Application of metagenomics in the human gut microbiome

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.

Figure 1

Application of metagenomics in the human gut microbiome. In studying the human gut microbiome, metagenomic analysis has the potential to provide sufficient information in the following research areas: The detection of microbial composition and diversity, novel genes, microbial pathways, functional dysbiosis, antibiotic resistance genes, and the determination of interactions and co-evolution between microbiota and host.

Figure 2

Comparison of different gut microbiome study approaches. The characteristics, limitations, and applications of different gut microbiome approaches from cultivation to metabolomics are presented. DGGE: Denaturing gradient gel electrophoresis.