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

Emu Full-length 16S rRNA metabarcoding analysis Microbiome

Journal

Journal of microbiological methods
ISSN: 1872-8359
Titre abrégé: J Microbiol Methods
Pays: Netherlands
ID NLM: 8306883

Informations de publication

Date de publication:
08 Apr 2024
Historique:
received: 26 12 2023
revised: 04 04 2024
accepted: 06 04 2024
medline: 11 4 2024
pubmed: 11 4 2024
entrez: 10 4 2024
Statut: aheadofprint

Résumé

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.

Identifiants

DOI: 10.1016/j.mimet.2024.106929 PMID: 38599390
pubmed: 38599390
pii: S0167-7012(24)00041-1
doi: 10.1016/j.mimet.2024.106929
pii:
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

106929

Informations de copyright

Copyright © 2024. Published by Elsevier B.V.

Auteurs

Yusuke Ota (Y)

Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan.

Kei Yasunaga (K)

Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan.

Samiratu Mahazu (S)

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.

Isaac Prah (I)

Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan.

Satoshi Nagai (S)

Fisheries Technology Institute, Japan Fisheries Research and Education Agency, Kanagawa, Japan.

Takaya Hayashi (T)

Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan.

Masato Suzuki (M)

Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.

Mitsunori Yoshida (M)

Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan.

Yoshihiko Hoshino (Y)

Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan.

Yukihiro Akeda (Y)

Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan.

Toshihiko Suzuki (T)

Department of Bacterial Pathogenesis, Tokyo Medical and Dental University, Tokyo, Japan.

Yoshiaki Gu (Y)

Department of Infectious Diseases, Tokyo Medical and Dental University, Tokyo, Japan.

Ryoichi Saito (R)

Department of Molecular Microbiology and Immunology, Tokyo Medical and Dental University, Tokyo, Japan. Electronic address: r-saito.mi@tmd.ac.jp.

Classifications MeSH