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

General arguments: (i) main goals of a metagenome study applied to the microbiome sciences; (ii) techniques and technologies for the metagenomes assessment, including bioinformatic and biostatistics; (iii) microbiome centrality for life, environmental microbiomes and host associated ones, eco and co-evolutionary trajectories; (iv) importance of microbiomes for the human biology, microbiome modernization and personalized medicine; (v) metagenomics of ancient DNA, applications in paleo-archeo microbiology and bioprospecting; (iv) innovation and perspectives in microbiome biotechnology and synthetic biology, applications in circular economy

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, de novo con construction of metagenomic species and genome scale metabolic models;
4. biostatistics: multivariate statistics, exploratory ordination, clustering, canonical correlation, discriminatory methods and machine learning, analysis of variance, permutation, networks construction and topology;
5. Ecological rules and dominant dynamics of microbial communities
6. The human microbiome, role in the human biology, co-evolutionary trajectory, modernization and personalized medicine
7. Earth microbiomes, ecological centrality, environmental and animal microbiomes, roles in the planted biology and connections with global changes
8. Paleometagenomics, from paleobioprospecting to paleoclimatic records and long term co-evolution
9. Microbiome biotechnology, microbiome-based applications for a more sustainable food production, set up of microbiome based bioprocess and bioconversions for side stream valorization in circular economy

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