PhD Courses in Denmark

Objectives of the course:
The aim of the course is to introduce participants to the fundamentals of rumen microbial ecology, the interactions between rumen microorganisms and their host and their relevance to sustainable livestock production. Thus, the course will cover the biological roles and functions of rumen microbes (bacteria, archaea, protozoa and virus) and relate these to ruminant nutrition, physiology, and production performance, as well as GHG emissions and the environmental footprint of animal production.

The course will further provide an introduction to experimental approaches used to study rumen microbial ecology, including experimental design, standardised sample collection and handling, and selected analytical approaches. Practical laboratory exercises, as well as a visit to the animal facilities, will complement the seminars. Participants will also work with pre-processed microbiome and metabolome example datasets  to explore selected standard bioinformatic analyses, focusing on an understanding of their underlying principles and the interpretation and discussion of results rather than on hands-on training in complete bioinformatic data-analysis workflows.  

Learning outcomes and competences:
At the end of the course, the participants should be able to:

• Describe and explain fundamental concepts and processes in rumen microbial ecology, including the biological roles and functions of major groups of rumen microorganisms and their interactions with the host.
• Relate rumen microbial processes to ruminant nutrition, physiology, and production performance, and discuss their contribution to GHG emissions in livestock production.
• Describe and discuss key considerations and challenges related to basic sampling and handling of rumen material from cattle for studies of rumen microbial ecology.
• Explain and evaluate how methodological choices can influence the observations and conclusions obtained in studies of rumen microbial communities and functions.
• Perform and assess the quality and validity of basic experimental measurements used in rumen microbial research, including microbial quantification and culturing and in vitro fermentation measurements.
• Process and handle example data sets from selected laboratory analyses in classical microbiology and molecular microbiology.
• Explain the principles of selected standard bioinformatic approaches used to analyse rumen microbiome (and metabolome) data and use these principles to interpret and discuss results, without requiring proficiency in bioinformatic workflows.
• Evaluate and discuss  experimental results and put the obtained findings into an applied context focusing on rumen ecology and functional processes, particularly in relation to nutrition and mitigation of the climatic impact of farming. 

Course parameters:
Language: English
Level of course: PhD course
Time of year: 12-23rd January 2027
No. of contact hours/hours in total incl. preparation, assignment(s) or the like: 80/128h
Capacity limits: min 10 participants, max 24 participants
Course fee: No course fee however a charge of 150€ to cover consumables.

Compulsory programme:
Participants will be required to give a short introductory presentation of their projects during the course, actively participate in the residential course and complete a written report at the end of the course. Report should not exceed 3-4 pages and must be submitted within 3 weeks of the completion of the course. 

Course contents:
The course will be a 10-day intensive workshop with a series of interactive seminars and theoretical exercises related to aspects of rumen ecology of ruminants, where teaching, and scientific seminars will be given by the organizers as well as by a number of local/internal (AU) and external (DK and international) lecturers. 

One of the aims of the course will be for those without classical microbiology training to understand current concepts of rumen microbiology. For students with a microbiological background, we aim to put rumen microbial research into context with environmental and nutritional drivers and production demands, encouraging cross-disciplinary thinking and reducing siloed perspectives.

The course will introduce the participants to relevant disciplines (i.e., rumen microbial ecology, physiology of rumen microbes and environmental and nutritional drivers), as well as state-of-the-art analytical methods (e.g., molecular microbiota analysis, bacterial cultivation, and rumen in vitro systems). 

The seminars will address selected topics within the following areas: a) fundamentals of rumen physiology including nitrogen metabolism b) experimental design, c) sampling methodologies, d) rumen microbial ecology, e) microbiome sequencing technologies and microbiome data analysis, f) Rumen microbiome in relation to feed efficiency, hydrogen utilization, animal genetics, feeding strategies and metabolomics, g) physiology of rumen microbes, and h) analytical tools for studying rumen microbiology

The exercises will introduce participants to sampling and handling of rumen digesta, in vitro rumen fermentation, bacterial quantification and identification and the analysis of pre-processed example data sets

Prerequisites:
This is an introductory course to rumen microbial ecology suitable for early-stage microbiology PhD students or non-microbiologists.

This course targets PhD students and post docs within animal nutrition, production animal, agricultural and animal genetics, working with scientific questions related to rumen biology and environment.

Name of course organizers and lecturers(tentative):
Samantha Joan Noel (org). Associate Prof., Dept. Animal and Veterinary Sciences (ANIVET), AU, Viborg
e-mail: samantha.noel@anivet.au.dk

Anna A. Schönherz (org). Associate Prof., Dept. Animal and Veterinary Sciences (ANIVET), AU, Viborg
e-mail: anna.schonherz@anivet.au.dk

Ole Højberg (org), Senior Researcher, Dept. Animal and Veterinary Sciences (ANIVET), AU Viborg 
e-mail: ole.hojberg@anivet.au.dk 

Mogens Larsen (Lecturer) Senior Researcher, Dept. Animal and Veterinary Sciences (ANIVET), AU Viborg
e-mail: mogens.larsen@anivet.au.dk

Type of course/teaching methods:
A 2-week (10 days) physical attendance course with seminars and practical exercises

Literature:
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:
https://anivet.au.dk/uddannelse/rumen-microbial-ecology#c1196810

Course assessment:
Participation in residential course (min 90% attendance) as well as an accepted written report

Special comments on this course:
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 (served by public busses)

We can offer travel scholarships to support up to 10 course participants to attend the course, including 6 for international students and 4 for domestic students. The scholarship will be a fixed sum of 9800 Dkr/1310 eur for international applicants and 5800 Dkr/775 eur for domestic applicants that live more than 2 hours away. The travel scholarship can be used towards flights, accommodation and internal travel costs. Travel scholarships can be applied for when applying for the course and grantees will be notified when the participant list is sent out. Priority being given to RUMEN Gateway network partners. The number of international and domestic scholarships can be altered within the budget allowance depending on the number and requirements of the applicants.

Participants will need to look up their own visa requirements, however most visitors will be able to enter on a free 3-month visitor visa.

Time:
January 12th-23rd 2027

Place:
The residential course will be held at AU-Viborg, Dept. Animal and Veterinary Sciences, Blichers Allé 20, DK-8830 Tjele, Denmark

Course fee:
The course is offered free of charge but participants cover their own travel and accommodation costs.
Course participants will however be charged a fee of 150 €to cover consumables. 

Registration:
Registration is open from 1st Sept 2026 to 16th Nov 2026 via e-mail to Emma Bonde Stanek (ebs@anivet.au.dk). All applicants will receive information regarding participation no later than 1st Dec 2026.

General registration must include a brief application with title and start year of PhD project, proposed title of participant presentation, address, and contact information. In addition, if a travel scholarship is sought, clearly indicate this in the request and include a paragraph on the relevance of the PhD course to your research and whether you or your institute is affiliated with the rumen gateway network.