93985 - Innovative Approach For Risk Assessment In Microbiome Food Value Chain

Learning outcomes

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.

Course contents

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.

Readings/Bibliography

Notes of lectures; scientific publications

Teaching methods

Oral lectures and scientific seminaries

Assessment methods

Theoretical knowledge will be tested in a oral examination

Teaching tools

projector, computer, instruments of microbiological laboratory

Office hours

See the website of Marco Candela