Learning objectives

The course aims to provide PhD students with a comprehensive and integrated overview of metabarcoding as a tool for microbiome research. Through an approach that combines theoretical, methodological, and applied aspects, the course will guide students from experimental design to the critical interpretation of results.
In particular, the course will explore the principles underlying metabarcoding and best practices for microbiome sampling, preservation, and analysis, highlighting the main sources of bias that may influence results. The course will then introduce and discuss the major bioinformatic approaches for metabarcoding data analysis, addressing challenges related to data management, normalization, and interpretation, while fostering the development of critical skills in the use of statistical and bioinformatic tools. A further component will focus on the role of taxonomy and nomenclature as key elements linking molecular sequences to microorganisms in natural environments, illustrating the use of specialized resources for the verification and updating of taxonomic names.

Prerequisites and basic notions

General Microbiology.

Program

Part 1 – Introduction to metabarcoding and microbiome studies
- Fundamental concepts of metagenomics and metabarcoding
- Molecular markers and their selection (16S, 18S, ITS, COI, etc.)
- Experimental design and best practices for sampling
- Sample preservation and DNA extraction
- Technical and biological sources of bias throughout the workflow
- Introduction to microbiome studies across different natural environments
Part 2 – Bioinformatic analysis of metabarcoding data
- Overview of analysis pipelines (QIIME2, mothur, DADA2, etc.)
- OTUs vs ASVs: principles, advantages, and limitations
- Sequence filtering, denoising, and quality control
- Taxonomic assignment methods and reference databases
- Diversity analysis:
- Alpha diversity
- Beta diversity
-Data normalization and statistical challenges
-Ecological interpretation of results
Part 3 – Taxonomy, nomenclature, and discovery of new taxa
- Name lists as a link between molecular sequences and microorganisms
- Principles of microbial taxonomy and nomenclature
- Tools for taxonomic name validation:
- LPSN and other resources for prokaryotes and microbial eukaryotes
- Identifying novel taxa in microbiome datasets
- From sequence data to the formal description of new species

Bibliography

Didactic methods

lecture

Learning assessment procedures

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Assessment

Discussion with students

Criteria for the composition of the final grade

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Sustainable Development Goals - SDGs

This initiative contributes to the achievement of the Sustainable Development Goals of the UN Agenda 2030. More information on sustainability