Metagenomic methods for the analysis of human microbiota towards a clinical application.

Several microbial communities colonize different body areas constituting the human microbiota. Recently, several researches suggested the involvement of these bacteria in maintaining omeostasis of the human body, highlighting as a microbial dysbiosis may be implicated in numerous inflammatory conditions and human diseases. The high-throughput sequencing technologies applicate to the study of human microbiome allowed to achieve important results about the interactions between microorganisms and the host. Moreover, metagenomics studies extended scientists’ knowledge about the human microbiota and its implications in numerous human diseases. Since the 16S rRNA gene sequencing was shown to be an effective method to investigate microbial communities, recently our laboratory adopted this molecular approach to characterize the interactions between bacteria and host. Therefore, the present PhD work describes our experience in samples collection, experimental procedures and data analysis in studying the human microbiota by means of a metagenomics approach. Indeed, our studies allowed us to understand that to achieve a complete overview of microbial communities involved in a specific fisio-pathological condition, a standardization of experimental protocols and data analysis should be adopted to carry out metagenomics surveys. Moreover, the taxonomic evaluations through 16S rRNA gene sequencing are just a first step for elucidating the roles of bacteria in the host’s health. Integrating the metagenomics data which those obtained by metatranscriptomic, metaproteomic, and metametabolomic represents a promising approach to develop new noninvasive bacterial-related diagnostic tools.