Journal article
Reconstruction of ancient microbial genomes from the human gut
Joslin Diabetes Center1
Boston Children's Hospital2
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark3
University of Nebraska-Lincoln4
EURAC Research5
Edmund Mach Foundation6
Harvard University7
Max Planck Institute for the Science of Human History8
University of Trento9
Instituto Nacional de Medicina Genomica10
National Food Institute, Technical University of Denmark11
University of Montana12
Northern Arizona University13
Pahrump Paiute Tribe14
Consolidated Group of Tribes and Organizations15
...and 5 moreLoss 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.
Language: | English |
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Publisher: | Nature Publishing Group UK |
Year: | 2021 |
Pages: | 234-239 |
Journal subtitle: | International Weekly Journal of Science |
ISBN: | 0306479834 , 1402004443 , 904815944x , 9780306479830 , 9781402004445 and 9789048159444 |
ISSN: | 14764687 and 00280836 |
Types: | Journal article |
DOI: | 10.1038/s41586-021-03532-0 |
ORCIDs: | 0000-0001-7678-5447 , 0000-0001-9140-7559 , 0000-0002-7533-8802 , 0000-0002-0453-980X , 0000-0003-2845-6475 , Pamp, Sünje Johanna , 0000-0002-0030-7788 , 0000-0002-1583-5794 , 0000-0002-5801-9180 and 0000-0002-0837-4360 |
Anti-Bacterial Agents Archaeology, Metagenomics, Microbiome Bacteria Biodiversity Biological Evolution Chronic Disease Developed Countries Developing Countries Diet, Western Feces Gastrointestinal Microbiome Genome, Bacterial History, Ancient Host Microbial Interactions Humans Industrial Development Methanobrevibacter Mexico Sedentary Behavior Southwestern United States Species Specificity Symbiosis