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, food production and connections with food quality and the risk assessment.

Course contents

1. General introduction to the study of microbiomes: microbiomes and metagenomes (definitions, importance and applications), main technical aspects of next-generation sequencing assessment

2. Next-generation sequencing: 16S rRNA amplicon sequencing, shotgun metagenomics and other omics, operational steps (sampling, DNA extraction from different matrices (e.g., soil, air, water and biological samples), library preparation, sequencing)

3. Bioinformatics and biostatistical analysis: demultiplexing, quality filtering, binning into OTUs/ASVs, alpha and beta diversity, read mapping, contig reconstruction, taxonomic/functional assignment (Greengenes/SILVA, KEGG, etc.), multivariate statistics and microbial networks

4. Microbiomes in food systems: microbiomes of food system actors, microbiome circulation in food systems and link to food quality and safety, microbiomes and risk assessment in food and food production, modulation of food system microbiomes for better food

Readings/Bibliography

Lecture notes and scientific publications

Teaching methods

Lectures supported by explanatory slides

Assessment methods

Theoretical knowledge will be verified by an oral test

Teaching tools

PC, projector

Office hours

See the website of Silvia Turroni