Bioinformatics for microbiome research: Concepts, strategies, and advances

Abstract

Advances in next-generation sequencing technologies allow comparative analyses of the diversity and abundance of whole microbial communities, and of important ecosystem functional genes, at far greater depths than ever before. However, the current major challenge for the use of this immense amount of genetic information is undoubtedly how to convert the information into rational biological conclusions. As an attempt to solve this issue, we now rely on a set of complex computational/statistical analyses, the use of which, however, could be a drawback for most researchers in the biological sciences. In this chapter, we outline the main approaches applied for microbiome studies based on high-throughput sequencing technologies and we introduce the most commonly used strategies for data handling, sequence clustering, taxonomic and functional assignment, and microbial community comparisons. We also draw readers' attention to recent advances in the microbiome research field, illustrating the Brazilian case.