Week 2: Analyzing our DNA Sequences

This is my final week at the Advanced Bacterial Genetics course at Cold Spring Harbor Lab. During the first two weeks we created mutants with desired phenotypes, such as targocil resistance or bacteriophage plaque formation. Once we created our mutants, we prepared the DNA for sequencing and sent it off to a sequencing center. This week we got back most of our sequences and we started our analysis. Without the sequences we can only see phenotypic changes, but now we can actually figure out what specific changes in certain genes created that phenotype.

One of our experiments involved changing a gene in a bacteriophage. Bacteriophages are viruses that infect and often kill bacteria. The bacteriophage we were interested in, ICP1, specifically infects V. cholera, and it can often be found in stool samples of patients with cholera. We were interested in changes genes in ICP to access how that affected the ability to infect V. cholera. Understanding how bacteriophages function could have eventually have a positive clinical impact. Although we generally think of infection as a bad thing, it could be possible to use viruses to kill the harmful bacteria in our body. Bacteriophages could be used in complement with antibiotics. There is also some interest at HSS in using bacteriophages on orthopaedic implants to help prevent infection.

We also got to sequence unknown bacteria that we collected from the environment. This was perhaps the most fun and open-ended experiment we did. My course mates chose bacteria from a variety of sources such as old coffee grounds, seawater, a rusty pipe, and a rotten strawberry. I went down to the beach and collected some seawater and sediment. When we received our sequences back, the first thing we did was to check the 16s ribosomal RNA. The 16s ribosomal RNA works as a kind of genetic barcode. A portion of the 16s ribosomal RNA is highly conserved, so this portion can be easily recognized. There is also a region of the 16s ribosomal RNA that undergoes rapid changes, so that section can be used to differentiate bacterial species from each other. My 16s ribosomal RNA identified my bacterium as vibrio, but the exact species wasn’t clear. I am now working on an in-silico DNA-DNA hybridization to compare the genome of my unknown bacteria to the genome of known species. The results aren’t back yet, but I may have discovered a new species of bacteria! Although this experiment was mostly meant to be exploratory, some of our findings could have public health implications. One course mate found a known human pathogen in the seawater.

Overall, this course has made me feel so much more comfortable with microbiology. At times it overwhelming, but it was always helpful. I am so excited to bring what I have learned to HSS next week!