Human Microbiota and Host-Interactions
A.Y. 2025/2026
Learning objectives
The teaching aims to provide a deep knowledge of the microbiota functions, both from the microbiological point of view (bacterial composition and function) and from an immunological perspective (protective role of the microbiota and microbiota-host interaction). The teaching has the objective to broaden and consolidate the knowledge related to:
- role and composition of the main bacterial components of the human microbiota, in particular of the gastro-intestinal tract;
- differences between commensal and pathogenic bacteria in terms of virulence factors and interaction with immune system, with particular reference to foodborne diseases;
- dysbiosis definition and characterization by omics-technologies, and the use of probiotics as therapeutic approach to manipulate dysbiosis.
The learning objectives of the practical laboratory activities are to acquire basic cellular microbiology techniques related to the study of host-bacteria interaction, in order to understand the different interactions between pathogen or commensal bacteria and host immune system, and to acquire the ability to critically analyze the results obtained.
- role and composition of the main bacterial components of the human microbiota, in particular of the gastro-intestinal tract;
- differences between commensal and pathogenic bacteria in terms of virulence factors and interaction with immune system, with particular reference to foodborne diseases;
- dysbiosis definition and characterization by omics-technologies, and the use of probiotics as therapeutic approach to manipulate dysbiosis.
The learning objectives of the practical laboratory activities are to acquire basic cellular microbiology techniques related to the study of host-bacteria interaction, in order to understand the different interactions between pathogen or commensal bacteria and host immune system, and to acquire the ability to critically analyze the results obtained.
Expected learning outcomes
By the end of the course, students will be able to define the differences between commensal bacteria and pathogens, to understand the mechanisms of bacterial pathogenicity and interaction with the immune system. Students will be able to define the human microbiota in terms of composition and function, and describe in depth the different mechanisms of host-microorganism interaction underlying the innate and adaptive immune system. Students will acquire detailed knowledge and understanding of the gut-microbiota dysbiosis and dysbiosis-driven disease processes.
Through the practical laboratory activities students will be able to use basic methods of cellular microbiology and to apply the cultural skills acquired on the host-microorganism interaction mechanisms. By discussing the results obtained during practical laboratory activities students will develop analytical and scientific communication skills.
Through the practical laboratory activities students will be able to use basic methods of cellular microbiology and to apply the cultural skills acquired on the host-microorganism interaction mechanisms. By discussing the results obtained during practical laboratory activities students will develop analytical and scientific communication skills.
Lesson period: Second semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course can be attended as a single course.
Course syllabus and organization
Single session
Responsible
Lesson period
Second semester
Course syllabus
Microbiology of the Human Microbiota: Fundamentals of microbiology with specific reference to human microbial ecology. Classification and taxonomy of bacteria relevant to the human microbiota. Structural and accessory components of the bacterial cell in relation to strategies of colonization, persistence, and interaction with the host. Definition and differentiation of commensals, symbionts, opportunistic organisms, and pathogens.
Foodborne bacterial infections: pathogenicity and virulence factors; bacterial toxins and their mechanisms of action.
The Human Microbiota: Composition and biodiversity of the microbiota across major anatomical sites: intestinal, oral, cutaneous, respiratory, and urogenital. Predominant phyla and classification into enterotypes. Factors influencing microbiota composition: genetic, environmental, dietary, and pharmacological variables.
Functions of the Microbiota and Host Interaction: Metabolic functions (e.g., production of short-chain fatty acids, vitamin synthesis, digestion of complex nutrients). Structural functions and maintenance of epithelial barrier integrity. Protective functions: competitive exclusion of pathogens and production of antimicrobial compounds. Immunomodulatory functions: interaction with components of both the innate and adaptive immune systems.
Interaction Between the Microbiota and the Immune System: Activation of the innate immune system by the microbiota: role of epithelial cells, pattern recognition receptors (PRRs), and the production of antimicrobial peptides. Interaction with macrophages, neutrophils, and dendritic cells: immune tolerance and controlled inflammatory responses. Interaction with the adaptive immune system: modulation of T cell activation (Th17, Treg, Th1 subsets) and B cell responses; antigen presentation in the context of stable microbial colonization. Mechanisms of immune evasion and modulation by pathogens, and strategies used by pathogens to elude the microbiota's protective functions.
