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Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community

View ORCID ProfileSvetlana Lyalina, Ramunas Stepanauskas, Frank Wu, Shomyseh Sanjabi, View ORCID ProfileKatherine S. Pollard
doi: https://doi.org/10.1101/2021.12.13.472402
Svetlana Lyalina
1Gladstone Institutes, San Francisco, CA, USA
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Ramunas Stepanauskas
2Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
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Frank Wu
1Gladstone Institutes, San Francisco, CA, USA
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Shomyseh Sanjabi
1Gladstone Institutes, San Francisco, CA, USA
3Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
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Katherine S. Pollard
1Gladstone Institutes, San Francisco, CA, USA
4Department of Epidemiology & Biostatistics, Institute for Human Genetics, and Institute for Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
5Chan-Zuckerberg Biohub, San Francisco, CA, USA
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  • ORCID record for Katherine S. Pollard
  • For correspondence: katherine.pollard@gladstone.ucsf.edu
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Abstract

Laboratory mice are widely studied as models of mammalian biology, including the microbiota. However, much of the taxonomic and functional diversity of the mouse gut microbiome is missed in current metagenomic studies, because genome databases have not achieved a balanced representation of the diverse members of this ecosystem. Towards solving this problem, we used flow cytometry and low-coverage sequencing to capture the genomes of 764 single cells from the stool of three laboratory mice. From these, we generated 298 high-coverage microbial genome assemblies, which we annotated for open reading frames and phylogenetic placement. These genomes increase the gene catalog and phylogenetic breadth of the mouse microbiota, adding 135 novel species with the greatest increase in diversity to the Muribaculaceae and Bacteroidaceae families. This new diversity also improves the read mapping rate, taxonomic classifier performance, and gene detection rate of mouse stool metagenomes. The novel microbial functions revealed through our single-cell genomes highlight previously invisible pathways that may be important for life in the murine gastrointestinal tract.

Competing Interest Statement

The authors have declared no competing interest.

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 December 13, 2021.
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Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community
Svetlana Lyalina, Ramunas Stepanauskas, Frank Wu, Shomyseh Sanjabi, Katherine S. Pollard
bioRxiv 2021.12.13.472402; doi: https://doi.org/10.1101/2021.12.13.472402
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Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community
Svetlana Lyalina, Ramunas Stepanauskas, Frank Wu, Shomyseh Sanjabi, Katherine S. Pollard
bioRxiv 2021.12.13.472402; doi: https://doi.org/10.1101/2021.12.13.472402

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