Saturday, December 6, 2014

Another AmGut Comparison

I am just loving this recent flood of American Gut Project results!  Commenter "Kate" just found her results and shared them.  She was one of the early potato starch experimenters. She describes herself as very healthy, no antibiotics since 2012, and eats a good, healthy diet.  We don't have before-and-after tests, just this one, after several months of 4TBS/day potato starch.  At first glance, it looked very un-impressive.  It looked similar to the SAD dieter I showed you in the last blog.  But the bar-charts are deceiving!

Now let's look at the microbes dominating these two gut biomes:

F. prausnitzii
Not detected
     'Top-5' dominating species highlighted in red.  

Suprising to me was that Kate did not have much Bifidobacteria.  But she did have lots of Lactobacillus, the first time I've ever seen it on anyone's AmGut report in more than just a fraction of a percent.

All of Kate's 'Top-5' are associated with butyrate production and good health.  The 'ancestral core' as many describe.

On the SAD 'Top-5' you see fewer of the butyrate producing core and a few that should probably not belong in a dominating role.

Megasphaera, in particular, quite disturbing. Known as a "Negativicute," but I think more due to its Gram-negative classification.

Akkermansia, as we discussed quite a bit in the comments of the last blog, may not be best to have in a dominate role.

While I have no idea why Kate's biome showed very little Bifidobacteria, it highlights the fact that we are all very unique in what we will grow.

I like to think that Kate exemplifies a healthy gut microbiome, and I also like to think that this shows that potato starch at 4TBS a day did nothing but ensure a healthy gut. One that has a friendly environment for beneficial bacteria and has kept the pathogens, if present, to a very small population.

Thanks, Kate, for sharing and I appreciate that you did the test.  It's a shame these results took 15 months to get here, but we're all in this for the long run, aren't we?


  1. Yeah, a before picture would have been great. Is Kate active or relatively sedentary? Just curious. What other pre-bio's does she consume regularly besides the PS?

  2. Could Kate be genetically lactose intolerant? The lactobacilus may be there sopping up any undigested lactose. According to 23and me, I'm lactose intolerant as is my sister. She gets symptoms when eating almost any dairy at all. I tolerate normal amounts just fine. Large amounts, I do not. I suspect I have more lactobacilus than she does.

  3. In Finland, it is known fact that you can't use people who eat real pure sourdough rye bread as a control for Bifidobacteria experiments as these people have already too much of them in the beginning.
    My DNA has a FUT2 negative mutation so I do not harbour Bifidobacteria unless I supplement regularly.
    Kate might have a FUT2 negative mutation or her Bifidobacteria loves extensive sourdough bread usage which at least for me is absolutely unbearable due to bloating, gas and pain.

    1. FUT2 mutation leads to no bifido? Do you have a reference? That's interesting and make a lot of sense!


    3. I have 3 FUT2 genes mutated red FUT2/card15 which leads to low BIFDIO... in studies you will also so these people tend to have HIGH CANDIDA , which if your having milk problems, or soy or grain all these (MILK) cassien resembles yeast. soy sauce made from mold(fungi) grains hwp1 .... add in any HLA DQ 2/8 genes your screwed.... I have several. Im playing in this area now for over a year... cured , but slowly trying to get my bifido up... my experiment is will my RED mutated genes FLIP------ and become normal when the bifido is finally stuck in :) then we have something for science :)

    4. "Flip" the genes?
      Hey Eddie, are you talking about epigenetic methylation and gene expression or what?

    5. Hello Edward, I have similar mutations in FUT2 (3 of them) and HLA DQ2. My story is so similar like yours and it took years for me to figure this out. Can I reach out to over email? I have a few questions...

  4. A little back story. I sent in my sample in Sept 2013. (It took a long time to process). In April of that year I had started supplementing about a teaspoon of inulin with a probiotic. Bumped into tatertot's discussion at perfect health diet, which led me to free the animal, and in May starting potato starch (ditching the inulin). I worked up to 4 tablespoons pretty quickly. I believe I was sporadically taking taking probiotics at the time and occasional sauerkraut.

