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. ecological models of microbial communities: cooperation, cross-feeding and competition; cell-to-cell signaling; metabolic networks; metagenome, metatranscriptome, metabolome

2. microbial communities of holobionts: phylosymbiosis; role in host physiology, adaptation and evolution; connection with the environment and environmental metacommunities; microbial communities for sustainable food systems

3. the human gut microbiome in human evolution, a co-evolutionary perspective

4. assessment of microbial communities: sampling and DNA extraction from different ecosystems (soil, tissues and sea); NGS sequencing, second-and third-generation NGS platforms, library preparation

5. Bioinformatic analysis of the microbiome: sequences quality filtering, assignment in metagenome sequencing and phylogenetic profiling (QIIME, read-mapping approach VS assembling approach); usage of reference databases (KEGG, COGS, greengenes and SILVA)

6. biostatistical analysis of microbial communities: alpha and beta diversity; multidimesional analysis; clustering; model prediction algorithm; biological networks and co-abundance groups

Testi/Bibliografia

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