Aarhus Universitets segl

Objectives and content

Objectives of the course

The aim of the course is to introduce the students to gastrointestinal ecology (nutrition, immunology, microbiology, host-pathogen interactions, gut-brain axis) and its influence on health and disease in animals, in short ”Gut Biology and Health”.

Learning outcomes and competences

After finalizing the course, the students will be able to:

  • Understand and use fundamental terms and notions related to disciplines like nutrition, immunology, and microbiology in relation to gut biology and health.
  • Understand challenges related to basic sampling and handling of gastrointestinal material (tissue and digesta) from pigs and potentially other monogastric animals.
  • Process and handle pre-generated examples of data from selected laboratory analyses in classical microbiology, molecular microbiology, bioinformatics, and immunology.
  • Analyse, evaluate and discuss the data sets, and put the obtained results into an applied context focusing on gastrointestinal health and disease (e.g., dysbiosis) of animals.

Compulsory programme

Active participation in the residential course incl. oral presentation of own field of work (PhD project). A final written report is required for completion of the course.


The course will be a 10-day intensive workshop with a series of interactive seminars and theoretical exercises related to aspects of gut biology and health of farm animals, where teaching, and scientific seminars will be given by the organizers as well as by a number of national (DK) and international lecturers.

The course aims at introducing the participants to relevant disciplines (i.e., immunology, nutrition, and microbiology), as well as state-of-the-art analytical methods (e.g., molecular microbiota analysis, flow cytometry and in vitro cell culturing).

The seminars will thus be covering topics within a) gut microbiology; b) gut immunology; c) livestock nutrition (including early life) and health; d) feeding strategies; e) alternatives to antibiotics and zinc); f) animals as models for human studies; g) analytical tools for studying gut microbiology and immunology.

The exercises will introduce e.g., sampling and handling of gut tissue and digesta, selected laboratory analyses, and processing of pre-generated data sets.


Participants are expected to deliver 128 working hours divided between:

  • Pre-course preparation: literature, own presentation (24h).
  • Residential course: 8 days in June/July 2022, including lectures, exercises, participant presentations and group work (80h).
  • Written report after finalizing residential course (24h)

Before arrival at the venue, the participating students are expected to have made themselves familiar with a number of papers, textbook chapters and reviews focusing on gut biology and health; the organizers will provide a literature list. The participants should further prepare a short presentation (approx. 5 min) of their own field of work (PhD project) and put it into the frame of the course syllabus.

At the residential course, the students will process data for writing a report on the exercises and the addressed techniques/methodologies. The report should be submitted for evaluation no longer than 2 weeks after the end of the residential course. The exact curriculum will be adjusted from year to year, based on an updated publication list as well as on suggestions from the invited lecturers.



This course targets PhD students and post docs within veterinary, production animal, agricultural and health sciences, working with scientific questions related to gut biology and health.