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

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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.

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Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

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Fast gapped-read alignment with Bowtie 2.

Ben Langmead, Steven L Salzberg (2012)

As the rate of sequencing increases, greater throughput is demanded from read aligners. The full-text minute index is often used to make alignment very fast and memory-efficient, but the approach is ill-suited to finding longer, gapped alignments. Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.

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DADA2: High resolution sample inference from Illumina amplicon data

Benjamin J. Callahan, Paul McMurdie, Michael Rosen … (2016)

We present DADA2, a software package that models and corrects Illumina-sequenced amplicon errors. DADA2 infers sample sequences exactly, without coarse-graining into OTUs, and resolves differences of as little as one nucleotide. In several mock communities DADA2 identified more real variants and output fewer spurious sequences than other methods. We applied DADA2 to vaginal samples from a cohort of pregnant women, revealing a diversity of previously undetected Lactobacillus crispatus variants.

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Author and article information

Contributors

Jorge Joven: Role: Academic Editor

Journal

Journal ID (nlm-ta): Biomolecules

Journal ID (iso-abbrev): Biomolecules

Journal ID (publisher-id): biomolecules

Title: Biomolecules

Publisher: MDPI

ISSN (Electronic): 2218-273X

Publication date (Electronic): 02 April 2021

Publication date Collection: April 2021

Volume: 11

Issue: 4

Electronic Location Identifier: 530

Affiliations

[1 ]Department of Marine Science, School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing 210044, China; wintergb@ 123456hotmail.com

[2 ]Metaorganism Immunity Section, Laboratory of Immune Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; chil2@ 123456nih.gov

[3 ]Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA; y3zhu@ 123456ucsd.edu

[4 ]Department of Environmental Ecological Engineering, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing 210044, China; 20201248131@ 123456nuist.edu.cn (X.S.); wsshen@ 123456nuist.edu.cn (W.S.)

[5 ]Department of Food Science and Nutrition, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China; tupengcheng1@ 123456163.com

[6 ]Suzhou Industrial Park Environmental Law Enforcement Brigade (Environmental Monitoring Station), Suzhou 215021, China; lbing@ 123456sipac.gov.cn

[7 ]Department of Hydrometeorology, School of Hydrology and Water Resources, Nanjing University of Information Science and Technology, Nanjing 210044, China; jy.junyin@ 123456foxmail.com

[8 ]Department of Biotechnology, School of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, China; ngao@ 123456njtech.edu.cn

[9 ]Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, Nanjing 210044, China

[10 ]Department of Medicine, VA San Diego Healthcare System, San Diego, CA 92161, USA

Author notes

[* ]Correspondence: beschnabl@ 123456health.ucsd.edu ; Tel.: +1-858-822-5311

Author information

Bei Gao https://orcid.org/0000-0002-3321-2339

Pengcheng Tu https://orcid.org/0000-0001-8920-7478

Article

Publisher ID: biomolecules-11-00530

DOI: 10.3390/biom11040530

PMC ID: 8066849

PubMed ID: 33918473

SO-VID: a0b3bc3f-996c-4064-9b0a-9815e9786ac2

License:

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( https://creativecommons.org/licenses/by/4.0/).

History

Date received : 27 January 2021

Date accepted : 29 March 2021

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

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Microbiology Independent Research Journal (MIR Journal)

Most cited references 139

Trimmomatic: a flexible trimmer for Illumina sequence data

Fast gapped-read alignment with Bowtie 2.

DADA2: High resolution sample inference from Illumina amplicon data

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