85300 - METAGENOMICS

Conoscenze e abilità da conseguire

Al termine del corso lo studente conosce: i) i principali metodi per la profilazione tassonomica, l'analisi funzionale e il confronto della comunità di genomi e trascrittomi estratti da un campione ambientale o da una biopsia. Conosce come descrivere la biodiversità di qualunque nicchia ambientale attraverso l'analisi del materiale genetico in essa presente.

Contenuti

1. General Introduction: 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 andlibrary 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)
4. biostatistics: multivariate statistics, exploratory ordination, clustering, canonical correlation, discriminatory methods and machine learning, analysis of variance, permutation, biological networks and co-abundance groups
5. Ecological rules and dominant dynamics of microbial communities
6. The human microbiome, from recent co-evolution to personalized medicine
7. Earth microbiomes, ecological centrality, microbiome for climate change and microbiomes biotechnology (microbiomes for food security, microbiomes for biodiscovery and synthetic biology)
8. Paleometagenomics, from paleobioprospecting to paleoclimatic records and long term co-evolution

Testi/Bibliografia

Lesk Introduction to Bioinformatics (V Edition_2019)

Metagenomics, perspectives, methods and applications, M Nagarajan (2017)

R in action, third edition

Multivariate analysis of ecological data with ADE4

Brook, biology of microorganisms 15^th edition

Papers and reviews suggested by the teacher

Laboratory notes

Metodi didattici

Frontal lessons and laboratory experiences

Modalità di verifica e valutazione dell'apprendimento

Oral examination

Strumenti a supporto della didattica

Board, projector and bioinformatic lab

Orario di ricevimento

Consulta il sito web di Marco Candela