MICROBIOLOGY

This course is granted to non-biological students to learn about microbiology and microbiology applications. Although relatively simple and primitive, microorganisms are considered the most successful life form. They are practically everywhere and are indispensable for life on Earth. Microorganisms deeply affect the world in which we live: they are essential for maintaining the balance of every ecosystem, living in symbiosis with plants and animals, essential for the fermentation of food, play an important role in various industrial applications, for the purification of water and environmental bioremediation. Some of them are pathogenic and therefore novice and dangerous for plants, animals and humans. For these reasons it becomes important to study them and to know their cellular, molecular and metabolic mechanisms. During the course, new discoveries in microbiology and microbial mechanisms used in biotechnology and nanotechnology applications will be investigated.

The main objective of the course is to provide students with the concepts for understanding the structural and functional and molecular mechanism inside the microbial world, as well as their main biotechnological and nanotechnological applications that impact the human society and environment. At the end of the course, students will be able to:
-Understand the fundamental concepts of microbiology and the importance of microorganisms;
-Describe the metabolic diversity of prokaryotes and how these organisms obtain energy, electrons and carbon from the environment;
-Describe the molecular biology mechanisms of microorganisms
-Discuss the main options for the control of microbial growth in vitro and in vivo;
- Have a good understanding of common and advanced procedures in microbiology laboratories, including bacterial isolation and purification and bacterial identification based on biochemical and molecular tools
-Evaluate potential benefits and harm caused by microorganisms;
-Knowledge of microbial tools for new application in biotechnology and nanotechnology
-Present and discuss scientific data retaining and applying the specialized language of microbiology

No prerequisites are required for this course, but it is recommended that students have a basic understanding of organic chemistry and biochemistry

1. MICROBIAL CELLULAR AND MOLECULAR BIOLOGY
a. Importance to study microorganism. Cell structure: prokaryotes vs eukaryotes; bacterial morphology; the cytoplasmic membrane: structure and functions; bacterial wall: Gram + and Gram- structure, peptidoglycan and LPS; cell wall synthesis and cell division.
b. Surface cell structures: capsules and mucous layers, fimbriae and pili. Cell inclusions; gas vesicles; endospores: structure and sporulation cycle.
c. Microbial locomotion: Flagella and motility; gliding motility; microbial taxes: chemotaxis, phototaxis.
d. Microbial DNA, replication, transcription and bacterial translation; mutations; gene transfer in bacteria; gene recombination; transformation; transduction; conjugation; transposons; CRISPR

2. DIVERSITY OF MICROBIAL METABOLISM. Macro and micro nutrients; cellular transport; energy classification of microorganisms; principles of bioenergetics;
Catabolism. glycolysis and fermentation; respiration: citric acid and glyoxylate cycles, electron carriers; electron transport and proton motive force.
Anabolism: polysaccharide biosynthesis and gluconeogenesis; amino acids-nucleotides, lipids.
Autotrophy: Calvin cycle and other CO2 fixation pathways; phototrophy; nitrogen fixation; Hydrogen oxidation; iron and sulfur oxidation; nitrification; nitrate reduction and denitrification; sulfur reduction; 1-carbon metabolism; acetogenesis and methanogenesis, fermentations.

3. MICROBIAL GROWTH. Nutrients; classical microbiology: cultivation techniques and microbial count; binary division and microbial growth cycle; continuous culture; environmental effects on microbial growth: temperature, pH, osmotic pressure and oxygen; controlling microbial growth: heat, chemical and physical agents; antibiotic resistance.

4. SOCIAL BACTERIAL BEVIOURS. Stage of biofilm formation; different type of biofilm; the biofilm matrix; the matrix as a communal external digestion system; heterogeneity in biofilm; bacterial social interactions; bacterial cooperation and competition; tolerance and resistance to, antimicrobials; biofilm adhesion on surfaces; biofilm

5. HUMAN MICROBIOME. Microbiome composition; diversity of human microbiotas; the central rule of gut microbiome; microbiome-host coevolution; microbiome in health and diseases; gut microbiome-host axis; microbiome intervention

6. BACTERIAL COMMUNICATION. Quorum sensing; type of quorum sensing systems; cell to cell communication; intra and inter bacterial communication

7. MICROBIAL ADVANCED TECHNIQUES. FISH, Flow cytometry, 16S rRNA sequencing, shotgun metagenomics, single cell sequencing, Ecological parameters

8. BACTERIAL INGENEERING. Biofuels production, microbial fuel cells, materials design by synthetic biology; bottom-up approaches for single cell and microbial community

9. Journal club: students will present research articles in microbiology field related to new discovery in human microbiome, single-cell sequencing, outer membrane vesicles, engineering biofuels, synthetic bacterial cells, bioremediation

Madigan M.T., Bender K.S., Buckley D.A., Sattley W.M, Stahl D.A. Brock, Biology of Microorganisms, 16th Edition. ISBN-13: 9781292404790.

Research Articles and Research Reviews are provided by the Professor.

The exam will be divided of tree parts. The first part will consist to present a research article on new discoveries of microbiology. The second part will include the evaluation of the activities carried out during the laboratory sessions and will assess the student's understanding of what was covered during these sessions through a written test with the possibility of multiple-choice questions and/or open questions. The last part will consist of an oral test that will evaluate all the topics covered during the course.

The teaching will be organized in lectures that will cover different aspects of microbiology. The lectures will be supported by laboratory sessions that will help illustrate the practical concepts. The lessons will be interactive, and students will be encouraged to discuss their observations and points of view on the theoretical and practical concepts of the course. The journal club sessions will do during the course on topics addressed during the lessons to help the students to improve their skills in microbial and science communication. The laboratory exercises will consist of real experiments and will provide students with the opportunity to gain practical experience on the concepts illustrated during the lectures.

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