Dysbiosis and Its Clinical Implications: Definition of dysbiosis: qualitative and/or quantitative alterations of the microbiota. Clinical conditions associated with intestinal dysbiosis: irritable bowel syndrome (IBS), inflammatory bowel diseases (IBD), celiac disease, type 1 and type 2 diabetes mellitus, obesity, and cardiovascular diseases. Dysbiosis of the respiratory microbiota and chronic inflammatory airway diseases: asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis. Dysbiosis and neurodegenerative disorders: the role of the gut microbiota in multiple sclerosis and Parkinson's disease.
Technologies for the Study of the Microbiota: Metagenomic and metatranscriptomic approaches; Next Generation Sequencing (NGS), 16S rRNA gene sequencing, shotgun metagenomics, RNA-seq. Integration of multi-omic datasets and systems biology methodologies. Elements of bioinformatics: analysis pipelines and major reference databases (e.g., SILVA, Greengenes, KEGG, MG-RAST).
Inter-organ Communication Axes:
Gut-brain axis: interaction between the intestinal microbiota and the central nervous system. Gut-lung axis: influence of the intestinal and respiratory microbiota on pulmonary immune responses.
Therapeutic Interventions Targeting the Microbiota:
Prebiotics, probiotics, postbiotics, and engineered probiotics: definitions, mechanisms of action, and immunological impact. Fecal microbiota transplantation (FMT): rationale, clinical applications, and future perspectives.
Foodborne bacterial infections: pathogenicity and virulence factors; bacterial toxins and their mechanisms of action.
The Human Microbiota: Composition and biodiversity of the microbiota across major anatomical sites: intestinal, oral, cutaneous, respiratory, and urogenital. Predominant phyla and classification into enterotypes. Factors influencing microbiota composition: genetic, environmental, dietary, and pharmacological variables.
Functions of the Microbiota and Host Interaction: Metabolic functions (e.g., production of short-chain fatty acids, vitamin synthesis, digestion of complex nutrients). Structural functions and maintenance of epithelial barrier integrity. Protective functions: competitive exclusion of pathogens and production of antimicrobial compounds. Immunomodulatory functions: interaction with components of both the innate and adaptive immune systems.
Interaction Between the Microbiota and the Immune System: Activation of the innate immune system by the microbiota: role of epithelial cells, pattern recognition receptors (PRRs), and the production of antimicrobial peptides. Interaction with macrophages, neutrophils, and dendritic cells: immune tolerance and controlled inflammatory responses. Interaction with the adaptive immune system: modulation of T cell activation (Th17, Treg, Th1 subsets) and B cell responses; antigen presentation in the context of stable microbial colonization. Mechanisms of immune evasion and modulation by pathogens, and strategies used by pathogens to elude the microbiota's protective functions.
Dysbiosis and Its Clinical Implications: Definition of dysbiosis: qualitative and/or quantitative alterations of the microbiota. Clinical conditions associated with intestinal dysbiosis: irritable bowel syndrome (IBS), inflammatory bowel diseases (IBD), celiac disease, type 1 and type 2 diabetes mellitus, obesity, and cardiovascular diseases. Dysbiosis of the respiratory microbiota and chronic inflammatory airway diseases: asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis. Dysbiosis and neurodegenerative disorders: the role of the gut microbiota in multiple sclerosis and Parkinson's disease.
Technologies for the Study of the Microbiota: Metagenomic and metatranscriptomic approaches; Next Generation Sequencing (NGS), 16S rRNA gene sequencing, shotgun metagenomics, RNA-seq. Integration of multi-omic datasets and systems biology methodologies. Elements of bioinformatics: analysis pipelines and major reference databases (e.g., SILVA, Greengenes, KEGG, MG-RAST).
Inter-organ Communication Axes:
Gut-brain axis: interaction between the intestinal microbiota and the central nervous system. Gut-lung axis: influence of the intestinal and respiratory microbiota on pulmonary immune responses.
