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  Reconstruction of ancient microbial genomes from the human gut

Wibowo, M. C., Yang, Z., Borry, M., Hübner, A., Huang, K. D., Tierney, B. T., et al. (2021). Reconstruction of ancient microbial genomes from the human gut. Nature, s41586-021-03532-0. doi:10.1038/s41586-021-03532-0.

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The Supplementary Information includes an Ethics Statement, Supplementary Information sections 1-12, Supplementary Figures 1-3, Supplementary Table 11, and Supplementary References. - (last seen: June 2021)

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 Creators:
Wibowo, Marsha C., Author
Yang, Zhen, Author
Borry, Maxime1, Author              
Hübner, Alexander1, Author              
Huang, Kun D., Author
Tierney, Braden T., Author
Zimmerman, Samuel, Author
Barajas-Olmos, Francisco, Author
Contreras-Cubas, Cecilia, Author
García-Ortiz, Humberto, Author
Martínez-Hernández, Angélica, Author
Luber, Jacob M., Author
Kirstahler, Philipp, Author
Blohm, Tre, Author
Smiley, Francis E., Author
Arnold, Richard, Author
Ballal, Sonia A., Author
Pamp, Sünje Johanna, Author
Russ, Julia, Author
Maixner, Frank, Author
Rota-Stabelli, Omar, AuthorSegata, Nicola, AuthorReinhard, Karl, AuthorOrozco, Lorena, AuthorWarinner, Christina1, 2, Author              Snow, Meradeth, AuthorLeBlanc, Steven, AuthorKostic, Aleksandar D., Author more..
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              
2Kostbare Kulturen, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2591692              

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Free keywords: Archaeology, Metagenomics, Microbiome
 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.

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Language(s): eng - English
 Dates: 2021-05-12
 Publication Status: Published online
 Pages: 30
 Publishing info: -
 Table of Contents: Ethics
Overview of samples
Reference-based taxonomic composition
De novo genome reconstruction
Methanobrevibacter smithii tip dating
Functional genomic analysis
Discussion
Online content
Methods
 Rev. Type: Peer
 Identifiers: DOI: 10.1038/s41586-021-03532-0
Other: shh2939
 Degree: -

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Title: Nature
  Abbreviation : Nature
Source Genre: Journal
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Publ. Info: London : Nature Publishing Group
Pages: - Volume / Issue: - Sequence Number: s41586-021-03532-0 Start / End Page: - Identifier: ISSN: 0028-0836
CoNE: https://pure.mpg.de/cone/journals/resource/954925427238