I am in the process of teaching a course on “DNA sequence based studies of microbial diversity” and I thought it would be of use to some people to post about it. So here goes. I have made a landing page for the course and for slides and such material here.
This course is being offered this quarter at UC Davis via the Evolution and Ecology department (my home department). And I will be posting slides and recordings of class there as well. The course is summarized in Lecture 1 where I provide an outline of the course.
Slides I used in Class 1 are available via Slideshare.
The general outline for the course is to cover what I consider to be the four eras of DNA sequence based studies of microbial diversity:
- Era 1: The Tree of Life
- Era 2: rRNA Surveys from Environments
- Era 3: Genome Sequencing
- Era 4: Metagenomics
The main approach I take in the course is reading and discussing key papers on
- The pioneering work of each “Era”
- The scope of what is possible in the era
- Case studies of specific ecosystems or recent papers
I also have one lecture on DNA sequencing methods.
In the 1st class I basically cover and outline of where we are going and also do a brief “background” discussion on phylogenetic trees. There is a paper that I use to cover the scope of Lecture 1, though it is not ideal:
Eisen JA (2007) Environmental Shotgun Sequencing: Its Potential and Challenges for Studying the Hidden World of Microbes. PLoS Biol 5(3): e82. doi:10.1371/journal.pbio.0050082
Anyway – will be posting more about each “lecture”.