Gut Biology and Health

Gut Biology and Health (2017)

Course title:



ECTS credits


Course parameters

Language: English

Level of course: PhD course

Semester/quarter: ultimo August 2017

Capacity limit: 20 students


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 monogastric animals.

-          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 disease (gut dysbiosis) 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 (e.g. gut epithelium cell lines); 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

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, evening sessions will be organized where 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.


Participants are expected to deliver 134 working hours divided between:

·         Pre-course preparation: literature, own presentation (24h).

·         Residential course: 10 days in August 2017, 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 scientific questions related to gut biology and health.


Name of lecturers:

The course organizers are:

Ole Højberg, Senior scientist, Dept. Animal Science, AU-Foulum, Aarhus University,


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


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



The invited external key lecturers of the course will be:

Prof Mike Baily, Bristol University, Bristol, United Kingdom

Prof Hauke Smidt, Wageningen Agricultural University, Wageningen, The Netherlands

Ass Prof Paolo Trevisi, University of Bologna, Bologna, Italy

Dr Jordi Estelle, INRA, Jouy-en-Josas, France


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 15 June 2017.


Course homepage:


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. (accommodation information will be specified in due time)

The course is organised as a joint event with a training school under the EU Cost Action FA1401 “PigGutNet” (Link).



14-25 August 2017



Residential course will be held at Department Animal Science, Aarhus University, AU-Foulum, Blichers Allé 20, DK-8830 Tjele, Denmark



Open from 1 March to 1 June 2017 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 15 June 2017.