The Human Microbiome - Experiments

Course content

In this course the students will study their own microbiome and hence get hands on experience with all steps involved in studying the human microbiome. Humans harbour ten times more bacterial cells than human cells. Different parts of the human body are inhabited by specific microbial communities forming the human microbiome. Within recent years it has become clear that the human microbiome interacts extensively with their human host and is important for human health.

This course will give students a thorough understanding of and hands on experience with the experimental approaches, molecular methods, and bioinformatic analysis used to study microbial communities in and on humans. This includes: DNA extractions from complex microbiome samples, PCR amplification of the 16S RNA gene and other phylogenetic marker genes, and all other steps needed to prepare samples for next generation DNA sequencing. The bioinformatic analysis from initial quality filtering to final biological analysis of obtained data is a substantial part of the course. Students will be introduced to the basic principles of next generation DNA sequencing and finally get hands on experience with the bioinformatic analysis from initial quality filtering, OTU binning and final biological analysis of obtained data. Students will obtain detailed knowledge on the different microorganisms shaping the microbiome of key human habitats and the methods used to study them.


MSc Programme in Biochemistry
MSc Programme in Biology

Learning outcome

By the end of the course students are expected to be able to master:


  • describe the main steps involved in DNA extraction from complex microbiome samples
  • describe the pros and cons of using 16S RNA gene amplicon sequencing approaches
  • describe the pros and cons of using a shot gun DNA sequencing approach
  • describe the key steps involved in bioinformatic analysis of next generation sequencing data from the human microbiome
  • describe principles of quantitative analyses of human microbiome sequence data
  • describe methods to compare microbiome samples


  • perform DNA extraction from complex microbiome samples
  • prepare DNA samples for Illumina-based sequencing
  • perform basic bioinformatic analysis on microbiome data from16S RNA gene sequencing
  • perform basic statistical data analyses in R
  • present orally and in writing key aspects of different experimental approaches to study the human microbiome and its effects on human health
  • propose studies for investigating the human microbiome and its interactions with the human host


  • evaluate the molecular methods used to investigate the human microbiome
  • evaluate the basic bioinformatic methods used to investigate the human microbiome
  • independently retrieve and evaluate information from the primary scientific literature
  • discuss original scientific articles and reviews on the human microbiome
  • present a coherent essay on a specific topic on the human microbiome

In general, two hours of lectures and seven hours of laboratory practicals per week for the first five weeks. The lectures will introduce the overall approaches currently used to study the human microbiome. The practicals will include introductions to experimental methods followed by hands on laboratory experiments studying the microbiome of the students followed by relevant bioinformatic analyses. It should be emphasized that data handling and bioinformatic analyses takes up approx. 50% of the course time. In weeks six and seven, students will prepare an individual report based on data obtained during the practicals.

Scientific papers. See Absalon.

It is recommended that the student has passed the course "NBIK15016U The Human Microbiome" or equivalent.

Academic qualifications equivalent to a BSc degree is recommended.

Continuous feedback during the course of the semester
Feedback by final exam (In addition to the grade)
Peer feedback (Students give each other feedback)
7,5 ECTS
Type of assessment
Oral examination, 60 minutes without preparation time
Type of assessment details
The exam is a group (max. 4 students in a group) oral examination without preparation time. It consists of two parts: The first part of the exam is a discussion of the submitted report and the second part consists of questions based on the Learning Outcome of the course. For the first part the students will be expected to individually present relevant parts of the report and answer the following questions. The second part of the exam will be a group discussion where all group members are expected to participate. Based on the two parts the students will be individually evaluated and graded.

The oral examination weighs 100% of the grade.
Exam registration requirements

To participate in the exam the student must hand in a group report, which have to be passed before the exam.

Only certain aids allowed

Students can bring their own notes.

Marking scale
7-point grading scale
Censorship form
No external censorship
Several internal examiners

Oral examination, 30 minutes without preparation time.

The re-exam consists of two parts: The first part of the exam is a discussion of the submitted report and the second part consists of questions based on the Learning Outcome of the course. Based on the two parts the students will be evaluated and graded. 

If the requirements of handing in a passed group report is not fulfilled, the student must hand in a new individual report, which have to be passed, no later than three weeks before the re-exam.

Criteria for exam assessment

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

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 10
  • Preparation
  • 120,5
  • Practical exercises
  • 35
  • Project work
  • 40
  • Exam
  • 0,5
  • English
  • 206,0


Course number
7,5 ECTS
Programme level
Full Degree Master

1 block

Block 4
The number of places might be reduced if you register in the late-registration period (BSc and MSc) or as a credit or single subject student.
Study Board for the Biological Area
Contracting department
  • Department of Biology
Contracting faculty
  • Faculty of Science
Course Coordinators
  • Søren Johannes Sørensen   (3-8279824f71787e3d7a843d737a)
  • Joseph Nesme   (12-73787c6e797137776e7c766e496b727837747e376d74)

Anders Priemé, Dennis Sandris Nielsen, and guests from hospitals and research institutions.

Saved on the 14-02-2024

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