Instruction of microbiome taxonomic profiling based on 16S rRNA sequencing

Hyojung Kim; Sora Kim; Sungwon Jung

doi:10.1007/s12275-020-9556-y

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Instruction of microbiome taxonomic profiling based on 16S rRNA sequencing: Hyojung Kim ¹, Sora Kim ², Sungwon Jung ^1,2,3; Journal of Microbiology 2020;58(3):193-205.
DOI: https://doi.org/10.1007/s12275-020-9556-y
Published online: February 27, 2020

¹Department of Health Sciences and Technology, Gachon University, Incheon 21999, Republic of Korea, ²Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon 21565, Republic of Korea, ³Department of Genome Medicine and Science, Gachon University College of Medicine, Incheon 21565, Republic of Korea¹Department of Health Sciences and Technology, Gachon University, Incheon 21999, Republic of Korea, ²Gachon Institute of Genome Medicine and Science, Gachon University Gil Medical Center, Incheon 21565, Republic of Korea, ³Department of Genome Medicine and Science, Gachon University College of Medicine, Incheon 21565, Republic of Korea

Corresponding author: Sungwon Jung , Tel: +82-32-458-2740,

Received: 19 November 2019 • Revised: 3 February 2020 • Accepted: 14 February 2020

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Abstract

Recent studies on microbiome highlighted their importance in various environments including human, where they are involved in multiple biological contexts such as immune mechanism, drug response, and metabolism. The rapid increase of new findings in microbiome research is partly due to the technological advances in microbiome identification, including the next-generation sequencing technologies. Several applications of different next-generation sequencing platforms exist for microbiome identification, but the most popular method is using short-read sequencing technology to profile targeted regions of 16S rRNA genes of microbiome because of its low-cost and generally reliable performance of identifying overall microbiome compositions. The analysis of targeted 16S rRNA sequencing data requires multiple steps of data processing and systematic analysis, and many software tools have been proposed for such procedures. However, properly organizing and using such software tools still require certain level of expertise with computational environments. The purpose of this article is introducing the concept of computational analysis of 16S rRNA sequencing data to microbiologists and providing easy-to-follow and step-by-step instructions of using recent software tools of microbiome analysis. This instruction may be used as a quick guideline for general next-generation sequencing-based microbiome studies or a template of constructing own software pipelines for customized analysis.

Keywords: microbiome;next-generation sequencing;16S rRNA;bioinformatics;software pipeline

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Instruction of microbiome taxonomic profiling based on 16S rRNA sequencing

J. Microbiol. 2020;58(3):193-205. Published online February 27, 2020

DOI: https://doi.org/10.1007/s12275-020-9556-y

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