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Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity

View ORCID ProfileNicholas D. Youngblut, Jacobo de la Cuesta-Zuluaga, Georg H. Reischer, Silke Dauser, Nathalie Schuster, Chris Walzer, Gabrielle Stalder, Andreas H. Farnleitner, Ruth E. Ley
doi: https://doi.org/10.1101/2020.06.05.135962
Nicholas D. Youngblut
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076 Tübingen, Germany
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  • ORCID record for Nicholas D. Youngblut
  • For correspondence: nyoungblut@tuebingen.mpg.de
Jacobo de la Cuesta-Zuluaga
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076 Tübingen, Germany
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Georg H. Reischer
2TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Gumpendorfer Straße 1a, A-1060 Vienna, Austria
3ICC Interuniversity Cooperation Centre Water & Health, 1160 Vienna, Austria
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Silke Dauser
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076 Tübingen, Germany
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Nathalie Schuster
2TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Gumpendorfer Straße 1a, A-1060 Vienna, Austria
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Chris Walzer
4Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
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Gabrielle Stalder
4Research Institute of Wildlife Ecology, University of Veterinary Medicine, Vienna, Austria
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Andreas H. Farnleitner
2TU Wien, Institute of Chemical, Environmental and Bioscience Engineering, Research Group for Environmental Microbiology and Molecular Diagnostics 166/5/3, Gumpendorfer Straße 1a, A-1060 Vienna, Austria
3ICC Interuniversity Cooperation Centre Water & Health, 1160 Vienna, Austria
5Research Division Water Quality and Health, Karl Landsteiner University for Health Sciences, 3500 Krems an der Donau, Austria
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Ruth E. Ley
1Department of Microbiome Science, Max Planck Institute for Developmental Biology, Max Planck Ring 5, 72076 Tübingen, Germany
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Abstract

Large-scale metagenome assemblies of human microbiomes have produced a vast catalogue of previously unseen microbial genomes; however, comparatively few microbial genomes derive from other vertebrates. Here, we generated 4374 metagenome assembled genomes (MAGs) from gut samples of 180 predominantly wild animal species representing 5 classes. Combined with existing datasets, we produced 5596 non-redundant, quality MAGs and 1522 species-level genome bins (SGBs). Most SGBs were novel at the species, genus, or family levels, and the majority were enriched in host versus environment metagenomes. Many traits distinguished SGBs enriched in host or environmental biomes, including the number of antimicrobial resistance genes. We identified 1986 diverse and largely novel biosynthetic gene clusters. Gene-based assembly revealed tremendous gene diversity, much of it host or environment specific. Our MAG and gene datasets greatly expand the microbial genome repertoire and provide a broad view of microbial adaptations to life within a living host.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • http://ftp.tue.mpg.de/ebio/projects/animal_gut_metagenome_assembly/

  • https://github.com/leylabmpi/animal_gut_metagenome_assembly

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 4.0 International license.
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Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity
Nicholas D. Youngblut, Jacobo de la Cuesta-Zuluaga, Georg H. Reischer, Silke Dauser, Nathalie Schuster, Chris Walzer, Gabrielle Stalder, Andreas H. Farnleitner, Ruth E. Ley
bioRxiv 2020.06.05.135962; doi: https://doi.org/10.1101/2020.06.05.135962
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Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity
Nicholas D. Youngblut, Jacobo de la Cuesta-Zuluaga, Georg H. Reischer, Silke Dauser, Nathalie Schuster, Chris Walzer, Gabrielle Stalder, Andreas H. Farnleitner, Ruth E. Ley
bioRxiv 2020.06.05.135962; doi: https://doi.org/10.1101/2020.06.05.135962

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