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Copyright ©The Author(s) 2015. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Gastroenterol. Jan 21, 2015; 21(3): 803-814
Published online Jan 21, 2015. doi: 10.3748/wjg.v21.i3.803
Application of metagenomics in the human gut microbiome
Wei-Lin Wang, Shao-Yan Xu, Zhi-Gang Ren, Liang Tao, Jian-Wen Jiang, Shu-Sen Zheng
Wei-Lin Wang, Shao-Yan Xu, Zhi-Gang Ren, Liang Tao, Jian-Wen Jiang, Shu-Sen Zheng, Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang Province, China
Author contributions: Wang WL and Xu SY contributed equally to the writing of the paper; Ren ZG, Tao L and Jiang JW revised the paper and prepared the figures; and Zheng SS is the supervisor of the study.
Supported by National Basic Research Program (973 Program) of China, No. 2013CB531403.
Open-Access: This article is an open-access article which was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/
Correspondence to: Shu-Sen Zheng, PhD, MD, Department of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Road, Hangzhou 310003, Zhejiang Province, China. shusenzheng@zju.edu.cn
Telephone: +86-571-87236466 Fax: +86-571-87236466
Received: July 15, 2014
Peer-review started: July 16, 2014
First decision: September 15, 2014
Revised: September 30, 2014
Accepted: November 7, 2014
Article in press: November 11, 2014
Published online: January 21, 2015
Processing time: 188 Days and 21 Hours
Abstract

There are more than 1000 microbial species living in the complex human intestine. The gut microbial community plays an important role in protecting the host against pathogenic microbes, modulating immunity, regulating metabolic processes, and is even regarded as an endocrine organ. However, traditional culture methods are very limited for identifying microbes. With the application of molecular biologic technology in the field of the intestinal microbiome, especially metagenomic sequencing of the next-generation sequencing technology, progress has been made in the study of the human intestinal microbiome. Metagenomics can be used to study intestinal microbiome diversity and dysbiosis, as well as its relationship to health and disease. Moreover, functional metagenomics can identify novel functional genes, microbial pathways, antibiotic resistance genes, functional dysbiosis of the intestinal microbiome, and determine interactions and co-evolution between microbiota and host, though there are still some limitations. Metatranscriptomics, metaproteomics and metabolomics represent enormous complements to the understanding of the human gut microbiome. This review aims to demonstrate that metagenomics can be a powerful tool in studying the human gut microbiome with encouraging prospects. The limitations of metagenomics to be overcome are also discussed. Metatranscriptomics, metaproteomics and metabolomics in relation to the study of the human gut microbiome are also briefly discussed.

Keywords: Human gut microbiome; Metabolomics; Metagenomics; Metaproteomics; Metatranscriptomics

Core tip: Metagenomics plays a role in understanding the human gut microbiome, including the diversity of the gut microbiome, identifying novel genes, and determining the etiology of functional dysbiosis. A combination of metagenomics, metatranscriptomics, metaproteomics and metabolomics can also promote an understanding of the functional activity of the human gut microbiome and possibly provide a new strategy for disease diagnosis and treatment.