- Docente: Marco Candela
- Credits: 6
- SSD: CHIM/11
- Language: English
- Teaching Mode: Traditional lectures
- Campus: Bologna
- Corso: First cycle degree programme (L) in Genomics (cod. 9211)
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 15th 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
SDGs
This teaching activity contributes to the achievement of the Sustainable Development Goals of the UN 2030 Agenda.