METHODS FOR ANALYSIS OF ENVIRONMENTAL MICROBIAL COMMUNITIES

Teachers: 
Credits: 
3
Site: 
PARMA
Year of erogation: 
2021/2022
Unit Coordinator: 
Disciplinary Sector: 
General Microbiology
Semester: 
First semester
Year of study: 
3
Language of instruction: 

Italian

Learning outcomes of the course unit

The aim of the course is to give the student a certain familiarity with the most modern methods of analysis of microbial communities to enable him to read, in a critical way, scientific articles on the subject and to give him the tools to evaluate, through these analyzes, the impact that various external factors (pollution, climatic variations, anthropogenic activities of various kinds, etc.) can have on environmental processes in which microorganisms play a fundamental role.

Course contents summary

The course aims to provide a multidisciplinary approach (genomic, ecological and bioinformatics) to the study of biodiversity and the analysis of microbial communities. At the end of the course the student will have acquired the basic knowledge concerning the study of microbial ecosystems. In particular, the student will be able to: know the main cultivation and molecular techniques for the identification of microorganisms, the methods of phylogenetic analysis, the principles of applied omics technologies, the description of microbial communities as well as the methods for the study of their activities functional.

Course contents

Structure of a microbial community, biodiversity indices of microbial communities, microorganism-microorganism and microorganism-host interactions.
Traditional methods of analysis based on cultivation in pure culture: isolation and identification of microbial species by biochemical, physiological and serological methods.
Molecular methods applied to microorganisms isolated in pure culture: PCR, analysis by agarose gel electrophoresis, real-time PCR, genetic fingerprinting: RAPD, ERIC, PFGE analysis. Fluorescent in situ hybridization (FISH, CARD-FISH). Microarrays. Flow Cytometer.
DNA sequencers and development of technology, sequencing of marker sequences, sequencing of the entire bacterial genome.
Application of molecular techniques to the study of microbial communities, without cultivation of microorganisms (metagenomics): isolation of environmental DNA.
High-throughput sequencing techniques and their application to the study of microbial communities: 16S-rRNA gene microbial profiling, shotgun metagenomics for taxonomic and functional analyzes through the use of different databases. Nanopore long-reads sequencing and field applications.

Recommended readings

The teaching material will be provided by the teacher. Reference will be made to the most up-to-date scientific literature.

Teaching methods

The course will include theoretical lessons and practical exercises through which the teacher will illustrate some types of in silico analysis of DNA sequences, searches in databases, creation of phylogenetic trees, analysis of bacterial genomes, analysis of metagenomic results etc. so that the student becomes familiar with the basic tools that are normally used in this type of research. Some of the most common molecular techniques described in the theoretical part will be illustrated through videos and practical activities in the classroom (environmental DNA extraction, PCR, digestion with restriction enzymes, agarose gel electrophoresis) together with bioinformatics analysis and subsequent post-processing and visualization of the results via Office package.

Assessment methods and criteria

The exam will be conducted through an oral interview in which students' knowledge of the contents on the entire program explained and presented in class will be verified. The exam will verify the level of competence reached by the student and the autonomy of judgment.