Bioinformatics in Microbiome Analysis

Publication date: Available online 10 October 2017 Source:Methods in Microbiology Author(s): Yuhan Hao, Zhiheng Pei, Stuart M. Brown Diseases driven by pathogens have been studied for decades, but the mechanisms of those diseases are still not completely understood. Next-generation sequencing provides a powerful technology with which to observe changes of pathogens at a genome level and the composition of microbial communities. This in turn has facilitated investigation on the associations between the microbiome and diseases. This chapter first will discuss bioinformatics applications under the “one pathogen to one disease” paradigm. Next, it will introduce the 16S rRNA sequencing method and how it facilitates the determination of the taxonomy of a community. Next it will present metagenomic shotgun sequencing data and several metagenomic bioinformatic tools and examples of associations between human disease and microbial communities. It discusses commonly used analytical approaches for metagenomic data, with aspects of statistics, machine learning and network analysis. Finally, it will summarize different sequencing platforms and provides future prospectives about integrating different omics sequencing technologies and longitudinal samples.
Source: Methods in Microbiology - Category: Microbiology Source Type: research