**3. Conclusions**

The study of how microbial communities contribute to environmental functions and the physiology of the host was limited to cultivable microorganisms. As, the free culture techniques based on molecular markers developed (AFLP, RFLP, and DGGE), this knowledge expanded. However, the knowledge obtained from these was quite limited. But now with the techniques of massive sequencing, it has been possible to obtain a better understanding of the role of microorganisms in different types of environments and hosts, both from the taxonomic and functional point of view.

The use of bioinformatic programs has allowed not only the reconstruction of the molecular phylogeny but also has allowed them to be studied from the functional point of view, showing the great potential for the future biotechnological exploitation of this microbial metabolic diversity such as enzymes with different catalytic activities from uncultivable organisms. Several combined methodologies that uses NGS techniques along with culture-based methods have been used to

#### *Metagenomics - Basics, Methods and Applications*

obtain new bacterial strains using specific culture media or through the functional screening using specific primers in order to isolate the genes of interest.

Current research is now been carried out in order to obtain more precise metagenomic and metatranscriptomic assemblages, with new software specially designed (MetaVelvet, TriMetAss, and MetaAmos) to obtain complete genomes and transcriptomes of the bacterial communities. These protocols along with the integration of other "omic" techniques and systems biology could allow a better understanding of the complex metabolic and trophic networks that operates in an organism or environment.
