Monday, May 11, 2015

Bacteroides plebeius and me

 Japanese people are able to digest sushi better than other people thanks to enzymes in Bacteroides plebeius, a bacterium that was first discovered in 2005 and later found to be common in Japanese guts. The 2010 paper in Nature that analyzed this could find no non-Japanese who harbored it, providing some speculation that the microbe has co-evolved with Japanese people, perhaps over thousands of years, to let them digest carbohydrates present in the nori seaweed that wraps the sushi.

Well, I appear to be an exception, according to my uBiome results. I don’t have any Japanese ancestry, but I do have a ton of B. plebeius, an incredible 16% of all the species identified in my October sample. (uBiome was only able to identify about 65% of the species present, so 16% is quite high).

This doesn’t seem to be a fluke in the uBiome data. After seeing my free RuBiome tools, many people have sent me their own uBiome results, but of the dozen or so I’ve analyzed, none of them (all North Americans, like me) have any B. plebeius. If the uBiome test didn’t accurately identify this species, I’d expect at least some of these other users to find in it in their guts too.  Nope, I appear to be unique.

The obvious answer is that I picked it up sometime during the ten years I lived in Tokyo during the 1980s and 90s. I love eating new things, and I certainly ate my share of raw konbu and other types of seaweed. Guess I must have brought home more than just the memories of good meals.

I don’t eat nearly as much sushi and seaweed as I used to, though my kids and I enjoy good, high-quality Japanese koshihikari rice a few times each week, often wrapped with toasted nori. That’s probably not as good for my plebeius as the raw stuff, and come to think of it, my latest February uBIome results show much lower amounts: down to less than 1%.

 Okay, I know what’s on my shopping list the next time I’m at a Japanese grocery.


Tuesday, May 05, 2015

My gut diversity through time

Clark Ellis posts a nice summary of his uBiome results over at the uBiome Blog and now, with more detail at The Self-Taught Author blog. A long period of antibiotic use has made him acutely interested in the understanding gut diversity, so he asks others to post their uBiome diversity results too.

Here’s mine:


A few caveats:

  • These values only represent the identified results, which generally bounce from about 70% (at the genus level) to 95% (phylum). There could well be dozens, perhaps thousands, of other unique bacteria that are simply too rare to be counted by the uBiome technology.
  • A single bacterium can have a big effect, so it probably doesn’t mean much to look at raw counts. Remember that the mammalian genus canis includes wolves, coyotes, and jackals in addition to your trusty dog Fido. Simply knowing there’s a canis at the door tells you nothing about whether it’s safe to go out.
  • Species information is (probably) meaningless. uBiome uses 16S rRNA technology that can’t differentiate below the genus level. They don’t even post species information on their web viewer; you have to uncover it from the raw data like I did. They claim it’s “experimental”, which I interrupt to mean they apply some statistical “guess”, perhaps based on general trends. Anyway, you shouldn’t rely on it.

Something strange happened in my June sample, which was taken three weeks after the one from May, in what was frankly a boring period of my life (no travel, no unusual food, no camping, etc.). It’s possible that result was simply a mistake.

Note: all of my data is posted on GitHub, and you’re welcome to explore it and compare to your heart’s content as long as you promise to let me know if you find anything interesting!

Saturday, April 25, 2015

Potato starch doesn't help my sleep

I've been experimenting with the relationship between sleep and resistant starch, taking a few tablespoons of Bob's Red Mill potato starch, which some people think improves sleep by feeding the helpful Bifidobacterium that may play a role in producing up to 80% of the body's serotonin.

There’s no question the potato starch raised my Bifido levels:
Sprague Bifido over time

But it seems not to have changed my sleep, either in overall hours:
Sprague Z vs potato starch
or in a more precise measure, like REM:
Sprague REM vs potato starch
You can see from these charts that I did notice some fantastic nights of sleep after starting potato starch, but there were plenty of other nights when my sleep was back to normal and sometimes worse. If I hadn’t measured so carefully, I’d be tempted to overplay the good and underplay the not-so-good. If there’s a psychosomatic effect, then yeah it may have made me feel better, but in terms of actual sleep time, resistant starch doesn’t seem to have helped.

