Reconstruction of ancient microbial genomes from the human gut.

Autor: Wibowo MC; Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.; Department of Microbiology, Harvard Medical School, Boston, MA, USA., Yang Z; Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.; Department of Microbiology, Harvard Medical School, Boston, MA, USA.; Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario, Canada., Borry M; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany., Hübner A; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany., Huang KD; CIBIO Department, University of Trento, Trento, Italy.; Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy., Tierney BT; Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.; Department of Microbiology, Harvard Medical School, Boston, MA, USA.; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA., Zimmerman S; Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.; Department of Microbiology, Harvard Medical School, Boston, MA, USA., Barajas-Olmos F; Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico., Contreras-Cubas C; Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico., García-Ortiz H; Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico., Martínez-Hernández A; Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico., Luber JM; Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.; Department of Microbiology, Harvard Medical School, Boston, MA, USA.; Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA., Kirstahler P; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark., Blohm T; Department of Anthropology, University of Montana, Missoula, MT, USA., Smiley FE; Department of Anthropology, Northern Arizona University, Flagstaff, AZ, USA., Arnold R; Pahrump Paiute Tribe and Consolidated Group of Tribes and Organizations, Pahrump, NV, USA., Ballal SA; Department of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA., Pamp SJ; Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark., Russ J; Morrison Microscopy Core Research Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA., Maixner F; Institute for Mummy Studies, EURAC Research, Bolzano, Italy., Rota-Stabelli O; Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.; Center Agriculture Food Environment (C3A), University of Trento, Trento, Italy., Segata N; CIBIO Department, University of Trento, Trento, Italy., Reinhard K; School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, USA., Orozco L; Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico., Warinner C; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.; Department of Anthropology, Harvard University, Cambridge, MA, USA.; Faculty of Biological Sciences, Friedrich-Schiller University, Jena, Germany., Snow M; Department of Anthropology, University of Montana, Missoula, MT, USA., LeBlanc S; Peabody Museum of Archaeology and Ethnology, Harvard University, Cambridge, MA, USA., Kostic AD; Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA. aleksandar.kostic@joslin.harvard.edu.; Department of Microbiology, Harvard Medical School, Boston, MA, USA. aleksandar.kostic@joslin.harvard.edu.
Jazyk: angličtina
Zdroj: Nature [Nature] 2021 Jun; Vol. 594 (7862), pp. 234-239. Date of Electronic Publication: 2021 May 12.
DOI: 10.1038/s41586-021-03532-0
Abstrakt: Loss of gut microbial diversity 1-6 in industrial populations is associated with chronic diseases 7 , underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000-2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces.
Databáze: MEDLINE