Bioinformatics Approaches for Human Gut Microbiome Research

Abstract

The human gut microbiome has received great attention because many studies have revealed that it is associated with a variety of diseases. The extraordinary large datasets of microbiome studies indicate that bioinformatics approaches are crucial for their analyses. Here, we systematically reviewed bioinformatics tools that are commonly used in microbiome research, including a typical pipeline and software for sequence alignment, abundance profiling, enterotype determination, taxonomic diversity, identifying differentially abundant species/genes, gene cataloging, and functional analyses. We also reviewed the algorithms and methods used to define metagenomic species and co-abundance gene groups to expand our knowledge of unclassified and poorly understood gut microbes that are undocumented in the current genome databases. Additionally, we examined the methods used to identify metagenomic biomarkers based on the gut microbiome, which might help to expand the knowledge and approaches for disease detection and surveillance.