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Updated: Dec 27, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Microbial community analysis using high-throughput sequencing technology: a beginner's guide for microbiologists.

Jihoon Jo¹, Jooseong Oh¹, Chungoo Park²

¹School of Biological Sciences and Technology, Chonnam National University, Gwangju, 61186, Republic of Korea.

Journal of Microbiology (Seoul, Korea)

|February 29, 2020

Summary

Shotgun metagenomic sequencing (SMS) analyzes microbial DNA directly from environments. This review provides a practical bioinformatics protocol for microbial community analysis, aiding wet-lab researchers.

Keywords:

bioinformatics environmental DNA metagenomics microbiome shotgun metagenomic sequencing

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Last Updated: Dec 27, 2025

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

Published on: October 15, 2019

Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing

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Published on: March 19, 2018

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Exploring the Root Microbiome: Extracting Bacterial Community Data from the Soil, Rhizosphere, and Root Endosphere

Published on: May 2, 2018

Area of Science:

Environmental microbiology
Metagenomics
Bioinformatics

Background:

Microbial communities are crucial for ecosystems and human health.
Traditional methods for microbial identification have limitations.
Advances in DNA sequencing enable high-throughput analysis of environmental DNA.

Purpose of the Study:

To review environmental DNA analysis applications for microbial community profiling.
To introduce the shotgun metagenomic sequencing (SMS) approach.
To provide a practical bioinformatics protocol for SMS data analysis for wet-lab microbiologists.

Main Methods:

Review of historical environmental DNA analysis techniques.
Focus on shotgun metagenomic sequencing (SMS) for untargeted sequencing of microbial genomes.
Presentation of an in silico bioinformatics protocol for SMS data analysis.

Main Results:

SMS allows comprehensive analysis of microbial taxonomic composition and functional potential.
The provided protocol covers essential bioinformatics steps: data preprocessing, taxonomic profiling, functional annotation, and visualization.
This protocol aims to demystify in silico analysis for microbiologists.

Conclusions:

Shotgun metagenomic sequencing is a powerful, mainstream approach for microbial community analysis.
A practical bioinformatics protocol can significantly aid wet-lab researchers in analyzing SMS data.
This work facilitates a deeper understanding of microbial community structures and functions.