An assessment of Oxford Nanopore sequencing for human gut metagenome profiling: A pilot study of head and neck cancer patients

Thidathip Wongsurawat; Mayumi Nakagawa; Omar Atiq; Hannah N Coleman; Piroon Jenjaroenpun; James I Allred; Angela Trammel; Pantakan Puengrang; David W Ussery; Intawat Nookaew

doi:10.1016/j.mimet.2019.105739

An assessment of Oxford Nanopore sequencing for human gut metagenome profiling: A pilot study of head and neck cancer patients

J Microbiol Methods. 2019 Nov:166:105739. doi: 10.1016/j.mimet.2019.105739. Epub 2019 Oct 15.

Authors

Affiliations

¹ Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
² Department of Pathology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
³ Department of Internal Medicine, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Otolaryngology-Head and Neck Surgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
⁴ Cancer Clinical Trials and Regulatory Affairs Office, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
⁵ Bioinformatics and Systems Biology Program, School of Bioresources and Technology, School of Information Technology, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand.
⁶ Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA.
⁷ Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA; Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA. Electronic address: inookaew@uams.edu.

Abstract

Gut metagenome profiling using the Oxford Nanopore Technologies (ONT) sequencer was assessed in a pilot-sized study of 10 subjects. The taxonomic abundance of gut microbiota derived from ONT was comparable with Illumina Technology (IT) for the high-abundance species. IT better detected low-abundance species through amplification, when material was limited.

Keywords: Head and neck cancer; Microbiome; Next-generation sequencing; Shotgun metagenome sequencing; Third-generation sequencing.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Aged
Bacteria / classification*
Female
Gastrointestinal Microbiome / genetics*
Head and Neck Neoplasms / epidemiology*
High-Throughput Nucleotide Sequencing / methods
Humans
Male
Metagenome / genetics*
Middle Aged
Nanopore Sequencing / methods*
Pilot Projects
Sequence Analysis, DNA / methods

Abstract

Publication types

MeSH terms

Grants and funding