HMI-50806 Commensal and Pathogen Host-Microbe Interactions in the Intestine


Credits 6.00

Teaching methodContact hours
Independent study
Course coordinator(s)prof. dr. M Kleerebezem
Lecturer(s)prof. dr. M Kleerebezem
prof. dr. J Wells
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/Stage HMI.


The course aims to teach students the concepts involved in the science of host microbe interactomics 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 will be explained in the lecture series. The technologies that will be explained 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 latter technologies will include a demonstration (one afternoon) of the high-throughput high content microscopy set-up). During the case studies small groups of students work on a provided specific research question, and this should lead to research proposals that address the question posed.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- reproduce the relevant differences of the model systems employed in the field of host-microbe interactions;
- choose the appropriate model system to address questions related to the molecular interactions between the host and the intestinal microbiota;
- describe the technological approaches employed in these models to decipher the mechanisms of host-microbe and host-pathogen interactions;
- select and explain the appropriate technological approaches to address host microbe interactomics questions in research models;
- assess the scientific evidence underlying the mechanisms of molecular cross-talk between intestinal microbes, mucosal pathogens/pathobionts and the host;
- practice independent reading and interpretation of papers in this field;
- define 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. One or two of the lecture blocks (2 hours) will employ a debate set-up to stimulate discussions among the students related to the topics of the course. One topic that will be addressed in such a debate concerns probiotics, and the issues surrounding their beneficial effects on health. Another topic for debate relates to the issue of the cause and effect relationship between microbiota differences and the health effects they are associated with.
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 can be handled to deduce knowledge about biological pathways and processes. Several datasets will be collected and will be assigned to groups of students; 2-4 students per group depending on the total number of students registered for the course. The practical course is planned to run for two weeks for 2 hours per day (total time investment 20 hours) that are linked to the lectures and will be finalized by a presentation. The computer practical course is scheduled in the first half of the course.
The literature case studies are aimed at teaching students critically assess research publications in this field and will address (1) research background, (2) experimental approach (models and tools), (3) study results and discussion and relevance for the topic of the study. Selected publications will be assigned to groups of students; 2-4 students per group depending on the total amount of students registered for the course. The literature case study is planned to run for two weeks, and will be largely based on self-study, with blocks of contact hours with the supervisors of the course and will be finalized by a presentation. The literature case study is scheduled in the second half of the course.


- written examination (40%);
- computer practical presentation and discussion (30%);
- literature case study Presentation and Discussion (30%).
Students should score at least a 5.0 for each part of the examination to pass the exam.


Reader 'Commensal and pathogen host-microbe interactions in the intestine' + selected literature.