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MICR 336: Applied and Environmental Microbiology

Second Semester - 18 points

Course prescription

Microbial technologies, including production and purification of recombinant proteins in microbes, immune technologies, bioremediation and microbial biodegradation networks. Commercialisation of biotechnology products.

Course overview

cloverMost microbes are not pathogens, rather their diversity has been exploited for a range of beneficial purposes, with much of modern biotechnology studying and exploiting the ability of microbes to grow rapidly and to high levels in fermenters, to be manipulated genetically for the production of recombinant proteins, to be used in the environment for practices such as bioremediation and as technological stepping stones in discovery research. 

This course in Microbial Biotechnology focuses upon the growth, manipulation and use of microbes for beneficial purposes. In particular you will:

  1. develop your own commercialisable biotechnology idea
  2. investigate the use of recombinant bacteria and viruses for discovery, production of, and use as biotechnology products
  3. be aware of the molecular systems and technologies associated with the use of microbial metabolic pathways for bioremediation.

This course is for students interested in the use of molecular microbiology for the production of beneficial products and applications. It ranges from large-scale fermentation to recombinant protein expression and purification, to concepts underlying the commercialisation of biotechnology.

Lecture course overview

The MICR 336 lecture series typically includes lectures on: 

  • the commercialisation of biotechnology 
  • bioreactors for microbial fermentation
  • recombinant proteins and protein complexes from microorganisms
  • student team presentations on a biotechnology idea
  • the applications of bacteriophage biotechnology
  • bioremediation and biosensors.

Lab course overview

The MICR 336 lab classes will expose you to the use of molecular biology in biotechnology. In particular, during the 4-week lab course you will set up a gene for protein expression, express the protein in Escherichia coli and then purify the protein using a recombinant peptide tag built into the construct during cloning. You will also design your own process to isolate, express and purify a recombinant protein.


  1. Commercialization case study report (25%)
  2. Lab assessment (10%)
  3. Final written exam (65%)

Course prerequisites

MICR 221



Mondays and Wednesdays 1-1.50pm


Weeks 32-34, 36, Tuesdays 2-6pm, all day Wednesdays


There is no required text for this course but you will be directed to relevant scientific papers during lectures and you may like to read Molecular Biotechnology: Principles and applications of recombinant DNA by B.R. Glick and J.J. Pasternak, 2003 (3rd Edition), ASM Press, which is held in the Science Library.

Teaching staff

For more information

View the details of this paper on the University of Otago website

Students are encouraged to contact staff by email to make arrangements for a time to discuss course-related matters.

For more information on this course, please contact Dr Sergio Morales.