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My name is Richard Sprague and I am a long-time self-tracker. Today I’d like to show you something I presented a few months ago to the QS group in Seattle.
But first, my lawyers want me to read you this disclaimer. If you have any questions about health and its relationship to the microbiome, please see a real doctor (and if she has any answers, let me know because I have some questions too!)
Now a question: How many of you have had your genes sequenced? (through 23andme or another organization?)
I’ve always been interested in genetic testing but then I learned that most of the genes in our bodies is non-human!
In fact, if you look your body
By weight: you’re 99% human By cell count: it’s a lot more non-human By genes: as much as 99% of the genes in your body right now are from non-human microbes.
And collectively they seem to affect every aspect of our lives, and health.
Trillions of living microbes, many of them co-evolved with humans, inhabit every space of our bodies, adding up to a total of 3-5 pounds, about as much as your brain!.
You have millions of these organisms, and to sequence them all would have been completely impossible until some amazing new technology came on board a few years ago. Thanks to a clever engineering trick involving the “16S” portion of a bacterial genome, it’s now possible to find out which microbes are in you right now.
My favorite part about uBiome is that you get all the data, in raw form, so you can study it in as much detail as you like. Remember, we’re talking trillions of microbes, so turning this into usable data is not easy.
Here, I’ve taken a JSON form of the data, turned it into an Excel spreadsheet where I ran some numbers on it, and then converted it all to charts. For even more coolness, you can write simple Python scripts to do highly sophisticated anaysis.
These days you hear about the microbiome everywhere. The best part is that now I feel a connection to everyday science news.
When an interesting discovery is made, like this relationship between a high sugar diet and learning – and its affect on the microbiome – I can look up the specific organism involved and see how it changed for me over time.
It’s a quantified selfer’s dream!
From Huffington Post: http://www.huffingtonpost.com/2015/06/24/gut-bacteria-brain-cognit_n_7644484.html
And here’s my favorite discovery.
I remember hearing something on NPR, about a species of bacteria that can metabolize seaweed. The scientist who discovered this was only able to find it in Japanese people, but when I looked up my uBiome results, I found the same one in me!
Here’s one experiment I tried: your body’s sleep-inducing hormones are actually made in the gut by a species of Bifidobacterium that loves to eat resistant starches, like the kind found in potato starch. Can I grow more Bifido?
The answer is yes! Here are the results of my uBiome tests before and after …
And the next question: would it help my sleep?
It seemed to help, at first. But over time the effect seemed to wear off. Maybe it was dependent on the dosage? Maybe on what other things I was eating or doing at the time?
Who knows? But to unwrap all the variables, what if I could start all over? Wipe the slate clean, and give myself all new bacteria – the ones I want to be there.
So, I thought: maybe there is a different kind of interaction going on. Maybe I need to start all over with a brand new microbiome.
Like every QS talk, my remarks center around these three questions.
I fasted for two days beforehand, to clear myself as much as possible.
So I got myself some supplies that would be familiar to anyone doing a colonoscopy prep Then I got a big jug of GoLytely, and a few other common household items.
I carefully tracked exactly what I ate before and after.
I used myFitnessPal to track of all the foods I ate, broken down to the macronutrient level. And I specifically stuffed myself with “foods that are supposed to be good for the microbiome”.
Here are the results: the standard uBiome web app gives you two views into your data. The top one is a breakdown of which organisms they found. You can see the big plunge on the day of the cleanse, followed by some gradual movement back to normal in the days and weeks afterward.
Of course I lost a bunch of bacteria – that was the point – but surprisingly I didn’t seem to gain anything really new, even after an aggressive attempt at re-seeding. I didn’t gain or lose a single phyla. and even at the very fine-grained Genus level, only two taxa that had been regularly present beforehand were now extinct. (Holdemania and Methanomassiliicoccus).
I also wrote some of my own Python/R software to do a deeper analysis. At the top is my diversity (measured using one common diversity score called ”inverse Simpson”)
The bottom chart shows the ratio of the two most common bacteria found in most Westerners. Some people think a lower ratio might correlate with body weight.
I was especially intrigued by five new taxa that appeared just once, the day after the cleanse, and then disappeared. Maybe I found some that ordinarily get lost in the noise of the microbiome and only show up when the rest of the forest has been cleared.
What do they do? Who knows!?
But these are some hardy guys and I’m glad I know their names and can watch for them again:
I learned a few things as a result of this experiment, but…
Biohackers Seattle June 2016 Microbiome Hacking
Hacking My Gut
June 4, 2016
I’m not a doctor
• The following presentation and discussion is not intended to diagnose, treat, cure, or prevent any disease.
• The material in my talk is provided for informational purposes only and is not medical advice.
• Always consult your physician before beginning any diet or exercise program.
• uBiome sampling kits and data is designed to be a tool for personal research - not a diagnostic tool. uBiome
cannot predict the implications of your results for your long-term health, nor will you be able to use your results
to diagnose, treat, cure, or prevent any medical condition.
• uBiome offers the opportunity to gain a better understanding of the human microbiome and see the bacteria in
your own samples.
• uBiome’s platform enables you to visualize your results, as they compare to other participant groups and your
own samples over time.
My new friends
Abiotrophia Bacillus Catonella
What I Learned
• My gut microbiome recovers quickly
• Amounts and ratios change, but not the
• A few intriguing, new organisms appeared.
• It’s hard to significantly change your