Manghina, Valeria (2016) Development of pipeline to create and validate metagenomic datasets enabling microbiota associations with host traits. Doctoral Thesis.
The microbiota can be depicted as a measurable organ consisting of microbial cells, and creating a unique ecosystem together with the host eukaryotic cells. Therefore, to understand the normal physiology and pathology of animal ecosystems, it is mandatory to tackle a comprehensive analysis of the host, the microbiota, and their interactions. Since over 99.8% of the microbes cannot be cultured, metagenomics offers a path to the study of their community structures and metabolic potential. These goals are achievable thanks to the recent advances in sequencing complex assortments of small genomes, through 16S and WGS approach. In spite of the great number of latest studies, there is not a defined and standardized pipeline to measure the microbial community; rather, significant efforts are needed to optimize sample preparation and data analysis workflows for metagenomics analysis of microbiome.
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