NBIK16000U CHANGED: The Human Microbiome - Experiments
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. 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.
CHANGED FOR THE STUDY YEAR 2018/19
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
- 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
Scientific papers. See Absalon.
It is recommended that the student has passed the course "NBIK15016U The Human Microbiome" or equivalent.
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.
- 7,5 ECTS
- Type of assessment
- Oral examination, 25 minutesThe 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 weights 100% of the grade.
- Exam registration requirements
To participate in the exam the student must hand in a 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
The same as the ordinary exam.
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 re-exam.
Criteria for exam assesment
In order to obtain the grade 12 the student should convincingly and accurately demonstrate the knowledge, skills and competences described under Learning Outcome.
- Practical exercises
- Project work