Strain-level profiling of viable microbial community by selective single-cell genome sequencing
Abstract 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 ge...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-03-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-08401-y |
| _version_ | 1818321028681564160 |
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| author | Masahito Hosokawa Taruho Endoh Kazuma Kamata Koji Arikawa Yohei Nishikawa Masato Kogawa Tatsuya Saeki Takuya Yoda Haruko Takeyama |
| author_facet | Masahito Hosokawa Taruho Endoh Kazuma Kamata Koji Arikawa Yohei Nishikawa Masato Kogawa Tatsuya Saeki Takuya Yoda Haruko Takeyama |
| author_sort | Masahito Hosokawa |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-12-13T10:34:24Z |
| format | Article |
| id | doaj.art-fa963ffd80a44f01b2b364938da93b2a |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-12-13T10:34:24Z |
| publishDate | 2022-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-fa963ffd80a44f01b2b364938da93b2a2022-12-21T23:50:46ZengNature PortfolioScientific Reports2045-23222022-03-0112111210.1038/s41598-022-08401-yStrain-level profiling of viable microbial community by selective single-cell genome sequencingMasahito Hosokawa0Taruho Endoh1Kazuma Kamata2Koji Arikawa3Yohei Nishikawa4Masato Kogawa5Tatsuya Saeki6Takuya Yoda7Haruko Takeyama8Department of Life Science and Medical Bioscience, Waseda UniversitybitBiome, Inc.bitBiome, Inc.bitBiome, Inc.Research Organization for Nano and Life Innovation, Waseda UniversityResearch Organization for Nano and Life Innovation, Waseda UniversitybitBiome, Inc.bitBiome, Inc.Department of Life Science and Medical Bioscience, Waseda UniversityAbstract 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.https://doi.org/10.1038/s41598-022-08401-y |
| spellingShingle | Masahito Hosokawa Taruho Endoh Kazuma Kamata Koji Arikawa Yohei Nishikawa Masato Kogawa Tatsuya Saeki Takuya Yoda Haruko Takeyama Strain-level profiling of viable microbial community by selective single-cell genome sequencing Scientific Reports |
| title | Strain-level profiling of viable microbial community by selective single-cell genome sequencing |
| title_full | Strain-level profiling of viable microbial community by selective single-cell genome sequencing |
| title_fullStr | Strain-level profiling of viable microbial community by selective single-cell genome sequencing |
| title_full_unstemmed | Strain-level profiling of viable microbial community by selective single-cell genome sequencing |
| title_short | Strain-level profiling of viable microbial community by selective single-cell genome sequencing |
| title_sort | strain level profiling of viable microbial community by selective single cell genome sequencing |
| url | https://doi.org/10.1038/s41598-022-08401-y |
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