    Why was I doing this? I am 56 years old. I have always been "healthy" according to conventional measures. Good weight and body composition, and no red flags on my lab work, including an "enviable" lipid profile according to one doc. Only real issue was insomnia, which I more or less managed with good sleep hygiene. I always tried to eat well, which for most of my thirties and forties included a lot of whole grain wheat. Basically carb heavy and low fat. On the positive side, I had kicked my sugar habit to the curb in college, and never regained a taste for the stuff.

    In my early forties I started to get headaches, sometime severe enough to vomit. I was teaching at the time and chalked it up to stomach flu spread by the students. Eventually my neurologist brother in law convinced me they were migraines, and my doctor concurred. These got worse, and eventually included a daily headache as well. Tried the gamut of conventional and alternative remedies. Various triptans, 5 different prophylactic drugs (all awful!) magnesium, riboflavin, fish oil, butterbur, acupuncture, feverfew, traditional chinese medicine herbs, and others. Nothing helped. Fast forward to my late forties, and I had developed joint pain, particularly in my hips, and had stomach issues, for which I was increasingly resorting to tagamet. I was also pre hypertensive. Relatively modest issues compared to those faced by others on this and other blogs, but annoying enough to me. One day I was trying to run with my dog, felt awful, and I decided to try a radically different diet.

    I started with a low carb diet. I was a little scared about giving up my pasta, ha, ha, but I did it. Within days my insomnia and stomach issues were gone. Totally. They have never come back. Headaches got significantly better, which was very exciting , but they were not eliminated. I played around with the low carb diet, but gained no further improvements. (In retrospect, I think it was ditching the wheat, and not the low carb aspect, that helped.) After some time I migrated into a paleo diet, and eventually found the Perfect Health Diet, where I have been ever since. Going to the Perfect Health Diet, improved my head again. For some months I thought I was on the way to a cure. However, the improvements leveled off, and headaches were still an issue. (Joint pain did eventually clear completely however)

    1. wheat is a strange monster.... you have 14 chromosome, 28 chromosome and 42 chromosome USA frankin wheat. 14 wheat is missing the ALPHA chain and some 28 ........ALL 42 has the alpha chain. If you ever try to experiment with wheat , baking over baked fish try (EINKORN) wheat 14 chromosome :) I bet you can eat it........................................................................

  5. Continued....In the course of implementing this diet I noticed that a hefty serving of Miso or beet Kvass could provoke a BIG migraine. I've been careful to eat only modest amount of ferments since then. So, anyway, my thinking back in the spring of 2013 was that maybe I could tweek my gut to better deal with histamine, tryamine, or whatever . The fact that I had such noticable improvements after dietary changes (first low carb, then Perfect Health Diet) suggested to me that there was gut involvement.

    My head is better, but I still have a lot of headaches. Since submitting my sample I have experimented with a variety of probiotics including SBOs and lots of bifido heavy ones. I also currently use a wilberesque mixture including potato starch, as well as cooked and cooled potatoes, legumes, and rice. Even if I never cure my headaches, tending to my microbiome has given me a wonderful calmness that I really enjoy.

    @ Brad, very active. I feel better when I'm active. In fact, I've been known to get up in the midddle of the night when I feel a bad headache brewing and shovel snow. Back in the day I used to run a lot and lift. Now that i'm not working I tend toward more fun stuff like gardening and lots and lots of golf (I walk a hilly course and usually carry my bag).

    @Oliver. Don't know. I did stop drinking milk when my mom starting mixing it with half powdered milk as a cost cutting measure. I use cream in my coffee, and occasionally eat cheese. I've never reacted to dairy in an obviously negative way.
    @Anonymous. I lived in Germany off and on the the eighties and nineties. Used to love the sour rye bread from the bakery. When I think back to my bread eating days that's the only thing I miss!

    1. Thanks for agreeing to be 'on the spot' here, Kate! I think that seeing reports and hearing the story is very helpful.

  6. HI Tim, You and Dr BG seem to be going into antithesis at the moment with regards to the relative importance of Akkermansia and Bifidobacteria especially Bifidobacteria longum. ?????

    1. The science behind all of this is relatively new. I'm of the mind that we are pretty much stuck with a certain microbiome, but we can influence it greatly by eating lots of high fiber foods that are known to create butyrate and other SCFAs, a lower pH, and overall better environment that favors beneficial microbes over pathogens.

