Friday, October 17, 2014

Comparing uBiome data through time

Like I said previously, the data (and tools) at the uBiome site are fantastic, and it’s taking me a long time to understand what meaningful conclusions I can make. But first, one basic question I had is how stable the results are. If the microbiota changes all the time, then maybe you can’t really conclude much unless you track long-term trends.

In an excellent study published over the summer, Lawrence David at Duke University followed two subjects, measuring their microbiota and zillions of other variables every day for a year. His team concluded that although illness or travel can dramatically change microbiota composition in a single day, and different foods cause levels to fluctuate by up to 15% per day, generally things stay pretty stable.

So what happens if I send two samples, taken a few weeks apart, to uBiome? That’s what I tried, keeping close track of exactly what I ate and did in the meantime.

Here are the results for the first sample (the one I posted before)


Here’s the newer sample, taken three weeks later:


Hmmm. As you can see, these results seem quite different – far more than the 15% daily fluctuation from the Lawrence study.

No special travel or other unusual activity during those three weeks. Nothing unusual in my diet. I’m still analyzing what I ate, but for example here’s the amount of fiber per day, starting the week before the first test.


Nothing super unusual there. Note that I am a completely healthy male, normal/stable weight, no history of anything. Last antibiotic use was a long time ago.

Incidentally, Tina Saey (@thsaey) sent the same sample to two labs (uBiome plus American Gut Project), and got dramatically different results. uBiome wrote a detailed response – my takeway was that the differences can be mostly explained by how each lab handles the samples but that you can correct for that (mostly).

Still more analysis ahead of me. Meanwhile, I’ve sent them a third sample to compare further.