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MRGM: a mouse reference gut microbiome reveals a large functional discrepancy for gut bacteria of the same genus between mice and humans

Nayeon Kim, Chan Yeong Kim, Sunmo Yang, Dongjin Park, Sang-Jun Ha, View ORCID ProfileInsuk Lee
doi: https://doi.org/10.1101/2021.10.24.465599
Nayeon Kim
1Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea
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Chan Yeong Kim
1Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea
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Sunmo Yang
1Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea
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Dongjin Park
2Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea
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Sang-Jun Ha
2Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea
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Insuk Lee
1Department of Biotechnology, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, Korea
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  • ORCID record for Insuk Lee
  • For correspondence: insuklee@yonsei.ac.kr
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ABSTRACT

The gut microbiome is associated with human diseases and interacts with dietary components and drugs. In vivo mouse models may be effective for studying diet and drug effects on the gut microbiome. We constructed a mouse reference gut microbiome (MRGM, https://www.mbiomenet.org/MRGM/) that includes newly-assembled genomes from 878 metagenomes. Leveraging samples with ultra-deep metagenomic sequencing (>130 million read pairs), we demonstrated quality improvement in assembled genomes for mouse gut microbes as sequencing depth increased. MRGM provides a catalog of 46,267 non-redundant genomes with ≥70% completeness and ≤5% contamination comprising 1,689 representative bacterial species and 15.2 million non-redundant proteins. Importantly, MRGM significantly improved the taxonomic classification rate of sequencing reads from mouse fecal samples compared to previous databases. Using MRGM, we determined that reliable low-abundance taxa profiles of the mouse gut microbiome require sequencing >10 million reads. Despite the high overall functional similarity of the mouse and human gut microbiomes, only ~10% of MRGM species are shared with the human gut microbiome. Although ~80% of MRGM genera are present in the human gut microbiome, ~70% of the shared genera have <40% of core gene content for the respective genus with human counterparts. These suggest that although metabolic processes of the human gut microbiome largely occur in the mouse gut microbiome, functional translations between them according to genus-level taxonomic commonality require caution.

Key Points

  1. MRGM provides 46,267 genomes comprising 1,689 bacterial species of mouse gut microbiome.

  2. Despite high overlap of genera, functional discrepancy between mouse and human gut microbiota is large.

  3. Lineage-specific markers underestimate the completeness of assembled genomes for uncharacterized taxa.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • https://www.mbiomenet.org/MRGM/

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 4.0 International license.
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Posted October 24, 2021.
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MRGM: a mouse reference gut microbiome reveals a large functional discrepancy for gut bacteria of the same genus between mice and humans
Nayeon Kim, Chan Yeong Kim, Sunmo Yang, Dongjin Park, Sang-Jun Ha, Insuk Lee
bioRxiv 2021.10.24.465599; doi: https://doi.org/10.1101/2021.10.24.465599
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MRGM: a mouse reference gut microbiome reveals a large functional discrepancy for gut bacteria of the same genus between mice and humans
Nayeon Kim, Chan Yeong Kim, Sunmo Yang, Dongjin Park, Sang-Jun Ha, Insuk Lee
bioRxiv 2021.10.24.465599; doi: https://doi.org/10.1101/2021.10.24.465599

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