Science, Medicine, & Healthcare

My Microbiome Experience from Start to Results

Everyday I'm Samplin'For the past couple of years my Twitter feed, Facebook wall, and this 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.

uBiome Kit

Sleek uBiome kit

 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.

uBiome the Whole Kit and Caboodle

The whole kit and caboodle

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).

VirulentB skin sampling for uBiome

Let the swabbing begin!

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.

Creepy nostril sampling

Oh yeah, this is creepy

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.

In the meanwhile…


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.

Processing my uBiome samples

Science is happening

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.

uBiome gut sequencing results

Never one for “average”

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.


Microbiomics for Everyone from “Gut Check: Exploring your Microbiome”

Gut microbiome from Scientific American

Scientific American image

For all the microbiome scientists, aficionados, and dabblers out there, I would highly recommend “Gut Check: Exploring your Microbiome” on Coursera. Developed and presented by American Gut researchers Dr Rob Knight, Dr Jessica Metcalf, and Dr Katherine Amato, the six module course opens with, “What are microbes?” and continues through the development of and applications of microbiomics. The course covers all the usual uses of microbiome data for health, such as autoimmune disease and obesity research, but also stretches into less widely known applications like forensics. The liberal incorporation of interviews with field experts gives the course vitality and lots of directions for “independent study”. (Speaking of independent study, I would suggest Jeff Leach’s engaging and blunt blog posts for his The Human Food Project here.)

“Gut Check” is perhaps more academic than necessary in presentation style, a little more animation from the presenters would have been appreciated, and many of the slide deck snippets from the interviewees are above the level of a general audience; but the beauty of an on-line course is the ability to pause, fast forward, and skip at will.

The data analysis-heavy nature of several of the modules may surprise some students. Microbiomics is not just cool bugs but is actually a big data field. We must make sense of the deluge of data pouring out of the sequencers to unlock the health and wellness potential of our bacterial ecology. The sections are presented in simple terms with plenty of visual aids (and generous use of Giant Microbes) so invest the time in these modules.

Michael Pollan's American Gut DataWeek 6 focuses on the American Gut project and walks you through the process of participating, which is much more fun than an instruction sheet. They also guide you through interpreting the data you receive, including how to compare yourself to Michael Pollan. I don’t know if American Gut is suggesting he is a super-human prototype, but it is a fabulous idea that everyone gets to see how he or she stacks up against the famously omnivorous author.

If after joining the American Gut Project and acing Gut Check you still want more microbiome, check out Bik’s Picks: MicrobiomeDigest for a clearinghouse of microbiome news and research. TED has several excellent talks such as those from Jonathan Eisen, Joe DiRisi (infectious disease detection), Jessica Green, Jeroen Raes, and Rick Stevens.

There is a glut of information out there so happy hunting and remember to feed your gut-brain axis frequently.
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The world of fecal microbiota transplants

Poop pills or bacteria pills

Not to be confused with these poop pills, FMT requires transplantation directly into the colon

This is the link to my most recent post for uBiome on fecal microbiota transplants (FMT).

A little taste:

Fecal microbiota transplant (FMT) is the therapeutic process of transplanting feces from a healthy individual to an ailing recipient. Despite the obvious “ick” factor of receiving healthy poop from your sister, husband, or friend, people suffering from debilitating Clostridium difficile bacterial infections are overlooking the ick in hopes of a C. difficile cure. Currently the only indication for which FMT is approved by the FDA is C. difficile colitis and there is contention as to the efficacy of FMT for C. difficile treatment.”

Thank you from California Academy of Sciences

Oral swabbing for uBiome by Cal Academy

Angus Chandler, Academy postdoc, and Sean Edgerton, graduate student at SFSU, demonstrate oral swabbing

Check out my blog post on the wonderful thank you letter we received at uBiome from the California Academy of Sciences.  Visit both uBiome and the Cal Academy at Bay Area Discovery Days November 1, 2014.