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.           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 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)

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

Readings/Bibliography

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

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