HMI-20306 Microbiomes and Health


Credits 6.00

Teaching methodContact hours
Group work10
Course coordinator(s)dr. ir. HH Kranenbarg-Stolte
Lecturer(s)dr. ir. P van Baarlen
dr. A Lammers
dr. VCJ de Boer
dr. ir. HH Kranenbarg-Stolte
Examiner(s)prof. dr. J Wells

Language of instruction:



This course is aimed at teaching students the fundamentals of microbiome function, emphasising the major contributions of the collective of commensal bacteria (the microbiota) to host physiology and health. The course will provide an overview of the main terminology and concepts, will outline how gut microbes break down the food, harvest energy from breakdown products and make nutrients available to host, how microbiota "train" the host immune system from newborn to adult and influence host behaviour via the gut-brain axis. It will explain the concepts of (co-)infections, disease complexes and emerging diseases. The course will also describe the microbial origins of antibiotics and outline how microbiota-encoded antimicrobial resistance (AMR) has contributed to the current problems in resistance and global call for a One-Health approach to tackle AMR. Lastly, the course will handle current methodologies to study microbiomes including metagenomics and other -omics technologies, modelling, culturing, and application of sequencing in infectious disease and AMR diagnostics.

Learning outcomes:

After successful completion of this course students are expected to be able to:
- apply the main concepts and terminology used to describe microbiome functionality;
- understand the diverse ways by which microbiota contribute to host metabolism and health;
- apply laboratory techniques to identify and characterise host-associated microbes and antibiotic resistance;
- design and present testable hypotheses how a microbe(s) could impact on host health;
- demonstrate understanding of the approaches used to study microbiomes.


Lectures; a practical featuring culturing host-associated microbes and assessing antibiotic resistance; group work concluded with symposium examining diverse aspects of microbiota functionality.


A written examination on the contents of reader and lectures, consisting of short open answer questions (65%). Individual practical report (20%). Presentation of the group work (15%) (mark per group). Completion of practical and group work is obligatory to pass the course; the minimum pass mark is 5.5. The minimum pass mark for the entire course is 5.5. Results from practicals and tutorials are valid for three academic years following the academic year in which the results were attained.


A reader covering the background to the lectures and a handbook to the practical will be provided. Lectures and associated materials will be made available in Brightspace.

Compulsory for: BASAnimal SciencesBScB: Biological Functioning of Animals5MO