**Abstract**

Through millions of years, the multicellular organisms have coexisted and coevolved with the surrounding microorganisms, in an almost symbiotic relationship forming a complex entity known as holobiont. The composition and functions of these microbial communities were limited during many years to only a mere fraction, due to the use of culture-based techniques. The advent of molecular-based techniques allowed the identification of uncultured organisms in a culture-free manner. In recent years, the development of next generation sequencing techniques have allowed the high-throughput study of microbial communities allowing the identification and classification of otherwise uncultured microorganisms in a given environment, tissue or host through metagenomics. The next generation sequencing techniques have been used in the functional study of microbial assemblages and were able to identify the role of the microorganisms in biogeochemical cycles, pathogenic processes, metabolism and development, through metatranscriptomics. Taken together, the next generation sequencing based-studies have shown the existence of a complex metabolic network in different hosts and environments, with the microbial communities. This chapter will focus in different available bioinformatic tools that are suitable to study symbiosis and coevolution processes in a given sample.

**Keywords:** next generation sequencing, bioinformatics, metagenomics, metatranscriptomics, network analysis
