Microbial Quality and Safety in Food and Ecology of Human Microbiota

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. Elements of predictive microbiology. Definition and organization of Microbial Challenge Test.
Unit 2: Ecology of the human microbiota
Principles of ecology. The classification of living organisms and the taxonomy. The concept of bacterial species. The concept of holobiont. Next generation DNA sequencing technologies and their application in the study of microbial ecosystems: the 16S rRNA gene profiling and the shotgun metagenomics. Alpha- and beta-diversity. The microbiota associated with the human body: stability (concepts of perturbation, resistance, resilience, ecosystem service and dysbiosis). Biogeography of bacterial ecosystems in the human body: the cutaneous, vaginal, oral and intestinal microbiota. The dependence of the intestinal microbiota on dietary carbohydrates. The intestinal microbiota and obesity. The effect of antibiotics on the intestinal microbiota. Breast milk and bifidobacteria. Fecal microbiota transplantation. The reactions catalyzed by intestinal microbes on food-borne molecules: the case of melamine. The harmful activities of the intestinal microbiota. Relationship between diet-microbiota-human health: analysis of 7 case studies: [i] high-fat diet and liver cancer. The immune system. The hygiene hypothesis. [ii] high-salt diet and hypertension. [iii] dietary fiber and protection from intestinal polyps; refined inulin and liver cancer. [iv] carnitine/choline and atherosclerosis. [v] artificial sweeteners and glucose intolerance. [vi] food emulsifiers and the promotion of colitis and metabolic syndrome. [vii] milk fats and intestinal inflammation.