Therapeutic Interventions Targeting the Microbiota:
Prebiotics, probiotics, postbiotics, and engineered probiotics: definitions, mechanisms of action, and immunological impact. Fecal microbiota transplantation (FMT): rationale, clinical applications, and future perspectives.
Prerequisites for admission
Basic knowledge of microbiology is required.
Teaching methods
The teaching activities consist of interactive frontal lectures (6 CFU), supported by projected teaching materials. Attendance is strongly recommended, as active participation represents a fundamental prerequisite for the development and consolidation of students' critical thinking, analytical skills, and scientific reasoning.
The teaching material will be made available to the students through the dedicated ARIEL website.
The teaching material will be made available to the students through the dedicated ARIEL website.
Teaching Resources
To support the acquisition and consolidation of foundational knowledge, the following textbooks may be used as general references:
· Microbiologia generale (Prescott)
· Le basi dell'immunologia (Abbas - Lichtman - Pillai)
All teaching materials presented during the lectures will be made available in PDF format on the dedicated Ariel platform. In addition, a selection of scientific articles will be provided to students as supplementary resources for further study and in-depth exploration of the topics covered in class.
· Microbiologia generale (Prescott)
· Le basi dell'immunologia (Abbas - Lichtman - Pillai)
All teaching materials presented during the lectures will be made available in PDF format on the dedicated Ariel platform. In addition, a selection of scientific articles will be provided to students as supplementary resources for further study and in-depth exploration of the topics covered in class.
Assessment methods and Criteria
The acquisition of knowledge and the achievement of the expected learning outcomes will be assessed, for both attending and non-attending students, through an oral and a written test.
The oral examination, which contributes 20% to the final grade, will consist of a PowerPoint presentation and critical discussion of a scientific article, selected from a list provided by the professor, on a topic relevant to the course content. The purpose of the oral presentation is to evaluate the student's ability to understand, synthesize, and communicate complex scientific material in a rigorous and well-structured manner.
The written test, which accounts for 80% of the final grade, will last 90 minutes and will include one open-ended thematic question, three short open-ended questions, and ten multiple-choice questions.
Both components aim to thoroughly assess the student's understanding of the main mechanisms of interaction between the human microbiota and the host, with particular reference to the role of the microbiota in the regulation of immune, metabolic, and inflammatory responses. The questions will be designed to explore the student's ability to integrate knowledge of cellular microbiology and immunology with advanced concepts related to dysbiosis, homeostasis, and the implications of host-microbiota interactions in the development of microbiota-based therapeutic strategies.
The overall evaluation will take into account content accuracy, argumentative clarity, appropriate use of scientific terminology, and mastery of scientific language. The final grade will be expressed on a scale of 30/30. The results of the written exam will be communicated to students via e-mail at the time of registration.
The oral examination, which contributes 20% to the final grade, will consist of a PowerPoint presentation and critical discussion of a scientific article, selected from a list provided by the professor, on a topic relevant to the course content. The purpose of the oral presentation is to evaluate the student's ability to understand, synthesize, and communicate complex scientific material in a rigorous and well-structured manner.
The written test, which accounts for 80% of the final grade, will last 90 minutes and will include one open-ended thematic question, three short open-ended questions, and ten multiple-choice questions.
Both components aim to thoroughly assess the student's understanding of the main mechanisms of interaction between the human microbiota and the host, with particular reference to the role of the microbiota in the regulation of immune, metabolic, and inflammatory responses. The questions will be designed to explore the student's ability to integrate knowledge of cellular microbiology and immunology with advanced concepts related to dysbiosis, homeostasis, and the implications of host-microbiota interactions in the development of microbiota-based therapeutic strategies.
The overall evaluation will take into account content accuracy, argumentative clarity, appropriate use of scientific terminology, and mastery of scientific language. The final grade will be expressed on a scale of 30/30. The results of the written exam will be communicated to students via e-mail at the time of registration.
Professor(s)
Reception:
10am-12pm (by email appointment)
Department of Biosciences (Scientific Buildings) - 1st floor Tower B