Reconstruction of ancient microbial genomes from the human gut

Marsha C. Wibowo, Zhen Yang, Maxime Borry, Alexander Hübner, Kun D. Huang, Braden T. Tierney, Samuel Zimmerman, Francisco Barajas-Olmos, Cecilia Contreras-Cubas, Humberto García-Ortiz, Angélica Martínez-Hernández, Jacob M. Luber, Philipp Kirstahler, Tre Blohm, Francis E. Smiley, Richard Arnold, Sonia A. Ballal, Sünje Johanna Pamp, Julia Russ, Frank Maixner, Omar Rota-Stabelli, Nicola Segata, Karl Reinhard, Lorena Orozco, Christina Warinner, Meradeth Snow, Steven LeBlanc and Aleksandar D. Kostic ()
Additional contact information
Marsha C. Wibowo: Joslin Diabetes Center
Zhen Yang: Joslin Diabetes Center
Maxime Borry: Max Planck Institute for the Science of Human History
Alexander Hübner: Max Planck Institute for the Science of Human History
Kun D. Huang: University of Trento
Braden T. Tierney: Joslin Diabetes Center
Samuel Zimmerman: Joslin Diabetes Center
Francisco Barajas-Olmos: Secretaría de Salud, Instituto Nacional de Medicina Genómica
Cecilia Contreras-Cubas: Secretaría de Salud, Instituto Nacional de Medicina Genómica
Humberto García-Ortiz: Secretaría de Salud, Instituto Nacional de Medicina Genómica
Angélica Martínez-Hernández: Secretaría de Salud, Instituto Nacional de Medicina Genómica
Jacob M. Luber: Joslin Diabetes Center
Philipp Kirstahler: Technical University of Denmark
Tre Blohm: University of Montana
Francis E. Smiley: Northern Arizona University
Richard Arnold: Pahrump Paiute Tribe and Consolidated Group of Tribes and Organizations
Sonia A. Ballal: Hepatology and Nutrition, Boston Children’s Hospital
Sünje Johanna Pamp: Technical University of Denmark
Julia Russ: University of Nebraska-Lincoln
Frank Maixner: EURAC Research
Omar Rota-Stabelli: Fondazione Edmund Mach
Nicola Segata: University of Trento
Karl Reinhard: University of Nebraska-Lincoln
Lorena Orozco: Secretaría de Salud, Instituto Nacional de Medicina Genómica
Christina Warinner: Max Planck Institute for the Science of Human History
Meradeth Snow: University of Montana
Steven LeBlanc: Harvard University
Aleksandar D. Kostic: Joslin Diabetes Center

Nature, 2021, vol. 594, issue 7862, 234-239

Abstract: Abstract Loss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7, 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.

Date: 2021
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DOI: 10.1038/s41586-021-03532-0

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