C9520 - BIOTECNOLOGIE MICROBICHE PER L'OTTENIMENTO DI METABOLITI SECONDARI

Learning outcomes

Students will acquire advanced knowledge of the biosynthetic mechanisms underlying the production of secondary metabolites, integrated with an understanding of fermentation processes and the enzymatic complexes responsible for the synthesis of bioactive secondary metabolites. By the end of the course, students will have acquired a solid understanding of industrial fermentation processes, with particular emphasis on microbial growth kinetics and the biosynthetic mechanisms of secondary metabolites; knowledge of environmental microbiomes and their potential as sources of Biosynthetic Gene Clusters (BGCs) encoding the enzymatic complexes responsible for the production of bioactive secondary metabolites; knowledge of biodiscovery strategies for the investigation of microbiomes and the identification of novel biosynthetic gene clusters; and familiarity with the fundamental principles of synthetic biology and heterologous expression, with particular emphasis on the design of gene expression systems in microbial hosts, using either isolated microbial strains or gene sequences recovered from environmental metagenomes.

Course contents

The course covers the principles of microbial biotechnology for the discovery and production of secondary metabolites, moving from the fundamentals of microbial physiology and industrial fermentation processes to the most recent biodiscovery approaches based on microbiomes, metagenomics, and synthetic biology. Following an introduction to microbial growth kinetics, metabolic regulation, and fermentation processes, the course examines the molecular mechanisms underlying secondary metabolite biosynthesis, with particular emphasis on the organization and function of Biosynthetic Gene Clusters (BGCs). Students will explore microbiome bioprospecting strategies based on culturomics, next-generation sequencing (NGS), genome and metagenome mining for the identification of novel BGCs and bioactive metabolites. The course also introduces the principles of synthetic biology and the heterologous expression of biosynthetic gene clusters, supported by case studies on biodiscovery from extreme environments and the human microbiome. Finally, concepts of microbiome engineering and the rational design of synthetic microbial communities will be presented as emerging approaches for the development of innovative biotechnological processes.

Readings/Bibliography

• Brock Biology of Microorganisms. 16th Edition. Michael M. Madigan, Kelly S. Bender, Daniel Buckley, W. Matthew Sattley, David A. Stahl Pearson
• Synthetic Biology - A Primer. Revised Edition. Geoff Baldwin, Travis Bayer, Richard Dickinson, Tom Ellis, Paul S. Freemont, Richard I. Kitney, Karen Polizzi, Guy-Bart Stan. World Scientific Publishing Company.
• Introduction to Bioinformatics. Fifth Edition. Arthur Lesk. Oxford University Press
• Metagenomics. 1st Edition Perspectives, Methods, and Applications Muniyandi Nagarajan Academic Press Inc.(London) Ltd
• R in Action. Third Edition. Robert I. Kabacoff. Manning Publications
  
• Fermentation Microbiology and Biotechnology. Fourth Edition. E. M. T. El-Mansi, Jens Nielsen, David Mousdale, Ross P. Carlson. CRC Press
• Industrial Microbiology, an introduction. Michael J. Waites, Neil L. Morgan, John S. Rockey and Gary Higton. Blackwell Science.
• Lecture notes and selected scientific papers provided by the instructor during the course.

Teaching methods

Lectures

Assessment methods

The final assessment consists of an oral examination aimed at evaluating the student's acquisition of the theoretical knowledge covered in the course and their ability to integrate and critically discuss the different topics addressed.

Teaching tools

Lecture slides, selected scientific papers, case studies from the literature, bioinformatics databases and demonstration software for the analysis of genomes, metagenomes and Biosynthetic Gene Clusters.

Office hours

See the website of Simone Rampelli