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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
Published on: August 20, 2021
Oral bacterial genome sequencing using the high-throughput Roche Genome Sequencer FLX System
Nicholas C K Heng1, Jo-Ann L Stanton
1Faculty of Dentistry, Sir John Walsh Research Institute, University of Otago, Dunedin, New Zealand.
Methods in Molecular Biology (Clifton, N.J.)
|August 19, 2010
Summary
High-throughput sequencing technologies have revolutionized genomics, making whole-genome sequencing feasible for more researchers. This study provides protocols for oral bacterial genome sequencing using 454 pyrosequencing.
Area of Science:
- Genomics
- Microbiology
- Bioinformatics
Background:
- Sanger sequencing was the standard for DNA sequencing for over 30 years.
- Whole-genome sequencing using Sanger chemistry was previously labor-intensive, costly, and impractical for most research groups.
- Recent advancements in high-throughput sequencing (HTS) technologies have drastically reduced cost and increased speed and scale.
Purpose of the Study:
- To provide accessible laboratory and bioinformatic protocols for HTS of oral bacterial genomes.
- To enable average research groups to perform large-scale genomic analyses.
- To leverage 454 pyrosequencing technology for oral microbiome research.
Main Methods:
- Utilized the Roche Genome Sequencer FLX System, which employs 454 pyrosequencing technology.
- Developed and validated laboratory protocols for sample preparation and sequencing.
- Established bioinformatic pipelines for data analysis and genome assembly.
Main Results:
- Demonstrated the feasibility of HTS for oral bacterial genomes using 454 pyrosequencing.
- Generated reliable DNA sequence output at gigabasepair levels.
- Achieved a significantly lower cost per sequenced basepair compared to traditional methods.
Conclusions:
- HTS technologies, specifically 454 pyrosequencing, have democratized whole-genome sequencing for bacterial species.
- The provided protocols empower average research groups to conduct comprehensive oral bacterial genome sequencing.
- This facilitates deeper understanding of oral microbiome composition and function.
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