Make a single sheet with all your samples

I often read news about a fresh scientific discovery involving the microbiome and immediately wonder if the discovery applies to me. For example, I recently saw a study from Oregon State University that seemed to find a link between high sugar diets and “cognitive flexibility”, i.e. your ability to adapt and adjust to changing circumstances. The study’s author, Kathy Magnusson, a professor in the OSU College of Veterinary Medicine, found that mice who eat lots of sugar have elevated levels of Clostridiales bacteria, and that this seemed to relate to a slower ability to solve a maze. Hmmm, I thought — how much Clostridiales do I have?

If you have just one uBiome result, that’s easy: log into http://explorer.ubiome.com and search for it in the section “All My Bacteria”. But in my experience a single result doesn’t tell you much. You really need at least two and hopefully several uBiome results to see what might be actionable. In my case, I want to know how my Clostridiales may have changed over time.

I programmed a short Python script to generate a single Excel table with every bacteria I’ve ever found, and then a series of columns with the amount found in each sample. Something like this:

The data makes it easy to generate a chart showing how my Clostridiales changes over time:

Hmmm, in my case it looks like something happened since last fall to increase my Clostridiales levels. Maybe it was the potato starch I tried in order to hack my sleep? Was it my trip to Central America in February? And of course the biggest question: has the increase affected my cognitive flexibility? I’m not really sure. Whatever happened, the level of Clostridiales seems to have stabilized in the past couple of months.

uBiome has identified more than 900 unique taxa (groups of organisms) in the half-dozen samples I've submitted over the past year, and after running this script I have them all laid out on a single page. Now, armed with this one spreadsheet I can search anytime for a new microbe and quickly see if I have it now, or if it's ever been detected in a previous test. Reading news about microbiome has taken on a whole new personal meaning when I can see if the discovery relates to me.

If you know a little Python, you can make the same spreadsheet with your samples using the ubiome.py Python module on the ubiome-opensource GitHub repository; the script that generated my spreadsheet is there too as an example. And while you’re at it, please upload your own uBiome sample results to the same repository so we can compare.

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