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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
Published on: May 23, 2018
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Strain-level profiling of viable microbial community by selective single-cell genome sequencing
Masahito Hosokawa1,2,3,4,5, Taruho Endoh6, Kazuma Kamata6
1Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480, Japan. masahosokawa@aoni.waseda.jp.
Scientific Reports
|March 16, 2022
Summary
PMA-SAG-gel enables single-cell genome sequencing of viable bacteria, overcoming limitations of dead cells and free DNA. This method accurately characterizes surviving bacterial populations for applications in health and environmental studies.
Area of Science:
- Microbiology
- Genomics
- Molecular Biology
Background:
- High-throughput sequencing is vital for bacterial community analysis.
- Non-viable bacteria and free DNA complicate accurate community profiling.
Purpose of the Study:
- To develop a method for viable bacteria-targeted single-cell genome sequencing.
- To obtain comprehensive whole-genome sequences of surviving bacteria.
Main Methods:
- PMA-SAG-gel utilizes gel matrices for sequential enzymatic reactions.
- Enables cell lysis and genome amplification of viable single cells.
- Selectively sequences genomes from live bacteria, excluding dead cells.
Main Results:
- PMA-SAG-gel successfully removed signals from dead bacteria in model samples.
- Recovered near-complete single-amplified genomes (SAGs) from eight oxygen-tolerant bacteria in human feces.
- Identified distinct strains and their specific genes for metabolic function analysis.
Conclusions:
- PMA-SAG-gel provides strain-level survival profiles for understanding bacterial populations.
- Offers insights for quality assessment of live bacterial products and fecal microbiota transplantation.
- Aids in evaluating antimicrobial treatment effects and environmental adaptation.
