## ## Welch Two Sample t-test ## ## data: rik$ptile[rik$Fish.Oil == 0] and rik$ptile[rik$Fish.Oil > 0] ## t = -2.7736, df = 90.886, p-value = 0.006728 ## alternative hypothesis: true difference in means is not equal to 0 ## 95 percent confidence interval: ## -14.489218 -2.396073 ## sample estimates: ## mean of x mean of y ## 45.36170 53.80435
Sunday, March 22, 2015
Monday, March 16, 2015
- Taken on Jan 19th, almost exactly 3 months after my Oct 17th sample.
- During the 94 days between samples, I had 31 days where I took a dose of potato starch, a total of about 80 tablespoons.
- I had been taking 1 T daily, an hour before bedtime, for a week before this sample.
## missing.count_norm missing.tax_name ## 1 1257 Arthrobacter albus ## 2 573 Bacillus amyloliquefaciens ## 3 530 Enorma massiliensis ## 4 376 Ruminococcus lactaris ## 5 188 Subdoligranulum variabile ## 6 163 Adlercreutzia equolifaciens ## 7 145 Oligella urethralis ## 8 137 Clostridium sp. NML 04A032 ## 9 137 Desulfovibrio sp. oral clone BB161 ## 10 111 Streptococcus rubneri
## missing.count_norm missing.tax_name ## 1 5929 bacterium NLAE-zl-H436 ## 2 114 Dialister micraerophilus ## 3 101 Peptoclostridium difficile ## 4 88 Dehalogenimonas lykanthroporepellens ## 5 76 Bifidobacterium catenulatum ## 6 51 unidentified bacterium ZF5 ## 7 51 Veillonellaceae bacterium canine oral taxon 211 ## 8 51 Ruminococcus sp. 25F8 ## 9 51 Clostridium leptum ## 10 38 Peptoniphilus sp. gpac018A
## tax_name count_change ## 24 Bifidobacterium longum 7713 ## 39 Clostridium clostridioforme 8958 ## 78 Ruminococcus bromii 10663 ## 20 Bacteroides uniformis 11036 ## 23 Bifidobacterium animalis 13578 ## 69 Peptostreptococcaceae bacterium TM5 14151 ## 47 Coprococcus sp. DJF_CR49 19000 ## 36 Clostridium baratii 24955 ## 76 Roseburia sp. 11SE38 35712 ## 57 Faecalibacterium prausnitzii 89592
## tax_name count_change ## 17 Bacteroides plebeius -90998 ## 30 butyrate-producing bacterium A1-86 -88414 ## 38 Clostridium chartatabidum -41972 ## 11 bacterium NLAE-zl-P430 -23659 ## 22 Bifidobacterium adolescentis -18334 ## 10 bacterium NLAE-zl-H54 -9970 ## 62 Lactobacillus rogosae -8575 ## 27 Blautia faecis -7693 ## 56 Eubacterium siraeum -6040 ## 5 Alistipes onderdonkii -5878
## tax_name count_change ## 27 Dorea 3396 ## 42 Parasutterella 3473 ## 48 Pseudobutyrivibrio 5523 ## 34 Lachnospira 5895 ## 14 Blautia 6612 ## 12 Bifidobacterium 7769 ## 7 Anaerostipes 8565 ## 23 Coprococcus 18317 ## 52 Roseburia 34957 ## 29 Faecalibacterium 135557
## tax_name count_change ## 10 Bacteroides -87903 ## 3 Alistipes -12141 ## 41 Parabacteroides -9820 ## 53 Ruminococcus -9685 ## 35 Lactobacillus -8601 ## 28 Eubacterium -5785 ## 21 Clostridium -5212 ## 11 Barnesiella -3809 ## 17 Butyricimonas -2702 ## 26 Dialister -2410
|B. Longum as % of total Bifido||0.38%||NA||3.16%||14.39%|
Friday, March 13, 2015
After all that analysis and discussion with experts about my uBiome results, I had high expectations for the brand new set of answers that arrived today.
Here’s a comparison chart showing all four of my uBiome submissions:
In a word: argh!
If the January 19th sample had been my first and only uBiome test, I’d be tempted to read a lot into this. After all, it appears that my levels of proteobacteria are way outside the norm. That’s not all: look at some other oddities about this one:
- That bifido bloom I saw after sleep-hacking with potato starch: it’s all gone. Not a single bifidobacterium was found in this sample. Hmmm.
- Lots of prevotella (almost 3% of the sample), a species that didn’t appear in any of my previous samples, and a bit worrisome for a meat-eater like me.
- No more Clostridum, either. Commonly thought of as a pathogen, it may be good to get rid of this, but why did it disappear?
