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Review
. 2021 Apr 2;11(4):530.
doi: 10.3390/biom11040530.

An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies

Bei Gao  1 , Liang Chi  2 , Yixin Zhu  3 , Xiaochun Shi  4 , Pengcheng Tu  5 , Bing Li  6 , Jun Yin  7 , Nan Gao  8 , Weishou Shen  4   9 , Bernd Schnabl  3   10
Affiliations
Review

An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies

Bei Gao et al. Biomolecules. .

Abstract

The gut microbiome is a microbial ecosystem which expresses 100 times more genes than the human host and plays an essential role in human health and disease pathogenesis. Since most intestinal microbial species are difficult to culture, next generation sequencing technologies have been widely applied to study the gut microbiome, including 16S rRNA, 18S rRNA, internal transcribed spacer (ITS) sequencing, shotgun metagenomic sequencing, metatranscriptomic sequencing and viromic sequencing. Various software tools were developed to analyze different sequencing data. In this review, we summarize commonly used computational tools for gut microbiome data analysis, which extended our understanding of the gut microbiome in health and diseases.

Keywords: fungi; gut microbiota; virus.

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Conflict of interest statement

B.S. has been consulting for Ferring Research Institute, HOST Therabiomics, Intercept Pharmaceuticals, Mabwell Therapeutics, Patara Pharmaceuticals and Takeda. B.S.’s institution UC San Diego has received grant support from Axial Biotherapeutics, BiomX, CymaBay Therapeutics, NGM Biopharmaceuticals, Prodigy Biotech and Synlogic Operating Company.

Figures

Figure 1
Figure 1
Commonly used sequencing techniques for the gut microbiome study.
Figure 2
Figure 2
16S rRNA sequencing data analysis pipeline.
Figure 3
Figure 3
Shotgun metagenomic sequencing data analysis pipeline.
See this image and copyright information in PMC

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