Personal Science Week - 241128 Microbiome Cleanse
Restarting the microbiome, plus more links
A microbiome research trial recruited subjects in 2015 with the promise that participants would be given access to their own trial data.
This week the lab gave us the data at last!
Way, way back in 2015, I learned that a Stanford microbiology lab was recruiting subjects for a detailed study of the microbiome. This was right around the time that direct-to-consumer microbiome testing had first become a thing (the Silicon Valley startup uBiome was formed around then), and this new “Human Microbial Dynamics” (HMD) study wanted 100 volunteers who would agree to submit weekly gut (aka poop) samples over a six-month period. The study included different treatment “arms”: some would be given an antibiotic, some would undergo a pre-colonoscopy “colon cleanse”, and others would be given daily doses of potato starch as a prebiotic. The researchers would study the results—dozens and dozens of carefully-collected longitudinal samples—and develop a model of how the microbiome changes.
Despite the difficulties involved in the collection, I was eager to join for one big reason: the researchers promised each participant would have access to their own raw data. The opportunity to get dozens of microbiome samples studied for free seemed like more than enough incentive to a personal scientist like me, and so in the summer and fall of 2015 I was one of the subjects.
Since then I had the opportunity to do many other microbiome tests and much more as I dug deeply into personal science. Never having received the Stanford HMD results become less important over time, so imagine my surprise when this week the HMD principal investigator Les Dethlefsen contacted me with my data!
Better late than never.
Colon Cleanse
The big question I wanted to know at the time was what happens if I completely flush my gut microbiome and start over? We all do this as part of a colonoscopy prep, so I scheduled my HMD study to coincide with what I was doing anyway. I had also amassed a bunch of separate gut testing kits from another vendor (uBiome) partly as a sanity check to see if the two labs match.
tldr; the labs matched! In other words, I feel more confident in the rest of my 600+ uBiome lab tests, knowing that a completely independent lab offered pretty close results. I wish I had known this ten years ago!
Here’s my uBiome data
Which, at least to a first approximation matches pretty closely with my Stanford data
And what about the microbiome cleanse? What did I learn? Here’s what I wrote at the time:
My gut microbiome recovers pretty quickly. Unlike antibiotics, which are known to cause long-term (and possibly permanent) changes, losing bacteria this way seems to matter only for a day or two. The missing microbes sprout right back just like a haircut. In two weeks it was as if nothing had happened.
Amounts and ratios changed, but not the specific organisms. 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.
It’s pretty hard to make a significant change. These days a little googling will find plenty of web sites, books, diets, and supplements that claim to “fix” or “change” your microbiome. I’m a healthy, reasonably fit adult, so I’m not as motivated as somebody with a specific health problem, but I thought simply popping probiotics and eating a variety of new and fermented foods would have a big effect. Nope.
After the Stanford experiment, I went on to do zillions of other microbiome tests, which you can read about in my (free) online ebook: the Personal Science Guide to the Microbiome
Personal Science Links of Interest
Google Research used antennas in zillions of Android phones to crowdsource a map of the earth’s ionosphere. I didn’t look deep enough into the details to tell whether this was something you had to specifically opt-in for, or if enabling your phone’s GPS and other radio settings was enough to give Google permissions. But what I’d really like to know is if users can themselves access that ionosphere data. It’d be neat to see exactly how the ionosphere affects my own phone right now.
You know those lists of biases (“loss aversion”, “sunk cost”, “overconfidence”) that we’re all supposed to watch out for? The Serengeti Plain: Fallacies that aren’t fallacies offers a contrarian take on why some of those so-called “biases” are actually pretty smart ways to make a decision. For example, bailing just because it’s a “sunk cost” can also be an excuse for not trying harder.
Adam Mastroianni points to “This guy on Reddit claims to have cured his wife’s 20-year migraine by cleaning their HVAC system. If even one other person heals their headaches by dusting their ducts, this is way more impact than the average scientific paper.”
Gary Wolfe did a deep dive on sleep trackers and points to a recent academic review that appears to show the devices, though good for measuring overall sleep, have little utility for measuring sleep phases or wakeups, even for Oura Ring.
About Personal Science
One advantage personal scientists have over professionals is that we can say or believe whatever we want without fear of losing our jobs or becoming ostracized. We’re already open-minded to new ideas—even those that go against the received wisdom—and we’re skeptical, including about our own ability to discern. If it turns out we’re wrong, no biggie: people will dismiss us as the amateurs that we are. But if we’re right, we’ll reap benefits in our own person lives.
In a highly-recommended podcast last week, Peter Thiel spoke to Bari Weiss about the tension in science between consensus “dogma” and skepticism. Science needs a certain amount of consensus in order to coordinate activities: progress is difficult if every conclusion is constantly re-litigated. Today it’s easy to think of examples of scientific consensus (aka dogma): climate, vaccines. But it’s harder to think of areas where scientists are skeptical about a mainstream consensus—a situation that resembles the Medieval period when it was risky to be skeptical about the Church.
Pick your topic: vaccines, climate change, sexual or racial issues. We all know the “correct” answer, don’t we? One good way to tell if something is worth discussing is to ask what would happen if a famous professional scientist announced that he or she wants to study the issue. Or what happens if the scientist finds the “wrong” answer.
So when you hear a new claim, whether from a well-regarded expert or from a certifiable quack, you should feel comfortable keeping an open mind. Experts are sometimes wrong and quacks are sometimes right. But be skeptical either way. After all, as Amazon founder Jeff Bezos says “contrarians are usually wrong”.
We discussed this in more detail, with specific examples back in Unpopular Science 240303 (now with the paywall removed).
If you have questions or suggestions about anything in personal science, please let us know.
If a colon cleanse is a haircut, antibiotics are laser hair removal 😀