Thanks to Dr. Brooke Anderson-White for this guest post today!
For the past couple of years my Twitter feed, Facebook wall, and blog have been overrun with all things microbiome; however, until a couple months ago, I had yet to contribute my own microbial ecosystem to the growing dataset. While at uBiome, I joined the movement and quantified my own microbiome with their five site kit. My experience was not completely authentic since I missed out on the excitement of receiving the sleek, black kit in the mail and I gained the excitement of processing my own samples, but I still want to share and promote some citizen science at the end.
In the beginning…
Usually your sequencing adventure begins with ordering your kit online, but I sped up the process by bringing one home with me. When I opened the kit, the instruction card greeted me and directed me to register my kit online. Easy enough. With registration complete, I was ready to get started sampling. Not as easy. To get the most accurate representation of your microbiome, sampling should be done after about eight hours without microbial ecology disruption. This includes showering, brushing your teeth, kissing, swimming in a chlorinated pool, etc.
As my friends will attest, I would gladly use sampling as an excuse to delay a shower, but I sleep less than eight hours a night and leave no extra time in my morning routine, so avoiding everything for eight hours is tough. I decided to stay up a little later than usual and do everything at once; except for the fecal sample, that would come in its own time (though we runners do have our tricks).
The instructions on how to sample are both on the card and on-line but I found the Vimeo video demonstrating skin sampling far more fun and informative. Swabbing was easy aside from the issue of working in the small spaces of the nostril and mouth (I definitely got a tap of skin and teeth in the samples, respectively). The extra swab was appreciated to take a second tooth-biome free mouth sample.
When I ask my friends about their experience with swabbing, they unanimously complain about the nostril. Yeah, swabbing inside your nose is creepy, in a “send chills up your spin way,” but it isn’t painful. It just feels wrong.
No one ever mentions the fecal sample. It reflects our actual comfort with poop. If we are as bothered by poop as we assume we all are, diapers would never get changed and there wouldn’t be 14 “poop tracker” apps in the iTunes app store.
Usually the samples would be mailed back in the padded envelope provided, but I skipped USPS and brought them right back to the uBiome lab.
Once in the lab, the samples are entered into the system and the processing begins. A DNews video gives you a behind the scenes look at this part of the uBiome experience. Once again, I deviated from the typical experience, and processed my own samples.
As your samples make their way through the sequencing pipeline, you receive encouraging email updates to track your precious microbes. Eventually, you get the email you’ve been waiting for and your data are ready.
In the end.
Upon entering the data delivery site, my suspicions were confirmed: my microbiome falls outside the norm. I have far more Firmicutes and far fewer Bacteroidetes than the average Western population (and maybe would fit in better with the Hadza). This is most likely the result of my high fiber diet of fruits and vegetables. According to the Mayo Clinic, a woman needs about 25 grams of fiber per day, but Americans average 15 grams. I average 35-40 grams per day. My Firmicutes are well fed.
In addition to comparisons to the overall data set, there are other options on the uBiome site to play with your data, as well as phyla descriptions, but what I really want to know is how to apply this information. Unfortunately, this is where I hit a wall. Much of the research linking specific bacteria to conditions, like obesity, is based on correlative data and the findings from one study to another are often contradictory.
The young field of microbiomics isn’t ready to prescribe behaviors or lifestyle changes based on sequencing results now, but it will be. We can all contribute to this progress by acting as citizen scientists. If you start a new probiotic, decide to go Paleo, or start Couch to 5K, take the opportunity to advance microbiomics and sequence yourself before and after. uBiome is not the only option for sequencing your microbiome, but I would suggest that you pick one service and stick with it to ensure all results are comparable. Sequencing results can vary based on the methods used to generate the data. (Yes, this is problematic and groups are working to create a solution.)
In the meantime, I’ll stick with my fiber and exercise and quietly keep quantifying myself until science catches up and tells me how to live better through bacteria.