RT Journal Article
SR Electronic
T1 Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.12.13.472402
DO 10.1101/2021.12.13.472402
A1 Lyalina, Svetlana
A1 Stepanauskas, Ramunas
A1 Wu, Frank
A1 Sanjabi, Shomyseh
A1 Pollard, Katherine S.
YR 2021
UL http://biorxiv.org/content/early/2021/12/13/2021.12.13.472402.abstract
AB 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 StatementThe authors have declared no competing interest.