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Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform

by 1,2,3,4,5,†, 6,7,†, 8, 9,10, 11, 12, 8,* and 6,13,14,*
1
Division of Colorectal Surgery, Department of Surgery, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan
2
Cancer Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan
3
Translational Laboratory, Department of Medical Research, Taipei Medical University Hospital, Taipei Medical University, Taipei 110, Taiwan
4
Department of Surgery, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
5
Graduate Institute of Cancer Biology and Drug Discovery, Taipei Medical University, Taipei 110, Taiwan
6
PhD Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
7
Department of Laboratory Medicine, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan
8
Graduate Institute of Business Administration, College of Management. Fu Jen Catholic University, New Taipei City 242062, Taiwan
9
Department of Family Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
10
Department of Family Medicine, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan
11
Office of Information Technology, Taipei Medical University, Taipei 106, Taiwan
12
Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei 106, Taiwan
13
School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
14
Pulmonary Research Center, Wan Fang Hospital, Taipei Medical University, Taipei 116, Taiwan
*
Authors to whom correspondence should be addressed.
These authors contributed equally to this work.
Int. J. Mol. Sci. 2020, 21(19), 7110; https://doi.org/10.3390/ijms21197110
Received: 1 September 2020 / Revised: 18 September 2020 / Accepted: 25 September 2020 / Published: 26 September 2020
(This article belongs to the Section Molecular Informatics)
Accurate and rapid identification of microbiotic communities using 16S ribosomal (r)RNA sequencing is a critical task for expanding medical and clinical applications. Next-generation sequencing (NGS) is widely considered a practical approach for direct application to communities without the need for in vitro culturing. In this report, a comparative evaluation of short-read (Illumina) and long-read (Oxford Nanopore Technologies (ONT)) platforms toward 16S rRNA sequencing with the same batch of total genomic DNA extracted from fecal samples is presented. Different 16S gene regions were amplified, bar-coded, and sequenced using the Illumina MiSeq and ONT MinION sequencers and corresponding kits. Mapping of the sequenced amplicon using MinION to the entire 16S rRNA gene was analyzed with the cloud-based EPI2ME algorithm. V3–V4 reads generated using MiSeq were aligned by applying the CLC genomics workbench. More than 90% of sequenced reads generated using distinct sequencers were accurately classified at the genus or species level. The misclassification of sequenced reads at the species level between the two approaches was less substantial as expected. Taken together, the comparative results demonstrate that MinION sequencing platform coupled with the corresponding algorithm could function as a practicable strategy in classifying bacterial community to the species level. View Full-Text
Keywords: 16S rRNA; gut microbiota; MinION; MiSeq 16S rRNA; gut microbiota; MinION; MiSeq
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MDPI and ACS Style

Wei, P.-L.; Hung, C.-S.; Kao, Y.-W.; Lin, Y.-C.; Lee, C.-Y.; Chang, T.-H.; Shia, B.-C.; Lin, J.-C. Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform. Int. J. Mol. Sci. 2020, 21, 7110. https://doi.org/10.3390/ijms21197110

AMA Style

Wei P-L, Hung C-S, Kao Y-W, Lin Y-C, Lee C-Y, Chang T-H, Shia B-C, Lin J-C. Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform. International Journal of Molecular Sciences. 2020; 21(19):7110. https://doi.org/10.3390/ijms21197110

Chicago/Turabian Style

Wei, Po-Li, Ching-Sheng Hung, Yi-Wei Kao, Ying-Chin Lin, Cheng-Yang Lee, Tzu-Hao Chang, Ben-Chang Shia, and Jung-Chun Lin. 2020. "Characterization of Fecal Microbiota with Clinical Specimen Using Long-Read and Short-Read Sequencing Platform" International Journal of Molecular Sciences 21, no. 19: 7110. https://doi.org/10.3390/ijms21197110

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