Friday, December 11, 2015
I'm trying to rebuild a personal site using my own software and it's going more slowly than I'd like, so please be patient. One of these days it'll be great.
Meanwhile, if you are here hoping to find more info about my work with the microbiome, please contact me directly. I'm working on a major new project to make it easy for normal people to analyze and understand their microbiome test results, and I would be grateful if you could send me your data in return for some cool analysis. Just email me.
Friday, October 16, 2015
Anthropologists Gandhi Yetish, Hillard Kaplan and their colleagues just published the results of some experiments that show hunter gathers get much less sleep than the eight hours we supposedly need. In fact, their sleep patterns closely resemble mine, despite the conventional wisdom that my average 6.5 hours per night is too little. (There’s a nice summary by Anahad O'Connor in a New York Times Blog post)
A long-time fan of Zeo, I have carefully measured my sleep for many years and I know that my lifetime average is pretty close to 6.5 hours. That’s real sleep, measured by a brain wave detector strapped to my head. Like other lazy people, I sometimes lay in bed longer than that, but it’s a rare occasion when my sleep duration is longer than 7 hours, even when I’m loaded with potato starch to grow serotonin-helping bifidobacterium.
Because the new study appears to contradict the rest of conventional scientific wisdom about the importance of 8+ hours of sleep, I read it carefully, along with the data collected to see if I could spot any problems. So far I think everything adds up:
Plenty of participants: 100 people, spread among male/female at different ages, including some fairly old: 60+
Three separate, unrelated societies: from both Africa and South America, it’s hard to argue these people are somehow related at anything other than being hunter-gatherers.
Week-long observations: You might want a study like this to go on for weeks or years, but I think the duration, from a week to a month per person was just fine.
Good self-tracking hardware: the anthropologists used the Philips Actiwatch 2, strapped to subjects’ wrists with a tamper-proof hospital band. These are well-studied, medical-grade wearables and although they use actigraphy information, not perfect because it’s based on movements in the night, if anything these devices tend to overestimate the amount of sleep. I skimmed the data from the study and it looks good.
The authors conclude that ambient temperature, not daylight, is the most important signal that tells these hunter-gatherers it’s time to sleep. They note that these people sleep no the ground on skin mats, inside huts or in the outdoors, often covered with lightweight cotton blankets. This isn’t all that different from camping, when I tend if anything to sleep more.
Interestingly, when Zeo studied 5000 of their users back in 2011, they found an average sleep time of something closer to 8 hours, with my 6.5 hours falling out of the 95% confidence interval, making me (and the hunter gatherers) real outliers.
Note that although I rarely sleep longer than 6.5 hours, I feel great in the morning and I’m generally alert and feel reasonably fresh all day. Like the hunter-gatherers, I don’t nap and I rarely suffer from insomnia.
I’ll be watching the follow-ups to this research carefully but for now I’ll be much more satisfied that my current level of sleep is just fine.
Monday, September 28, 2015
So today, imagine my surprise when they sent me a nice note announcing that they’d re-run my latest skin sample and found something! The web site version only found two phyla, which at first didn’t seem very interesting:
The sample shows up as only two taxa: Actinobacteria (96%) and Firmicutes (the rest). Fortunately, by downloading the taxonomy data and converting to Excel, I was able to get more details. Here’s my skin at the genus level:
The vast, vast majority of microbes behind my ear are Propionibacteria, which appears to be true for most people and most skin types. This genus contains the special P. Acnes species known to be linked to acne. The species level information in my case only identified about half of all the taxa found in my sample, so although none of what was found was P. Acnes, it’s possible that it’s lurking in there someplace.
Since learning more about the microbiome, I’ve stopped using hand sanitizers, switched to shampoo that is free of sodium laurel sulfate, and I take other precautions to ensure i have the most “natural” skin microbiome I can get, but I don’t know if those actions have helped (or hurt). The only way to find out will be to send another sample so I can compare. Now that I know uBiome is able to process my skin type, I’ll be sure to do that.
Tuesday, September 15, 2015
The Gut Guardians podcast interview with Alanna Collen included an interesting reference to the FUT2 gene, which the podcast hosts says has been linked to response to high fiber diets. One of the alleles, referred to as the non-secretor type, offers a genetic immunity to infection by the Norwalk Norovirus, also known as the “cruise ship virus”.
Alas, I’m not immune to that particular virus, but if you have to choose I think it’s better to have the “secretor allele”, like me. Overall, secretors seem less susceptible to many influenza strains and pathogenic bacteria, perhaps due to our better response to high fiber.
What’s especially interesting is that how FUT2 also seems to be associated with your microbiome. Secretors have noticeably different levels of various bacteria, including missing Bifido species that are known to play a role in health. This is another example of how genes don’t have the final say: you may not get the full benefits of being a secretor if you don’t eat enough fiber.
If you have your 23andme results, you can check your FUT2 status too.