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Gut biology and health 2022

ECTS credits



Course parameters

Language: English

Level of course: PhD course

Time of year: June/July 2022

No. of contact hours/hours in total incl. preparation, reporting, etc.: 80h/128h

Capacity limit: Approx. 20 participants


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 the disciplines nutrition, immunology and microbiology in relation to gut biology and health.
  • Perform 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.

Course contents

The course will be a 10 days intensive workshop, covering exercises (practical sampling and handling of gut tissue and digesta, theoretical introduction to a series of laboratory analyses and processing of pre-generated data sets) and a series of interactive seminars/lectures related to aspects of gut biology and health of farm animals. 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 cultures).

The exercises covers:

Sampling and handling of gut tissue and digesta from pigs and poultry (hands-on). Theoretical introduction to a range of analyses and methodologies like: a) isolation and growth of gut bacteria and archaea; b) physiological and molecular characterization of gut bacteria; c) analysis of microbial metabolites (e.g. short-chain fatty acids, gaseous compounds); d) genotypic characterization of the gut microbiota; e) in vitro systems for studying gut biology; f) isolation and characterization of immune cells (e.g phenotyping and functional assessment by flow cytometry); g) quantification of immunoglobulins by ELISA; h) identification of markers of inflammation e.g. cytokines; i) characterization of gut morphology.

Introduction, teaching and scientific seminars will be given by the organizers as well as by a number of national (DK) and international lecturers. The seminars will be covering topics like: 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.



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 (max. 10 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.

Course organizers

  • Ole Højberg, Senior Researcher, Dept. Animal Science, AU-Foulum, Aarhus University
    e-mail: ole.hojberg@anis.au.dk

External key lecturer list (preliminary)

  • Prof Mick Baily, Bristol University, Bristol, United Kingdom
  • Prof Chris Stokes, Bristol University, Bristol, United Kingdom
  • Prof Thomas Thymann, University of Copenhagen,
  • Dr Prof Jürgen Zentek, Frei Universität Berlin, Germany
  • Dr Peader Lawlor, Teagasc, Ireland

Type of course/teaching methods: see course content


Original literature in the form of primary and review papers from international journals and textbooks. A literature list will be made available well in advance of the course.


Course homepage


Course assessment

Participation in residential course as well as an accepted written report


The course is provided by the research section Health, Department of Animal Science, Aarhus University, in collaboration with the Graduate School (GSTS) at the Faculty of Technical Sciences.

Special comments

Course participants have to pay direct costs for their own travel and accommodation. Rooms will be pre-booked by the organizers at a hostel in the city of Viborg, approx. 15 km from the institute (run by public busses)

Course participants will be charged a fee to cover consumables etc. (to be specified)

Approx. half of the available seats will be allocated to PhD students from the Innovative Training Network (ITN) ‘MonoGutHealth’ (link), funded by the European Commission under the Horizon 2020 Marie Skłodowska-Curie Action. This will strengthen the international aspect of ‘Gut Biology and Health’ and is in line with previous versions of the course, where more than half of the participants have been international PhD students e.g. from partners in the EU Cost Action F1401 “PiGutNet” (link).


27 June – 8 July 2022


The residential course will be held at AU-Foulum, Dept. Animal Science, Blichers Allé 20, DK-8830 Tjele, Denmark


Open from 1 February 2022 to 1 April 2022 via e-mail to Charlotte Kahlen Steffensen (cks@anis.au.dk), including a brief application with title and start year of PhD project, scientific keywords, proposed title of participant presentation, address and contact information.

All applicants will receive information regarding participation no later than 15 April 2022.

21856 / i43