Skip Navigation
Skip to contents

Journal of Microbiology : Journal of Microbiology

OPEN ACCESS
SEARCH
Search
Advanced Search
mobile menu button

Articles

Page Path
HOME > J. Microbiol > Volume 58(3); 2020 > Article
Journal Article
Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists
Jihoon Jo , Jooseong Oh , Chungoo Park
Journal of Microbiology 2020;58(3):176-192.
DOI: https://doi.org/10.1007/s12275-020-9525-5
Published online: February 27, 2020
School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of KoreaSchool of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
Corresponding author:  Chungoo Park , Tel: +82-62-530-1913, 
Received: 5 November 2019   • Revised: 11 December 2019   • Accepted: 16 December 2019
prev next
  • 44 Views
  • 0 Download
  • 43 Web of Science
  • 41 Crossref
  • 51 Scopus
Full Article

Abstract

Microbial communities present in diverse environments from deep seas to human body niches play significant roles in the complex ecosystem and human health. Characterizing their structural and functional diversities is indispensable, and many approaches, such as microscopic observation, DNA fingerprinting, and PCR-based marker gene analysis, have been successfully applied to identify microorganisms. Since the revolutionary improvement of DNA sequencing technologies, direct and high-throughput analysis of genomic DNA from a whole environmental community without prior cultivation has become the mainstream approach, overcoming the constraints of the classical approaches. Here, we first briefly review the history of environmental DNA analysis applications with a focus on profiling the taxonomic composition and functional potentials of microbial communities. To this end, we aim to introduce the shotgun metagenomic sequencing (SMS) approach, which is used for the untargeted (“shotgun”) sequencing of all (“meta”) microbial genomes (“genomic”) present in a sample. SMS data analyses are performed in silico using various software programs; however, in silico analysis is typically regarded as a burden on wet-lab experimental microbiologists. Therefore, in this review, we present microbiologists who are unfamiliar with in silico analyses with a basic and practical SMS data analysis protocol. This protocol covers all the bioinformatics processes of the SMS analysis in terms of data preprocessing, taxonomic profiling, functional annotation, and visualization.

  • Cite this Article
    Cite this Article
    export Copy Download
    Close
    Download Citation
    Download a citation file in RIS format that can be imported by all major citation management software, including EndNote, ProCite, RefWorks, and Reference Manager.
    Format:
    • RIS — For EndNote, ProCite, RefWorks, and most other reference management software
    • BibTeX — For JabRef, BibDesk, and other BibTeX-specific software
    Include:
    • Citation for the content below
    Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists
    J. Microbiol. 2020;58(3):176-192.   Published online February 27, 2020
    DOI: https://doi.org/10.1007/s12275-020-9525-5
    Close
Related articles
Journal of Microbiology : Journal of Microbiology
© The Microbiological Society of Korea.
TOP