In a previous post, I noted that I was currently working on identifying some environmental isolates I took from various locations. When I got my 16S sequences back, I had the ever so popular Micrococcus, Staphylococcus, and Bacillus bacteria in most of my samples. Two that stood out were Kocuria Kristinae (OTW) and Kocuria Rosea (OTCP). Of the Kocuria species, only one has been completed and published, Kocuria Rhizophilia. One other is in permanent draft, and another three are targeted. By using BLAST on my two samples 16S gene, I determined that both are 96% related at the 16S gene level to the published species. Because of this difference, both samples are fairly distantly related to Kocuria Rhizophilia.
Now came the hard question of which one to use for library construction. Both are very closely related and found in the same general type of environment. I checked my genomic DNA concentration of the two samples and it turned out that I did not have much genomic DNA of Kocuria Kristinae and had plenty genomic DNA (about 785 ng/µL) of Kocuria Rosea. Thus, it was more practical for me to use Kocuria Rosea for my library construction project.
To give you a little information on Kocuria Rosea, it is a type of soil bacterium that has been found in various locations such as a polluted soil, indoor environments, deep sea sediments, and a spacecraft. But mostly, it is isolated from soil and water. A paper online has also attributed it to a catheter-related bacterium.
As my first REAL research experience, I had no idea what to expect. Back in high school, I did a little research in my statistics class where I tested students’ memories based on the type of music they were listening. Obviously, the data I collected wasn’t going to be research paper worthy. Before I began working under the Eisen Lab, I thought to myself, “This is my chance to find some crazy new bacteria and name them after me!” (Spoiler: None of us have yet found a novel bacteria. Pretty disappointing, I know.) Eventually, Winter Quarter came along and the undergrads finally began researching.
It was a pretty rough beginning for those first few weeks. We didn’t know how to pipet – considering the only pipets we were exposed to were those plastic pipets in Chemistry labs; didn’t know the proper lab protocols for avoiding contamination; couldn’t perform a simple dilution streaking; didn’t know what was done and what needed to be done; and so on and so forth. After finally coming up with a good system, the research went by smoothly. And it actually has become a very fulfilling experience. I’ve really come to appreciate the variety and unique characteristics of bacteria in the world. Sometimes, I find myself looking at a surface and wondering what bacteria has made a home there.
Currently, each undergrad is isolating and extracting bacterial DNA from their choice of environment. I took a couple of swabs from a restaurant’s chair, table, couch, and counter in Davis. And I also took some swabs from a nursing home, and the Golden Gate Bridge in San Francisco. I’m really close to submitting some of my 16S DNA in for sequencing. I’m pretty excited to see what the results are.