Title |
Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists |
Author |
Jihoon Jo, Jooseong Oh, and Chungoo Park* |
Address |
School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea |
Bibliography |
Journal of Microbiology, 58(3),176-192, 2020,
|
DOI |
10.1007/s12275-020-9525-5
|
Key Words |
microbiome, environmental DNA, metagenomics,
shotgun metagenomic sequencing, bioinformatics |
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. |