SGBK23001U Host-Microbiota Multi-Omics

Volume 2024/2025

MSc Programme in Biology


The study of host-microbiota interactions has become a central element of various disciplines of biological sciences, ranging from human health to evolution. Today, we know that most complex organisms have a microbial community associated with them, which to a larger or lesser degree affects their biological features. The recent development of multi-omic tools (genomics, transcriptomics, proteomics, metabolomics) enables complex interactions between animal and plant hosts and their microbiota to be analysed in great detail. This course will provide students a thorough theoretical and technical understanding of why and how to study host-microbiota interactions using multi-omics.

Through lectures, seminars and exercises, students will learn key concepts such as hologenomics, host-microbiota interactions, and will acquire detailed knowledge on:


  • Biological and genetic properties of hosts (principally animals, including humans), microbes (mainly those in the gut) and their interactions.
    • Laboratory, bioinformatic and statistical techniques for the generation and joint multi-dimensional analysis of the molecular features of both hosts and microbes.
    • Basic and applied contexts for the implementation of host-microbiota multi-omics to address basic biological questions such as the impact of microorganisms in animal evolution, as well as global challenges that range from human health to environmental sustainability.


All this knowledge will equip students with technical skills to analyse multi-omic data, in the context of host-microbiota interactions and beyond.

Learning Outcome

After completion of the course, the students are expected to be able to:



  • Describe the biological and genetic properties of hosts and associated microorganisms.
  • Identify the main host-microbiota interactions that influence host biology.
  • Critically reflect on the hologenome theory of evolution and its implications.
  • Understand the available multi-omic data generation methods and critically assess their relevance under specific scientific contexts.



  • Critically assess primary literature in the field of microbiota and hologenomic research.
  • Manage and organise multi-omic data following Findability, Accessibility, Interoperability, and Reuse (FAIR) of digital assets principles.
  • Code and analysing multi-omic data in R.
  • Present complex biological results to a public audience.
  • Perform statistical analyses on multi-omic datasets.
  • Interpret host-microbiota multi-omic data and results within a biological context.
  • Analyse and visualise results derived from host-microbiota multi-omic data in the R environment.



  • Critically assess primary research and main undergoing scientific discussions in the field of host-microbiota interactions.
  • Select the most appropriate omic layers to address specific scientific questions.
  • Conduct statistical analyses and data visualisations in the R environment.
  • Design and execute a technical project in a team.

Relevant literature will be provided through Absalon including primary scientific publications.

Academic qualifications equivalent to a BSc degree in biology, or similar.
Experience in the R environment is recommended, but not necessary (basic support will be provided).
The course consists of short lectures, seminars, hands-on computational sessions and group exercises. The lectures will be supplemented with discussions in interactive groups. The seminars are based on discussions of scientific papers and involve student presentations of original research papers, lectures by invited guests, and, importantly, discussions between students, guest lecturers and teachers.
  • Category
  • Hours
  • Lectures
  • 29
  • Preparation
  • 116
  • Practical exercises
  • 19
  • Project work
  • 29,5
  • Seminar
  • 12
  • Exam
  • 0,5
  • Total
  • 206,0
Peer feedback (Students give each other feedback)
7,5 ECTS
Type of assessment
Oral examination, 30 minutes
Type of assessment details
The oral examination contributes 100% of the evaluation, but the individual assignment must be passed to be admitted to the oral exam.
Exam registration requirements

To be admitted to the oral exam, students must have delivered all the course exercises, have attended at least 80% of the classes and passed the individual written assignment.

The individual written assignment takes place during the last weeks of the course. Each group of students receives research data and relevant background of the study the data derived from. Students need to analyse the data following the methods learned in the practical exercises. The project work is conducted both during class hours (when direct help from teachers is available) and asynchronously. The individually written assignment in the form of a 1000-2000 character essay, in which the results of research data are interpreted and discussed using the knowledge acquired throughout the course, is handed in approximately 1 week before the individual oral exam.

Without aids
Marking scale
7-point grading scale
Censorship form
No external censorship
Several internal examiners.

Re-submission of the written assignments followed by an oral defence.

Criteria for exam assesment

In order to obtain the grade 12, the student should convincingly and accurately demonstrate the knowledge, skills and competencies described under Learning Outcomes.