The human microbiome plays an important role in health and disease, but the structure of the bacterial communities and their interaction with the human body are still poorly understood. The recent introduction of next-generation sequencing technologies allows for the first time an unbiased and in-depth characterization of a microbiome based on the sequence of certain marker genes. However, analysis of the huge amount of sequence data generated in microbiome studies poses a considerable challenge to the individual researcher. Here we provide an overview of the steps involved in the characterization and comparison of complex microbial communities starting with sequence preprocessing on to taxonomic classification ending in statistical evaluation and visualization of the analysis results. A selection of different tools and techniques of each working step is introduced and discussed. Additionally, different sequencing approaches ahead of the bioinformatics analysis are considered. Furthermore, the application of microbiome analysis in medical research is shown by selected medical studies.
The chapter is addressed to microbial ecologists or medical researchers without or little bioinformatics background as well as to bioinformatics scientists who are interested in the overall microbiome workflow, and its tools and techniques.