Bioinformatics for DNA Sequence-based Microbiota Analyses

Microbiota samples are often complex and difficult to define with respect to organism content. The emergence of growth-independent DNA-based techniques, however, has made data generation from microbiota samples relatively easy. The most widely used approach to generate DNA sequence data is to PCRamplify the gene encoding RNA in the small ribosomal subunit (16S rRNA) using primers targeting generally conserved regions of the gene. The individual components of the microbiota are subsequently characterized by cloning and DNA sequencing. Analysis of large clone libraries is a bottleneck for the understanding of ecological processes in the microbiota. This chapter presents both traditional and novel bioinformatics approaches for microbiota description and analysis based on DNA sequences.