85300 - METAGENOMICS

Learning outcomes

The successful student knows i) the principal methods for taxonomic profiling and functional analysis and comparison of genomes and transcriptomes extracted as a whole from an environmental sample or biopsy. ii) how to describe the biodiversity of any environment by analyzing of the genetic material encompassed in it.

Course contents

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

Readings/Bibliography

Papers and reviews suggested by the teacher

Laboratory notes

Teaching methods

Frontal lessons and laboratory experiences

Assessment methods

Oral examination

Teaching tools

Board, projector and bioinformatic lab

Office hours

See the website of Marco Candela