HMI-30306 Commensal and Pathogen Host-Microbe Interactions in the Intestine


Credits 6.00

Teaching methodContact hours
Independent study8
Course coordinator(s)prof. dr. M Kleerebezem
Lecturer(s)prof. dr. J Wells
prof. dr. M Kleerebezem
dr. ir. P van Baarlen
Examiner(s)prof. dr. M Kleerebezem

Language of instruction:


Assumed knowledge on:

Cell Biology, Human and animal physiology, Practical Biological Chemistry.

Continuation courses:

Thesis/Minor/Internship HMI.


The course aims to teach students the concepts involved in research on host microbe interactions rather than a detailed technological training in the field, which may be taught in follow-up MSc-thesis studies.
The intestinal tract is colonized with a highly diverse and dense microbial population, and intestinal host microbe interactions play a prominent role in host-health and disease. Over the past years this field has expanded dramatically, and starts to decipher the molecular basis of these interactions and their importance in the determination of specific aspects of the host’s physiology, including metabolism, immunity, and behaviour. It is the aim of the course on ‘commensal and pathobiont host-microbe interactions in the intestine’ to understand the model systems and technological approaches applied in this field.
The model systems, including several (germ-free) animal and human volunteer models, and their use is explained in the lecture series. The technologies presented in the lectures encompass both the holistic, ‘omics based approaches as well as the mechanistic, cell-based approaches that employ molecular markers and reporters in combination with imaging. The computer practical employs public and in house datasets and software modules to analyse them, aiming for hands-on experience in data analysis and extraction of biological understanding. During the case studies small groups of students work on a provided specific health and disease question, analyse the state-of-the-art (literature and public information sources), and present their findings in a plenary session at the end of the course.

Learning outcomes:

After successful completion of this course students are expected to be able to:

- describe and explain the differences in animal model systems employed in host-microbe interaction research;
- select the appropriate model systems to investigate specific questions on molecular interactions between the host and the intestinal microbiota;
- comprehend and apply data-mining approaches to decipher the mechanisms of host-microbe and host-pathogen interactions;
- describe, explain and select the appropriate technological approaches to investigate host microbe interactions in research models;
- interpret and judge the reliability of results obtained in experiments in the field of host-microbe interactions;
- evaluate and criticize the scientific evidence underlying the mechanisms of molecular cross-talk between intestinal microbes, mucosal pathogens/pathobionts and the host;
- independently read and evaluate scientific papers in this field;
- design concise research proposals to address specific questions in this scientific area.


15 blocks of lectures (2 lecture hours per block); Computer Practical; Literature Case studies.
The 30 lecture hours will provide an overview of the field of host microbe interactions in relation to health and disease. Several of the lecture blocks (2 hours) will include student group activities, to stimulate discussions among the students related to the topics of the course. One of the topics that addressed in such activity relates to mechanistic research and clinical trial design with probiotics. Another topic that is discussed is the design of research to resolve cause and effect relationships between microbiota differences and health effects.
The computer practical course aims to provide a flavor of the actual work involved in the post-genomic analysis of datasets obtained from various host-microbe and diet studies. It will show the students how large datasets are handled to deduce knowledge about biological pathways and processes. Students work in groups of 2 to 3, and investigate specific datasets using state-of-the-art software suits using a practical guide that also contains questions that have to be answered and handed-in. The computer practical course runs in the first two weeks of the course (total time investment 20 hours).
The topical case studies aim to teach students (independent group work in groups of 4-5 students) to investigate the role of the microbiota in a selected disease. Students will critically assess research publications related to their subject, using guiding questions that address (1) disease aetiology and prevalence, (2) host genetic predisposition, (3) involvement of the microbiome and/or diet, (4) mechanistic understanding of the role of the microbiota, and (5) are asked to define the next steps in the research on this subject. The case study runs in the second part of the course and is largely based on self-study, with short feed-back meetings with the supervisors, and will be completed by a (poster) presentation session.


- written examination (40 %);

- computer practical Q&A assignments (30 %);

- case study presentation and discussion (30 %).

Students should score at least a 5.5 for each part of the examination to pass the exam.


Selected scientific literature, and course lecture materials.

Restricted Optional for: MBIBiologyMScC: Spec. C - Health and Disease5AF