Strain-level profiling of viable microbial community by selective single-cell genome sequencing

Masahito Hosokawa*, Taruho Endoh, Kazuma Kamata, Koji Arikawa, Yohei Nishikawa, Masato Kogawa, Tatsuya Saeki, Takuya Yoda, Haruko Takeyama

*この研究の対応する著者

研究成果: Article査読

抄録

Culture-independent analysis with high-throughput sequencing has been widely used to characterize bacterial communities. However, signals derived from non-viable bacteria and non-cell DNA may inhibit its characterization. Here, we present a method for viable bacteria-targeted single-cell genome sequencing, called PMA-SAG-gel, to obtain comprehensive whole-genome sequences of surviving uncultured bacteria from microbial communities. PMA-SAG-gel uses gel matrixes that enable sequential enzymatic reactions for cell lysis and genome amplification of viable single cells from the microbial communities. PMA-SAG-gel removed the single-amplified genomes (SAGs) derived from dead bacteria and enabled selective sequencing of viable bacteria in the model samples of Escherichia coli and Bacillus subtilis. Next, we demonstrated the recovery of near-complete SAGs of eight oxygen-tolerant bacteria, including Bacteroides spp. and Phocaeicola spp., from 1331 human feces SAGs. We found the presence of two different strains in each species and identified their specific genes to investigate the metabolic functions. The survival profile of an entire population at the strain level will provide the information for understanding the characteristics of the surviving bacteria under the specific environments or sample processing and insights for quality assessment of live bacterial products or fecal microbiota transplantation and for understanding the effect of antimicrobial treatments.

本文言語English
論文番号4443
ジャーナルScientific reports
12
1
DOI
出版ステータスPublished - 2022 12月

ASJC Scopus subject areas

  • 一般

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