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A comprehensive analysis of the global human gut archaeome from a thousand genome catalogue

Cynthia Maria Chibani, Alexander Mahnert, Guillaume Borrel, Alexandre Almeida, Almut Werner, Jean-François Brugère, Simonetta Gribaldo, Robert D. Finn, Ruth A. Schmitz, View ORCID ProfileChristine Moissl-Eichinger
doi: https://doi.org/10.1101/2020.11.21.392621
Cynthia Maria Chibani
1Institute for Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
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Alexander Mahnert
2Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
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Guillaume Borrel
3Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
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Alexandre Almeida
4European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
5Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Almut Werner
1Institute for Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
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Jean-François Brugère
6Institut Universitaire de Technologie Clermont Auvergne, Université Clermont Auvergne, CNRS, UMR 6023 Laboratoire Microorganismes: Genome et Environnement, Clermont-Ferrand, France
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Simonetta Gribaldo
3Department of Microbiology, Unit Evolutionary Biology of the Microbial Cell, Institut Pasteur, Paris, France
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Robert D. Finn
4European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
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Ruth A. Schmitz
1Institute for Microbiology, Christian-Albrechts-University Kiel, Kiel, Germany
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  • For correspondence: christine.moissl-eichinger@medunigraz.at rschmitz@ifam.uni-kiel.de
Christine Moissl-Eichinger
2Diagnostic & Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Neue Stiftingtalstraße 6, 8010 Graz, Austria
7BioTechMed, Graz, Austria
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  • ORCID record for Christine Moissl-Eichinger
  • For correspondence: christine.moissl-eichinger@medunigraz.at rschmitz@ifam.uni-kiel.de
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SUMMARY

The human gut microbiome plays an important role in health and disease, but the archaeal diversity therein remains largely unexplored. Here we report the pioneering analysis of 1,167 non-redundant archaeal genomes recovered from human gastrointestinal tract microbiomes across countries and populations. We identified three novel genera and 15 novel species including 52 previously unknown archaeal strains. Based on distinct genomic features, we warrant the split of the Methanobrevibacter smithii clade into two separate species, with one represented by the novel Candidatus M. intestini.

Patterns derived from 1.8 million proteins and 28,851 protein clusters coded in these genomes showed substantial correlation with socio-demographic characteristics such as age and lifestyle. We infer that archaea are actively replicating in the human gastrointestinal tract and are characterized by specific genomic and functional adaptations to the host. We further demonstrate that the human gut archaeome carries a complex virome, with some viral species showing unexpected host flexibility. Our work furthers our current understanding of the human archaeome, and provides a large genome catalogue for future analyses to decipher its role and impact on human physiology.

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GRAPHICAL ABSTRACT

HIGHLIGHTS

  • The human gut archaeome analysis reveals a previously unseen active diversity

  • The most abundant methanogen, Methanobrevibacter smithii, splits into two species

  • Archaeal protein catalogue can predict geography, demographics and health aspects

  • Host-associated and environmental archaea show distinct genomic & functional traits

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵9 Lead contact

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 22, 2020.
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A comprehensive analysis of the global human gut archaeome from a thousand genome catalogue
Cynthia Maria Chibani, Alexander Mahnert, Guillaume Borrel, Alexandre Almeida, Almut Werner, Jean-François Brugère, Simonetta Gribaldo, Robert D. Finn, Ruth A. Schmitz, Christine Moissl-Eichinger
bioRxiv 2020.11.21.392621; doi: https://doi.org/10.1101/2020.11.21.392621
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A comprehensive analysis of the global human gut archaeome from a thousand genome catalogue
Cynthia Maria Chibani, Alexander Mahnert, Guillaume Borrel, Alexandre Almeida, Almut Werner, Jean-François Brugère, Simonetta Gribaldo, Robert D. Finn, Ruth A. Schmitz, Christine Moissl-Eichinger
bioRxiv 2020.11.21.392621; doi: https://doi.org/10.1101/2020.11.21.392621

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