NBIK16000U  The Human Microbiome - Experiments

Volume 2016/2017

MSc Programme in Biology
MSc Programme in Biochemistry


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. 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.

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 principles behind next generation DNA sequencing
  • 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 principles of quality control of raw data from Illumina-based sequencing
  • describe the key steps involved in bioinformatic analysis of next generation sequencing data from the human microbiome


  • perform DNA extraction from complex microbiome samples
  • perform 16S RNA amplification
  • prepare DNA samples for Illumina-based sequencing
  • perform basic bioinformatic analysis on microbiome data from16S RNA gene sequencing
  • 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

Scientific papers. See Absalon.

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. In weeks six and seven, students will prepare an individual report based on data obtained during the practicals.
The course is part of the qualification profile 'Microbiology'.
7,5 ECTS
Type of assessment
Oral examination, 25 minutes
The exam is an individual oral examination without preparation. 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.

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

To participate in the exam the student must perform a satisfactory presentation of a scientific paper, participate actively in the discussions of the papers, and hand in a report, which have to be passed.

Only certain aids allowed

Students can bring their own notes.

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

As ordinary exam.

If the requirements of the performing of a satisfactory presentation of a scientific paper is not fulfilled, the student must hand in a two page essay presenting a relevant scientific paper no later than two weeks before the registration period for the reeexams ends. If the requirements of handing in a passed report is not fulfilled, the student must hand in a new report, which have to be passed, no later than two weeks before the registration period for the reexams ends.

Criteria for exam assesment

The grade 12 is given for an excellent performance displaying a high level of command of all aspects of the relevant material, cf. the Learning Outcome of the course, with no or only a few minor weaknesses.

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