But here’s the thing: I don’t notice a single difference in my health or well-being over this time period. Same sleep, same weight, same general mood. Diet, bowel movements, skin – like everyone, I see minor day-to-day variations, but absolutely nothing about me is different enough to be noteworthy.
On the other hand, there are a few oddities in the sample itself. First, uBiome warned that their first run had too low levels of bacteria; the ones you see above came after they ran the sample again under more amplified settings. Second, I used an older kit, one that had been lying around the house for about a year. Finally, I also ran into trouble with the mail, so it sat around at the post office for several more weeks than normal. Shouldn’t really matter, but still…
Soooo, my bottom line is that I’m just not going to read much into this sample. I’m waiting on my next submission, one that was sent a few weeks after this one, and hopefully that will give me a much better picture.
The takeaway for you? Don’t read much into a single uBiome test. The science is too new, and there are so many other factors that go into the results. My advice: send in multiple kits, spread over several weeks or months, before jumping to conclusions.
Wednesday, March 11, 2015
That’s how I look at my uBiome test results and the wonderful and incredibly detailed analysis done for me by Dr. Grace Liu, who I consider to be one of the world’s best experts about the gut microbiome. Please read her blog, and listen to her Gut Guardians podcast, where she goes into far more detail, but here’s her conclusion about my results:
Unfortunately after amputating over 1/3 of his gut species, many of the phylogenetic core are depleted. The initial levels were awesome but after a high dose of single source of 'fiber', many on re-testing were gone and dramatically diminished numbers.She’s referring to my “sleep hacking” experiment using raw potato starch to improve my sleep. Another way to put this (in my own words):
Raw potato starch — which is not in any ancestral diet — is bad for health. It may temporarily improve sleep by feeding gut bacteria responsible for the production of most sleep hormones, but it also crowds out other, more important organisms, and opens the door for pathogens that can cause far more trouble.Sounds pretty dangerous, and of course I stopped all potato starch experimentation immediately after her warning.
Here’s my summary of the uBiome test results that drove her conclusion (pulled straight from my publicly available data)
|B. Longum as % of total Bifido||0.38%||NA||3.16%|
Her analysis compares only my May and October samples (she dismisses my Jun result as an anomaly) but what if that's not fair? True, there are some issues with the data for June (for some reason, uBiome computed a much smaller sample that time and you can see from the chart that a few items are missing), but it’s still data, and we can’t be sure that the other samples are any more (or less) accurate. To use the New York coffee shop analogy, when you have almost no information to begin with, are you better or worse off when you drop some data points? The answer is that it depends on what you’re trying to accomplish.
Dr. Liu is alarmed at the drop in some key species between May and October, a fact she attributes to my potato starch experiment. But all of those numbers were already dropping in June. The five months pre-potato starch between May and October coincided with seasonal changes (late Spring to Summer to early Fall), lots of travel, multiple camping trips, and of course the normal dietary shifts that happen as I gained access to the freshly-harvested fruits and vegetables of Summer. Was a week of a couple tablespoons of potato starch really the most important change?
In fact, in this table the only species that reversed course after the initial May-June samples and October were the bifidobacterium (often associated with good health and sleep, and up by a LOT) and the clostridioforme (a potential pathogen, down by a little).
I'm pretty healthy, thankfully, and there are no particular disorders I'd like to treat. Like anyone, I want to feel even better, but in my self-experimentation I certainly don't want to risk falling into some terrible dysbiosis or worse. Potato starch appeared on the surface to help -- the improvement in sleep seemed promising -- but I take Dr. Liu's advice and expertise seriously, so I stopped until I can see more uBiome results. I submitted one sample right after my last experiment, and another a few weeks after that. If potato starch really wrecked my gut, then I'll expect the new samples will show considerable worsening across the board. But if not, then, well, maybe it's okay to continue the experiment. Either way, I'll be taking her bionic fiber advice seriously.
To go back to the New York coffee shop analogy, I think we have to respect how very, very little is known about the terrain around us. When you know absolutely nothing about the critically important gut environment, then a tool like uBiome is such a precious gift of information that it's tempting to use it for much more than it is. We'll need much more data, from many more people, before we can use this information to get across town without falling in the river.
Sunday, March 01, 2015
Minimalism is wonderful. Why clutter your life with stuff you don’t need? Here, from the golden sayings of Epictetus are words from the original Stoic himself:
Take what relates to the body as far as the bare use warrants—as meat, drink, raiment, house and servants. But all that makes for show and luxury reject.
Wait a second…servants ? The ancient Greeks, in the philosophical school that invented minimalism, says you need servants as much as food and shelter?!