Microbial Quality and Safety in Food and Ecology of Human Microbiota
A.Y. 2025/2026
Learning objectives
Knowledge of the main molecular tools used to study the human microbiota. Knowledge of the microbial ecology principles. Knowledge of human oral microbiota. Knowledge of human microbiota-associated antibiotic-resistances.
Understanding of the microbiological risk factors present in food products. Guarantee of the microbiological safety and hygienic quality of food production chains. Knowledge of the current legislation and how control systems are structured.
Understanding of the microbiological risk factors present in food products. Guarantee of the microbiological safety and hygienic quality of food production chains. Knowledge of the current legislation and how control systems are structured.
Expected learning outcomes
At the end of the course the student will know the virulence factors related to foodborne pathologies, learn about the hygiene management regulations in food systems, estimate the survival / growth of a microorganism in a food. Furthermore, he/she will be able to prevent, control and manage the presence / activity of microorganisms (pathogens, hygiene indicators, alterative, pro-technological) in food systems and will have useful skills in the critical analysis of the functional role of the human microbiota and its interactions with the individual, will be able to critically analyze the role of the microbiota in mediating the effects of diet on human health.
Lesson period: First semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course cannot be attended as a single course. Please check our list of single courses to find the ones available for enrolment.
Course syllabus and organization
Single session
Responsible
Lesson period
First semester
Course syllabus
Unit 1: Microbiological quality and safety in food systems
Functional classification of microorganisms. Elements of parasitology: helminth infestations, protozoan food infections. Bacterial infections: Campylobacter, entero-pathogenic Escherichia coli, Listeria monocytogenes, Salmonella, Yersinia enterocolitica. Foodborne virus infections: Norovirus, HAV and HEV viruses. Food TSEs: vCJD. "sensu stricto" food-borne diseases: Bacillus cereus, Clostridium perfringens. Bacterial food poisoning: neurotoxins from Clostridium botulinum, enterotoxins from Staphylococcus aureus. Fungal food poisoning: mycotoxins. Guarantee of safety in food production and distribution: Good Hygienic Practices (GHP). European legislation on food safety: the Hazard Analysis Critical Control Point system, Risk Analysis, Traceability, Food safety objectives. Definition and meaning of microbiological limit. Design and structure of a sampling plan. Food safety criteria, process hygiene criteria. Markers of hygiene in food production: fecal indicators, markers of shelf-life. Spoilage bacteria, spoilage eumicetes (yeasts and molds). Pro-technological microorganisms: microbial cultures in food technologies. Natural mixed cultures and selected strain for microbial starters.
Unit 2: Ecology of the human microbiota
Principles of ecology. The classification of living organisms and taxonomy. The concept of bacterial species. The concept of holobiont. New nucleic acid sequencing technologies and their application in the study of microbial ecosystems: 16S rRNA gene profiling and shotgun metagenomics. Alpha- and beta-diversity. Human-associated microbiomes: stability (concepts of perturbation, resistance, resilience, ecosystem service, and dysbiosis). Biogeography of bacterial ecosystems in the human body: the cutaneous, vaginal, oral, airway, and intestinal microbiomes. The dependence of the intestinal microbiota on dietary carbohydrates. The relationship between diet, microbiota, and human health. Concepts of precision medicine. The intestinal microbiome and metabolic syndrome. The evolution of the human microbiome through different life stages. Fecal microbiota transplantation. Probiotics, postbiotics and prebiotics: how they can modulate the intestinal microbiota and their effects on humans. The effect of antibiotics on the intestinal microbiota. Fermented products and host health. The gut-organ axes.
Functional classification of microorganisms. Elements of parasitology: helminth infestations, protozoan food infections. Bacterial infections: Campylobacter, entero-pathogenic Escherichia coli, Listeria monocytogenes, Salmonella, Yersinia enterocolitica. Foodborne virus infections: Norovirus, HAV and HEV viruses. Food TSEs: vCJD. "sensu stricto" food-borne diseases: Bacillus cereus, Clostridium perfringens. Bacterial food poisoning: neurotoxins from Clostridium botulinum, enterotoxins from Staphylococcus aureus. Fungal food poisoning: mycotoxins. Guarantee of safety in food production and distribution: Good Hygienic Practices (GHP). European legislation on food safety: the Hazard Analysis Critical Control Point system, Risk Analysis, Traceability, Food safety objectives. Definition and meaning of microbiological limit. Design and structure of a sampling plan. Food safety criteria, process hygiene criteria. Markers of hygiene in food production: fecal indicators, markers of shelf-life. Spoilage bacteria, spoilage eumicetes (yeasts and molds). Pro-technological microorganisms: microbial cultures in food technologies. Natural mixed cultures and selected strain for microbial starters.
Unit 2: Ecology of the human microbiota
Principles of ecology. The classification of living organisms and taxonomy. The concept of bacterial species. The concept of holobiont. New nucleic acid sequencing technologies and their application in the study of microbial ecosystems: 16S rRNA gene profiling and shotgun metagenomics. Alpha- and beta-diversity. Human-associated microbiomes: stability (concepts of perturbation, resistance, resilience, ecosystem service, and dysbiosis). Biogeography of bacterial ecosystems in the human body: the cutaneous, vaginal, oral, airway, and intestinal microbiomes. The dependence of the intestinal microbiota on dietary carbohydrates. The relationship between diet, microbiota, and human health. Concepts of precision medicine. The intestinal microbiome and metabolic syndrome. The evolution of the human microbiome through different life stages. Fecal microbiota transplantation. Probiotics, postbiotics and prebiotics: how they can modulate the intestinal microbiota and their effects on humans. The effect of antibiotics on the intestinal microbiota. Fermented products and host health. The gut-organ axes.
Prerequisites for admission
Basic knowledge of microbiology and food microbiology.
Teaching methods
Teaching is provided through class lectures.
Teaching Resources
The teaching material consists of lesson slides, EU regulations, scientific articles provided by the teachers, available on the myARIEL platform.
Assessment methods and Criteria
Type of exam: written test with open-ended questions within a defined time limit; actual duration of 60 minutes. The exam is the same for all the teaching units that make up the course. Registration for the exam through the UNIMIA (formerly SIFA) service is mandatory.
Evaluation criteria: demonstration of knowledge acquisition; ability to organize knowledge discursively; correct use of specialist terminology.
Grading: score out of thirty.
Students with learning disabilities (DSA) and disabilities are requested to contact the instructor via email at least 10 days before the scheduled exam date to arrange any individualized measures. In the email addressed to the instructor, it is necessary to CC the respective University Services: serviziodsa@unimi.it (for students with learning disabilities) and ufficiodisabili@unimi.it (for students with disabilities).
Evaluation criteria: demonstration of knowledge acquisition; ability to organize knowledge discursively; correct use of specialist terminology.
Grading: score out of thirty.
Students with learning disabilities (DSA) and disabilities are requested to contact the instructor via email at least 10 days before the scheduled exam date to arrange any individualized measures. In the email addressed to the instructor, it is necessary to CC the respective University Services: serviziodsa@unimi.it (for students with learning disabilities) and ufficiodisabili@unimi.it (for students with disabilities).
AGR/16 - AGRICULTURAL MICROBIOLOGY - University credits: 7
Lessons: 56 hours
Professors:
Foschino Roberto Carmine, Gargari Giorgio
Professor(s)
Reception:
On appointment
Room 3006, via L. Vanvitelli n.32, 3rd floor