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.
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.
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.
