The Hallam Lab

Investigating microbial communities…


MICB 425 Microbial Ecological Genomics: From Genomes to Biomes, 2013

Rationale and Intended Users:

It is important to understand the genetic basis for microbial biodiversity, how it arose and continues to evolve. To do this, one must also understand the experimental logic, explanatory power, and the limitations of methods and approaches used in the study of microbial biodiversity. This course is intended for any student with sufficient genetic and biochemical background interested in understanding the nature, extent and importance of Earth’s unseen majority. It will inform basic and applied science students in majors as varied as genetics, microbiology, medicine, forestry, earth and oceans, engineering and computer science.

Course Description: This course explores the intrinsic and extrinsic forces driving genome evolution within the bacterial and archaeal domains of life. Content areas include barriers and gateways to horizontal gene transfer, microbial species concepts and community genome structure, function and dynamics, and the ecological and biotechnological impacts of microbial genome diversity. Drawing on primary scientific literature, the course emphasizes a problem solving approach using current experimental methods and design such as high throughput sequencing and screening methods, discovery and application of plasmids, phage and other mobile genetic elements.

Overall Learning Objectives: By the end of the course, students will be able to
  • Comment on the ecological and biogeochemical roles played by microbial communities now and through the deep expanse of evolutionary time.
  • Evaluate different methods for studying the taxonomic and functional diversity of microbial communities.
  • Explain interconnections between microdiversity, genomic diversity and metabolic potential and their relationship to microbial species concepts.
  • Discuss the roles of mobile elements in the generation of genomic diversity, microbial adaptation and response, and the development of new tools for gene discovery and genetic engineering.
  • Use statistical and computational approaches to describe microbial community structure along environmental gradients or in response to perturbation
Download the syllabus

Look at all microbiology courses on the UBC Microbiology and Immunology website

Teaching Philosophy

“Go to the people. Learn from them. Live with them. Love them. Start with what they know. Build with what they have. But the best of leaders when the job is done, when the task is accomplished, the people will all say we have done it ourselves.” Lao Tzu, 604 B.C.

I believe in a constructivist approach to learning in which the student is given the opportunity to develop his or her own knowledge based on prior and current experience. It is essential to recognize the personal nature of the educational journey, and I appreciate that each student comes to learning with his or her own individual gifts and style. At the same time, it is my responsibility as an educator to bring the solitary learner into a collaborative partnership, in which both students and teacher share, creating a flow and exchange of ideas. In this partnership, by providing an environment rich in possibility, I facilitate the acquisition of knowledge and nourish the life of the mind. In the context of new experience, I am there to give input and encouragement, offering direction when needed, and celebrating small steps as enthusiastically as giant strides. Accepting my responsibility for careful preparation and thorough grasp of subject matter, I expect that students will make a serious commitment to the learning process and accept responsibility for their academic success. I firmly believe that the role of the educator is not one of implantation, but evocation. It is my job to evoke from students that which is known but unsaid, to draw forth from wonder an articulate voice.