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- Title
Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution.
- Authors
Matsuo, Yoshiyuki; Komiya, Shinnosuke; Yasumizu, Yoshiaki; Yasuoka, Yuki; Mizushima, Katsura; Takagi, Tomohisa; Kryukov, Kirill; Fukuda, Aisaku; Morimoto, Yoshiharu; Naito, Yuji; Okada, Hidetaka; Bono, Hidemasa; Nakagawa, So; Hirota, Kiichi
- Abstract
Background: Species-level genetic characterization of complex bacterial communities has important clinical applications in both diagnosis and treatment. Amplicon sequencing of the 16S ribosomal RNA (rRNA) gene has proven to be a powerful strategy for the taxonomic classification of bacteria. This study aims to improve the method for full-length 16S rRNA gene analysis using the nanopore long-read sequencer MinION™. We compared it to the conventional short-read sequencing method in both a mock bacterial community and human fecal samples. Results: We modified our existing protocol for full-length 16S rRNA gene amplicon sequencing by MinION™. A new strategy for library construction with an optimized primer set overcame PCR-associated bias and enabled taxonomic classification across a broad range of bacterial species. We compared the performance of full-length and short-read 16S rRNA gene amplicon sequencing for the characterization of human gut microbiota with a complex bacterial composition. The relative abundance of dominant bacterial genera was highly similar between full-length and short-read sequencing. At the species level, MinION™ long-read sequencing had better resolution for discriminating between members of particular taxa such as Bifidobacterium, allowing an accurate representation of the sample bacterial composition. Conclusions: Our present microbiome study, comparing the discriminatory power of full-length and short-read sequencing, clearly illustrated the analytical advantage of sequencing the full-length 16S rRNA gene.
- Subjects
RIBOSOMAL RNA; HUMAN microbiota; BACTERIA classification; BACTERIAL communities; GUT microbiome; GENES; DIAGNOSIS
- Publication
BMC Microbiology, 2021, Vol 21, Issue 1, p1
- ISSN
1471-2180
- Publication type
Article
- DOI
10.1186/s12866-021-02094-5