lyn Oh
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE 68583, USA
| | - Jean F. Ruiz
- Department of Biology, University of Puerto Rico, Rio Piedras 00931, Puerto Rico
| | - Selena Rodriguez
- Department of Biology, University of Puerto Rico, Rio Piedras 00931, Puerto Rico
| | - Nan Shen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Se Jin Song
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Jessica Metcalf
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
| | - Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
- Howard Hughes Medical Institute, University of Colorado, Boulder, CO 80309, USA
| | - Gautam Dantas
- 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
| | - M. Gloria Dominguez-Bello
- 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
- Corresponding author. E-mail:
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