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!