Thursday, April 23, 2015

Upcoming talk: Your Microbiome, Your Health

If you’re in the Seattle area on April 29th, I hope you’ll come to a talk I’ll be giving for The STEAM Vent, a local science event organizer. I’ll present the latest that I’ve learned about the microbiome, including the results of a bunch of self-experiments I’ve done since last year to understand more and learn how to manipulate my own microbial environment.

I’m super-excited that uBiome has generously offered a bunch of prizes for attendees, including free uBiome gut kits (worth $89) and some t-shirts.

The event will be held at T.S. McHugh’s, an Irish Pub/Restaurant near the Space Needle. They’re offering a special “microbe-friendly” meal beforehand, an entrĂ©e that includes fresh sauerkraut and other healthy bacterial cultures for those who want to feed their microbes.

My talk starts at 7:30, and The STEAM Vent charges an admission fee of $10. But I strongly encourage you to come a little earlier for the meal ($25, including admission).

Find out more at the Meetup page.

Tuesday, April 07, 2015

Yup, statins make me smarter

After a fifteen day test, I’ve concluded that 20mg of simvastatin daily has a major effect on my results on Seth Robert’s Brain Reaction Time (BRT) test.

Statin affect on BRT

Notice the big changes on the days before and after taking the statin (the “treatment”). The two weeks before were “clean” – no fish oil, no other special vitamins, foods, travel, or other changes in daily habits – making the change even more obvious and sudden: just one day makes the difference. (The chart shows BRT measurements roughly 24 hours after treatment).
With n=33, here’s a simple T-Test to show the effect:
## Welch Two Sample t-test ## t = 7.0834, df = 28.313, p-value = 9.835e-08 ## alternative hypothesis: true difference in means is not equal to 0 ## 95 percent confidence interval: ## 15.88029 28.79244 ## sample estimates: ## mean of x mean of y ## 71.20000 48.86364
My fellow Seattle Quantified-Selfer Mark Drangsholt, who studied something similar on himself, says 2-3 weeks of treatment helped him reduce or eliminate brain fog and it appears to help me too. This is consistent with other research that shows that statins seem to benefit the brain.
Incidentally, the statin had no significant effect on my sleep (as measured with Zeo):
Sleep (n=33)Average (hrs)Standard Deviationw/Statin (n=15)
total sleep (Z) 6.418 0.625 6.424 (SD=0.58)
REM 1.796 0.416 1.814 (SD=0.44)
Deep 1.039 0.198 1.006 (SD=0.13)
I’ve already demonstrated that two or three Kirkland fish oil pills taken daily give me a statistically-significant higher score, while other obvious candidates like sleep or alcohol make no difference. Seth’s app clearly is measuring something. In my next experiments, I’ll try to pin down more precisely what that is as I refine the app to make it easier and faster to use.

Saturday, April 04, 2015

Data is not a substitute for strategy

When I was in grad school, my data sciences class assigned us this incredibly complex optimization problem where we were supposed to recommend the best place to locate a series of factories given expected product demand, availability of suppliers, distance to customers, wage and materials costs, etc. It was too complicated to solve on a normal PC with off-the-shelf software, so the other students simply gave up treating this as a data optimization problem and instead made recommendations based on strategic considerations.

Me? No, I used brute force: I rewrote the software to run on the more powerful and expensive campus mainframe, applying every trick I knew until I found the “correct” answer. It was tough, and at the time I was quite proud of my computer skills, thinking somehow I had bettered my fellow students.

But when I saw the other answers, I realized how silly I was to think that data could beat strategy. Sure, with sufficient computation power I was able to identify a mathematically-provable solution given today’s data. But who cares? Data keeps changing. It’ll be months, maybe years before some of those factories are operating, by which time all my data assumptions would have been irrelevant. Good strategic thinking, on the other hand, doesn’t depend on fluctuations in the data.

I’m reminded of that lesson in this post from Aaron Carroll (at the Incidental Economist blog), responding to Mark Cuban’s advice that everyone get their blood tested quarterly. Data, says Carroll, is not the problem. If you think that more data is always better, you will likely miss the forest for the trees. Or as the post says:

“Ordering a lab test is like picking your nose in public. If you find something, you better know what you’re going to do with it.”