Learning objectives
The successful student will know: (i) main goals of a metagenome study; (ii) techniques and technologies for the metagenomes assessment; (iii) role of microbiomes in food systems, connection with food quality and risk assessment.
Prerequisites
- - -
Course unit content
1. General Introduction the study of microbiomes: metagenomics, microbial ecosystems and microbiomes, definitions, importance and applications, main technical aspects, goals for a metagenome study, types of metagenome studies, NGS sequencing, second-and third-generation NGS platforms;
2. NGS sequencing: sampling, DNA extraction from different matrices (soil, air, water and biological samples), multiplexing and library preparation, NGS sequencing reaction; marker gene 16S sequencing and shotgun metagenomics;
3. bioinformatic analysis: demultiplexing, quality filtering, reads mapping, contigues reconstruction, assignment on reference databases (KEGG, COGS, greengenes and SILVA, alpha and beta diversity), multivariate statistics
4. microbiomes in food system: microbiomes of the food system actors, microbiomes circulation in food systems and connection with food quality and safety, food system microbiome modulation for a better food.
Full programme
. General Introduction the study of microbiomes: metagenomics, microbial ecosystems and microbiomes, definitions, importance and applications, main technical aspects, goals for a metagenome study, types of metagenome studies, NGS sequencing, second-and third-generation NGS platforms;
2. NGS sequencing: sampling, DNA extraction from different matrices (soil, air, water and biological samples), multiplexing and library preparation, NGS sequencing reaction; marker gene 16S sequencing and shotgun metagenomics;
3. bioinformatic analysis: demultiplexing, quality filtering, reads mapping, contigues reconstruction, assignment on reference databases (KEGG, COGS, greengenes and SILVA, alpha and beta diversity), multivariate statistics
4. microbiomes in food system: microbiomes of the food system actors, microbiomes circulation in food systems and connection with food quality and safety, food system microbiome modulation for a better food.
Bibliography
- - -
Teaching methods
Oral lectures and scientific seminaries
Assessment methods and criteria
Theoretical knowledge will be tested in a oral examination
Other information
- - -
