Beginner's guide to microbiome analysis: Bioinformatics guidelines and practical concepts for amplicon-based microbiome analysis.

Abstract

The advent of next-generation sequencing (NGS) allows to study living organisms by reading genetic materials in a high-throughput manner. The technology has opened up a field of microbial research in several areas such as medicine, agriculture, energy, and environment, to study a whole microbial community in an environment of interest without culturing. Bioinformatics analysis is a need in order to characterize and analyze microbiota in the studied samples. In this tutorial, we will give an overview of microbiome analysis based on high-throughput 16S rRNA genes sequencing, a commonly-used target sequence to classify bacteria and archaea. With biological and technology backgrounds, microbiome data from short-read sequencing platform will be elucidated followed by all important computational steps for microbiome analysis. The steps include data preprocessing, amplicon sequence variant analysis, taxonomy assignment, data normalization, and diversity analyses. Practical concepts and codes for the microbiome analysis will be demonstrated step by step providing a basic guideline for beginner.