Comparative evaluation of analytical pipelines for illumina short- and nanopore long-read 16S rRNA gene amplicon sequencing with mock microbial communities

Yusuke Ota; Kei Yasunaga; Samiratu Mahazu; Isaac Prah; Satoshi Nagai; Takaya Hayashi; Masato Suzuki; Mitsunori Yoshida; Yoshihiko Hoshino; Yukihiro Akeda; Toshihiko Suzuki; Yoshiaki Gu; Ryoichi Saito

doi:10.1016/j.mimet.2024.106929

Comparative evaluation of analytical pipelines for illumina short- and nanopore long-read 16S rRNA gene amplicon sequencing with mock microbial communities

J Microbiol Methods. 2024 Jun:221:106929. doi: 10.1016/j.mimet.2024.106929. Epub 2024 Apr 8.

Authors

Affiliations

¹ Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan.
² Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan; Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan.
³ Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Kanagawa, Japan.
⁴ Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan.
⁵ Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
⁶ Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
⁷ Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan.
⁸ Department of Bacterial Pathogenesis, Tokyo Medical and Dental University, Tokyo, Japan.
⁹ Department of Infectious Diseases, Tokyo Medical and Dental University, Tokyo, Japan.
¹⁰ Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan. Electronic address: r-saito.mi@tmd.ac.jp.

PMID: 38599390
DOI: 10.1016/j.mimet.2024.106929

Abstract

Utility of a recently developed long-read pipeline, Emu, was assessed using an expectation-maximization algorithm for accurate read classification. We compared it to conventional short- and long-read pipelines, using well-characterized mock bacterial samples. Our findings highlight the necessity of appropriate data-processing for taxonomic descriptions, expanding our understanding of the precise microbiome.

Keywords: Emu; Full-length 16S rRNA metabarcoding analysis; Microbiome.

Publication types

Comparative Study
Evaluation Study

MeSH terms

Algorithms
Bacteria* / classification
Bacteria* / genetics
Bacteria* / isolation & purification
DNA, Bacterial / genetics
High-Throughput Nucleotide Sequencing* / methods
Microbiota* / genetics
Nanopores
RNA, Ribosomal, 16S* / genetics
Sequence Analysis, DNA / methods