You know sometimes you use a working title for something for long enough that it becomes the title? Like “Snakes on a Plane”. That’s what happened in this case, we also meant to come up with a name for this class… never did and so the official name at the registrar is “Koala Poop”. Awesome.
So last Spring quarter Ashley Vater and I teamed up to teach a “Swabs to Genomes” class here at UC Davis. Our summary of the class, with course materials, can be found here at microBEnet. The big problems with that class were the cost and difficulty of genome sequencing in only 10 weeks. So this time, Ashley, Katie Dahlhausen and I decided to try a version that focused more on the microbiology, without genome sequencing. We also took ideas from a similar class taught by Cameron Thrash at LSU.
The background for this project is Katie’s PhD work which focuses on the koala gut microbiome. Her crowdfunded research project is looking how koalas (which require bacteria to break down tannins in their limited diet) respond to antibiotic treatment (for rampant Chlamydia infections). In this class, the students are attempting to isolate ~100 bacterial strains from koala feces under several combinations of conditions; anaerobic/aerobic, RT/37C, tannin positive/negative, BHI versus LB versus CBA media. They will isolate the bugs, extract DNA, perform 16S Sanger PCR, identify the bugs (including making phylogenetic trees), and then screen these isolates for resistance to 10 common antibiotics (including the two actually used with koalas).
As with the last class, we are requiring the students to blog here on microBEnet as part of the class, although this time we’re adding a “peer review” component to the process which will delay the posts a bit. Those blogs will be found on a dedicated page here, and at the end of the quarter I’ll post a summary of the class, along with the results and all the class materials.