Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community.
Svetlana LyalinaRamunas StepanauskasFrank WuShomyseh SanjabiKatherine S PollardPublished in: PloS one (2022)
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.
Keyphrases
- single cell
- microbial community
- rna seq
- genome wide
- flow cytometry
- antibiotic resistance genes
- high throughput
- copy number
- high fat diet induced
- minimally invasive
- affordable care act
- climate change
- single molecule
- healthcare
- dna methylation
- working memory
- gene expression
- risk assessment
- type diabetes
- human health
- machine learning
- transcription factor
- metabolic syndrome
- neural network
- solid state