Gut biology and health (2015)

Course name:

Gut biology and health

ECTS credits


Course parameters

Language: English

Level of course: PhD course

Semester/quarter: ultimo August 2015

Capacity limits: 20

Expected students from ANIS: 8

Objectives of the course

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

Learning outcomes and competences

After finalizing the course, the students will:

  • Understand and use fundamental terms and notions of the disciplines nutrition, immunology and microbiology in relation to gut biology and health.
  • Sample and handle gastrointestinal samples (tissue and digesta) from pigs and potentially other monogastrics.
  • Perform selected laboratory analyses in classical microbiology, molecular biology and immunology.
  • Analyse, evaluate and discuss the obtained data, and put the obtained results into an applied context focusing on gastrointestinal health and dysbiosis/disease of animals.


Compulsory programme

Active participation in residential course Monday-Friday (for two weeks) incl. presentation of own project. The final part of the course constitutes a written report.

Course contents

The present course will be a 10 days intensive workshop covering experimental exercises (including a pig trial related to gastrointestinal disease), seminars and round-table discussions related to aspects of gut biology and health of farm animals and humans. 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 techniques, flow cytometry and in vitro use of cell lines).

The experimental part includes a number of exercises covering:

Techniques for sampling and handling of porcine or rodent gut samples. Laboratory analyses: i) Isolation and growth of gut bacteria; ii) Physiological and molecular characterization of selected gut bacteria; iii) Analysis of microbial metabolites (short-chain fatty acids, gaseous compounds); iv) Genotypic characterization of the gut microbiota; v) In vitro systems for studying gut biology (gut epithelium cell lines and PIOC); vi) Isolation and characterization of immune cells (including phenotyping by flow cytometry); vii) ELISA.

Handling and statistical treatment of obtained data will be performed throughout the course period and in defined sessions supervised by the organizers, in order for the students to prepare the written reports (to be finalized in the post-course period)

Introduction, teaching and scientific seminars will be given by the organizers as well as invited national and international lecturers. This will be done in morning and afternoon sessions fitting into the practical work and covering topics like: i) Gut microbiology; ii) Gut immunology; iii) Nutrition (including early life) and health; iv) Feeding strategies; v) Alternatives to in-feed antibiotic growth promoters (AGP); vi) Aspects of bacterial antibiotic resistance; vii) Animals as models for human studies; viii) Analytical tools for studying gut microbiology and immunology.

During the course, one/two evening session(s) will be allocated in which each participant should give an oral presentation of her/his own field of work, and put it into the frame of the course syllabus.

Scientific and social event: A one-day excursion.

Before arrival at the venue, the participating students are expected to have read a number of papers, text book chapters and reviews focusing on gut biology and health; a literature list will be provided by the organizers (see below). The participants should further prepare a short presentation (approx. 10 min) of their own field of work. At the residential course, the students will sample and handle data for writing a report on the practical exercises and the involved techniques. The report should be submitted for evaluation no longer than 6 weeks after the end of the residential course. The exact curriculum will be adjusted from year to year, based on new publications as well as on suggestions from the invited lecturers. The expected work of the participants in order to read the curriculum is not less than 16h.


Participants are expected to deliver 134 working hours divided between:

  • Pre-course preparation: literature, own presentation (24h).
  • Residential course: 10 days in August 2015, including lectures, exercises participant presentations and group work (86h).
  • Written report after finalizing residential course (24h)


This course targets PhD students and post docs within veterinary-, agricultural- and health sciences working with animals, including animal model studies, experimentation, in zoo and animal parks, and with scientific questions related to pain biology.

Name of lecturers:

The course organizers are:

Ole Højberg, Senior scientist, Department of Animal Science, AU-Foulum, Aarhus University,


Tina Dalgaard, Academic staff, Department of Animal Science, AU-Foulum, Aarhus University,


Charlotte Lauridsen, Head of Research Section, Department of Animal Science, AU-Foulum, Aarhus University,


The invited external key lecturers of the course are:

Professor Christopher Stokes, Bristol University, Bristol, United Kingdom

Professor Wei-Yun Zhu, Nanjing Agricultural University, Nanjing, China

Type of course/teaching methods: see course content


Original literature in the form of reviews and papers from international journals and textbooks. A list of relevant reading material will be provided shortly after 1 July 2015.

Course homepage:

To be established

Course assessment:

Participation in residential course plus a written report


The course is provided by the Department of Animal Science, Aarhus University

Special comments on this course:

Course participants have to pay direct costs for accommodation, etc. (to be specified)

Course participants will be charged a fee (150€) to cover lab consumables etc.

The course will be organized as a joint event with a training school under the EU Food and Agriculture COST Action (FA1401): ‘European network on the factors affecting the gastro-intestinal microbial balance and the impact on the health status of pigs (PiGutNet)’.


17 - 28 August 2015


Residential course to be held at AU-Foulum, Department of Animal Science, Blichers Allé 20, DK-8830 Tjele, Denmark


Open from 1 March to 1 June 2015 via e-mail to, including form with title and start year of PhD project, scientific keywords, proposed title of participant presentation, animal species, address and contact information. Information regarding granted application is given to all by 1 July 2015.

Comments on content: 
Revised 16.05.2017