Techniques for the study of microbiota

Abstract

Gut microbiota is an exceptionally diverse, variable and dense microbial ecosystem that has been extensively studied in recent years. Numerous technological developments have facilitated the rapid progress of the field by the improvement of old and the emergence of new methods. Most of the available methods are based on the sequence of the small subunit ribosomal RNA and are suitable for assessment of gut microbiota composition. Others, such as metagenomics and metabolomics, provide information about gut microbiota function. In this chapter we systematically present the most widely used approaches including cultivation/culturomics, quantitative and profiling small subunit ribosomal RNA-based methods, sequencing technologies with specific focus on bioinformatics and data processing, finishing with omics that facilitate functional profiling. The advantages and limitations of each technology are presented, while examples of successful applications provide evidence that different scientific questions call for the application of different techniques.