Molecular Microbiology

Course content

Molecular Microbiology is a discipline that combines genetics, physiology, biochemistry, molecular biology and cytology with microbiology. These fields have undergone dramatic, in some cases almost explosive, developments during the last decade. In particular, the genetics of microorganisms has become very efficient with rapid methods of gene mutation and replacement and rapid whole genome sequencing; biochemistry has been revolutionized by methods for rapid protein purification and crystallization and high-throughput protein-protein interaction methods whereas cytology has been revolutionized by the introduction of fluorescent protein tags and a number of high-end methods to visualize the fluorescently tagged proteins within living cells. Last but not least, the genomics era has spawned a genuine revolution in microbiology, transforming it into an exact discipline. There are now more than 8,000 fully sequenced and annotated prokaryotic genomes available. Making use of this vast biological information it is now possible to classify prokaryotes numerically and thereby chose model systems of general importance.   

The present course in Molecular Microbiology is held by researchers belonging to the Centre for Bacterial Stress Response and Persistence that was generated by funding from the Danish National Research Foundation, the Novo Nordisk Foundation and the European Research Foundation. It is our aim with the course to give a broad overview of rapidly developing and exciting topics in Molecular Microbiology, with an emphasis on molecular mechanisms underlying bacterial stress physiology and survival. Each lecture will give an overview of a separate topic as described below. These topics will then be discussed in depth via recent research articles presented by the students and the teachers. Finally, in the laboratory part, relevant cutting edge techniques will be used to investigate research problems that we currently study. This comprehensive course will thus provide a strong platform for those students who wish to pursue or already are pursuing a research career in Molecular Microbiology and related fields.           

The theoretical part (lectures and colloquia) will contain an in-depth discussion of the following topics:

  • Basic bacterial physiology analysed with cutting edge technologies such as microarrays, deep RNA sequencing and ribosome profiling. The connection between growth rate, ribosome synthesis and translation
  • How bacteria under stress uses intracellular second messengers (ppGpp and cyclic-di-GMP) to reprogram their physiology
  • How bacteria under stress reprogram their transcription patterns using alternative RNA polymerase sigma factors
  • Molecular mechanisms underlying bacterial survival during stationary phase
  • Heterogeneity (stochasticity) in bacterial populations: sporulation, competence and persistence
  • Molecular mechanisms underlying bacterial persistence
  • How bacterial toxin – antitoxins contribute to survival during stress
  • Bacterial cell division and DNA segregation. Presentation of high-end cytological methods to study cell division in bacterial model organisms
  • Bacterial cell wall synthesis and its control
  • The coupling between stress response and cell wall synthesis

The practical part (lab exercises):

The practical part of the course will consist of a two-week lab course. During that time the students will be introduced to different techniques within the field of molecular microbiology. The lab exercises will include the following techniques:

  • Basic methods for propagation of bacteria in the laboratory
  • Purification of RNA and DNA (plasmid, genomic)
  • Analysis of gene expression by Norther hybridization
  • Using reporter genes to analyze gene expression
  • Construction and screening of gene libraries to identify regulatory genes
  • DNA sequencing and sequence analysis
  • Regulation of gene expression by the CRISPR/Cas9 system
  • In vitro analysis of DNA-protein interactions by electrophoretic mobility shift assay
  • In vivo analysis of protein-protein interactions using a two-hybrid system

BSc Programme in Biochemistry
BSc Programme in Biology
BSc Programme in Molecular Biomedicine

Learning outcome


  • Ability to describing and understanding genetics of model organisms
  • Understanding how whole genome sequences forwards rapid genetic analysis
  • Understanding how phylogeny and genomics allow for the design of projects aiming at answering important questions of general biological significance 
  • Describing and understanding how the use of fluorescent proteins has transformed cell biology
  • Describing and understanding cell division and DNA segregation in bacteria
  • Describing and understanding the biology and function of bacterial cell walls
  • Describing and understanding the transcription machinery in bacteria
  • Understanding and describing the translation machinery in bacteria.


  • Evaluate the stringent response in relation to bacterial physiology and pathogenesis
  • Know how to use phylogeny and genomics to design projects aiming at answering important questions of general microbiological significance 
  • Know how to use fluorescent reporter fusion proteins to obtain knowledge about the cellular dynamics of particular proteins.


  • Be able to read, understand and present cutting edge literature in the field of molecular microbiology
  • Be able to use standard phylogenetic analyses and web based databases to understand the biological importance of specific genes, proteins and metabolites.

Lectures, colloquia and lab exercises.

See Absalon.

Curriculum in 1. and 2. year courses are considered known.

Type of assessment
Written examination, 4 hours under invigilation
All aids allowed
Marking scale
7-point grading scale
Censorship form
External censorship
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
  • 20
  • Colloquia
  • 20
  • Practical exercises
  • 90
  • Exam
  • 4
  • Preparation
  • 278
  • English
  • 412