Hacking my sleep with uBiome

As a very special treat today, Richard Sprague has a guest blog post for you about hacking his sleep, with a surprising discovery. You can also find Richard on Twitter and at his brilliant blog. Let’s give Richard a warm welcome!

Here he is…

About a year ago, I started to notice my sleep becoming less regular. Nothing serious — thankfully, I’ve never had sleep problems — but I was waking up too early, and I didn’t seem to be quite as refreshed. Maybe it’s just a sign of age, I thought, until I read in Martin Blaser’s excellent book Missing Microbes (p.304) that most (80%) of the sleep- and mood-regulating neurotransmitter serotonin is made in the gut. Could my gut microbes affect my sleep?

A few internet searches later led me to evidence that B. infantis modulates tryptophan, the stuff in turkey that urban legends have long blamed for that sleepy feeling you get after Thanksgiving dinner. Seemed like a good target to check, and because I’m a long-time uBiome fan —- I supported them on Indiegogo almost two years ago – my first step was to look at my gut biome results to see my levels of bifidobacterium.

As I suspected, I had no B. infantis, and in fact my overall bifido numbers were pretty low as you can see from this item on my uBiome results sample explorer page:


You may already know about pre-biotics, foods that feed bacteria, as opposed to pro-biotics, which are simply pills or foods that already contain a bunch of (presumably) beneficial microbes. Lately a number of people have noticed that a particular kind of starch, so-called resistant starch is a prebiotic that acts like a yummy smorgasboard for bifido and other bacteria. I followed a protocol that uses plain ole Bob’s Red Mill Potato Starch (easy to find any nice grocery store): just a couple of tablespoons one hour before bedtime to give the starch time to make it to the upper colon where the bifido live.

Whoah! You wouldn’t believe how wonderfully I slept that night. Over 8 hours of rock-solid, uninterrupted sleep, and more vivid dreams than I’ve had in years. It was amazing!

After a few days of this, I submitted another sample to uBiome for testing:


Holy bloom, Batman! That’s just plain stratospheric: up from 0.847% before the potato starch, to over 5.87% afterwards. That 8x improvement it seems clearly explains my much-improved sleep.

But nothing’s free, right? If the bifido are increasing that much, then something else is decreasing. My sleep might be improving, but am I sacrificing some other aspect of my long-term health?

To find out, I wrote a couple of utilities to examine my uBiome results in more detail. One of the things I like most about uBiome is that they give users access to the raw data, which you can convert to work in Excel or another programming environment. If you’re interested in more details, you can read how I did this later, but here are some of the major species that went extinct after I took potato starch:

##   missing.count_norm                   missing.tax_name
## 1               8295        Bifidobacterium tsurumiense
## 2               4650          Subdoligranulum variabile
## 3               2074     Dialister sp. oral clone BS095
## 4                780 Desulfovibrio sp. oral clone BB161
## 5                475        Adlercreutzia equolifaciens
## 6                459               Ruminococcus sp. ID1

What do these microbes do? After a few more internet searches, my answer is: nobody knows! We have some guesses, but so far scientists just haven’t had enough samples from real people to understand much. That’s another reason I hope you’ll submit your samples to uBiome, to increase the number of data points that scientists can work with in hopes of understanding this better.

Meanwhile, my sleep continues to be much better than before I began this experiment, so I’ve stopped taking potato starch and have been substituing a few other foods that seem to affect the microbiome. I’ve already submitted my before-after samples to uBiome and will let you know what I find in a future post.


10 thoughts on “Hacking my sleep with uBiome

  1. Follias

    This stuff is so exciting. It really is one of the missing pieces in health maintenance. Yay for smart women promoting this venture. Looking forward to 23&me coordinating with Ubiome. Impressed by Indiegogo too. @phylogenomics , aka Johnathan Eisen, UCD, has tweeted about lack of recognition for women in this scientific community. Maybe for first time women will lead the business application side of things.

  2. DavisJD

    Interesting! It’s true that nobody knows, but it’s generally accepted that the more diversity the better, so extinction of multiple species is a bit of a concern. Thanks for sharing your experience.

  3. Alexandra Carmichael

    Thanks for your comments! We’ll be profiling more posts from Richard as well as other amazing microbiome self-experimenters in the weeks to come.

  4. Great job, Richard!

    Just two comments. 1. uBiome is probably not so reliable when it comes to species level identification, and 2. Looking at a the genus level should show everyone that a couple spoonfuls of raw potato starch is truly the ‘hack of the decade’ for improving the gut microbiome.

    I believe that increasing the abundance of butyrate producing bacteria AND bifidobacteria is a dead giveaway that potato starch is helpful to the gut. Did you also do a search for bacteria that was created? Not just ‘extincted’?

    Lots of connections with gut bacteria and sleep. Factor S, tryptophan, serotonin, etc..

    Good job…love your grasp of bioinformatics.


  5. Thanks Tim,
    I agree with both your comments. At the genus level, I had 57 extinctions, 12 inceptions, so numerically there was more die-off, but of course if the “bad” bugs died and “good” ones appeared, then I’m ahead. Like I said, who knows.


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  7. Greg

    I have been experiencing much longer sleep by simply eating a large bowl of popcorn in the evening. It has no calories and the gut bacteria seem to settle down working on the fibre.

    1. greg

      no more than 2000 calories per day; breakfast; late lunch; skip supper, eat popcorn; comprised of protein, fruit, veg; daily avocado; daily cooked tomatoes; daily cabbage family; Kimchi; snacks of one apple and a few almonds; minimal or no wheat; small serving of brown rice, wine, beer.

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