16S rRNA-Based Taxonomy Profiling in the Metagenomics Era

The coupling of next-generation sequencing (NGS) with metagenomics and phylogenetic markers has improved our understanding on how microbial communities build up, operate and evolve. A coherent taxonomic framework can be obtained with both targeted or untargeted approaches. Targeted approaches have dominated the meta-analyses for a long time, providing great insights into the structure and the dynamics of microbial populations. Such information is precious for verifying, complementing or even integrating the results obtained with metagenomics. In fact, taxonomic accuracy is a crucial aspect of every meta-approach. A multitude of methods have been proposed aimed at extracting taxonomic/phylogenetic information from untargeted sequencing, with the aim of reconstructing and evaluating the genomic complexity of environments. Yet, methods for targeted taxonomic profiling, although relatively poor in terms of achievable taxonomic depth, can give a broader perspective on microbial populations with respect to metagenomics. This chapter is therefore dedicated to the role of targeted approaches, in particular those related to 16S rRNA, in the advancing field of metagenomic knowledge.