Molecular tools used for metagenomic analysis. Review

Abstract

Metagenomics uses molecular biology techniques to analyze the diversity of microbial genomes (metagenomes). Metagenome diversity has been analyzed using molecular markers to classify bacteria and archaea into taxonomic groups at the genus level. Among the most widely used molecular markers are ribosomal genes, genes encoding subunits of cytochrome C, and certain constitutive genes (gyrB, rpoB, rpoD, recA, atpD, infB, groEL, pmoA, sodA). The most widely used marker for classifying bacteria and metagenomic samples is the 16S rRNA gene, although it does not allow certain sequences to be properly classified. However, all the sequences of the hypervariable regions can be identified with the sequencing of the complete 16S rRNA gene, and, therefore, this molecular marker has made it possible to classify them at the species taxonomic level. Next generation sequencing, also called mass sequencing or high throughput sequencing, has helped to describe complex metagenomes such as those of environmental samples, which have an ecological importance, as well as metagenomes growing in extreme environments. They have also proved helpful in studies related to animal and human health, and in the agro-food field. Specifically, both the 16S rRNA molecular marker and high throughput sequencing combined with bioinformatic tools for metagenomic analysis have been used to describe the ruminal metagenome, a microbial community of great importance because it is involved in animal production of meat and milk. Despite the many studies that have been conducted in this field, some microorganisms still remain to be discovered and characterized.