Up to Species-level Community Analysis of Human Gut Microbiota by 16S rRNA Amplicon Pyrosequencing

Jiro NAKAYAMA; Jiahui JIANG; Koichi WATANABE; Kangting CHEN; Huang NINXIN; Kazunori MATSUDA; Takashi KURAKAWA; Hirokazu TSUJI; Kenji SONOMOTO; Yuan-Kun LEE

doi:10.12938/bmfh.32.69

Note

Up to Species-level Community Analysis of Human Gut Microbiota by 16S rRNA Amplicon Pyrosequencing

Jiro NAKAYAMA, Jiahui JIANG, Koichi WATANABE, Kangting CHEN, Huang NINXIN, Kazunori MATSUDA, Takashi KURAKAWA, Hirokazu TSUJI, Kenji SONOMOTO, Yuan-Kun LEE

Author information

Jiro NAKAYAMA
Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Japan
Jiahui JIANG
Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Japan
Koichi WATANABE
Yakult Central Institute for Microbiological Research, Japan
Kangting CHEN
Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
Huang NINXIN
Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
Kazunori MATSUDA
Yakult Central Institute for Microbiological Research, Japan
Takashi KURAKAWA
Yakult Central Institute for Microbiological Research, Japan
Hirokazu TSUJI
Yakult Central Institute for Microbiological Research, Japan
Kenji SONOMOTO
Laboratory of Microbial Technology, Division of Applied Molecular Microbiology and Biomass Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Japan
Yuan-Kun LEE
Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore

Keywords: pyrosequence, 16S rRNA gene, human gut microbiota

JOURNAL FREE ACCESS

2013 Volume 32 Issue 2 Pages 69-76

DOI https://doi.org/10.12938/bmfh.32.69

Details

Abstract

Pyrosequencing-based 16S rRNA profiling has become a common powerful tool to obtain the community structure of gastrointestinal tract microbiota, but it is still hard to process the massive amount of sequence data into microbial composition data, especially at the species level. Here we propose a new approach in combining the quantitative insights into microbial ecology (QIIME), Mothur and ribosomal database project (RDP) programs to efficiently process 454 pyrosequence data to bacterial composition data up to the species level. It was demonstrated to precisely convert batch sequence data of 16S rRNA V6-V8 amplicons obtained from adult Singaporean fecal samples to taxonomically annotated biota data.

Corresponding author

Register with J-STAGE for free!