      After seeing the inaccuracies between uBiome, AmGut, and Genova Labs, I don't feel we can use these reports to create a perfect biome. Can you imagine the effort and money it would take to try to tweak Akkermansia or a single strain of Bifido?

      I think it's better to focus on the food, gut symptoms, and overall health. "Others" seem to think it's best to look at key marker species when determining gut health.

      But, to answer your question, I think the only real difference between Grace and I is that she does not like raw potato starch.

      I have no problem with her recommending other fibers, not everyone likes using potato starch, and many cannot tolerate it.

      To condemn potato starch in its entirety is a bit premature, I believe. It's dirt cheap and many do find it works quite well.

      From the very outset of my explorations of potato starch, I knew that the most vocal opponents would be people who want to sell more expensive prebiotics, such as custom blends of pectin, larch AG, inulin, etc...

      As far as I'm concerned, the science behind potato starch as a prebiotic is sound, it bears out in real life, but it's not for everyone.

    2. Doesn't she use PS? I am not a huge fan of her writing style (kind of all over the place and incomplete thoughts, in which you have to had already read the rest of her posts and reference material to fully understand) and have a hard time pulling everything she says together. That being said, isn't she advocating a blend of prebiotics due to the fact PS alone may cause an overgrowth of (beneficial) bacteria at the expense of other (beneficial) bacteria? Also, inulin/FOS is dirt cheap (though admittedly unpleasant) if you just eat chicory root straight.

    3. Not sure. I hate to even try speaking for Grace. Mark Sisson hit the nail on the head with this:

      "If that doesn’t work – but I imagine it would – and your gut is really compromised, I suggest trying Dr. BG’s gut healing protocol. It involves probiotics, prebiotics, and a number of other, more drastic but potentially necessary steps. The good doc is a bit wild, but in a good way. Just read her stuff at least twice and you’ll figure it out. Reading it out loud seems to help, too. She certainly has a way with language!

      Read more:"

      I have no idea where Grace will be with all this in another 12 months, but you can bet I will be stuck right where I am: A fiber-rich diet, supplemented with a variety of fibers you can tolerate.

      I have certainly not learned all there is to know, and I learn new stuff every day, that's what this blog is about.

      I see lots of people being helped with Grace's advice and I like that she questions everything. We all should.

      The more I look at supplementary fibers, the more I actually like raw potatoes and raw potato starch. Easy, cheap, effective, not foul tasting, easy to use. But should not be the sole source of one's fiber.

    4. Tate, thanks for beautifully articulating that. I kept thinking that I was a bit stupid whenever I read her posts, and that everybody else except me was getting it. Don't feel quite so stupid anymore!

    5. I think its obvious that her and Richard and Tim got into some sort of squabble and now Dr. Grace is trying to make them both look bad. She can't make up her mind if she likes potato starch or hates it and then when people ask about RS2 she backtracks all over the place.

      Sorry to gossip. I still like to read there, but now just to see what she is going to say next. Same reason I read Nickoley's blog.

  7. Kate - I think just looking at your profile and major genuses that you have very healthy guts, indeed. Shame about your headaches, though. So many things it could be.

    The headaches have persisted from your SAD days right through the diet changes?

    Do you ever get massages? I used to get tension headaches from work, then started taking Tylenol only to develop what I later learned were "rebound" headaches. Have you heard of that? My physical therapist told me that frequent headaches, non-migraine, are most often re-bounds.

    I would have loved to see a before gut test, but your after looks convincing enough to me, even though lacking bifido. I read recently that Lactobacillus is harder to get growing than Bifido as it requires a very narrow band of healthy pH.

    Here is the Mayo Clinic page on rebound headaches, maybe it will help you!
    Cheers, and thanks for sharing.

    1. Anonymous-thanks. Yes, the headaches have persisted, although overall they are better--less intense and occasional headache free days. Yes, I've definitely considered rebound. I don't take tylenol or NSAIDS for headache simply because they don't work for me. However, a few years back I was using triptans 3-4 times a week which is certainly more than recommended. I decided to test the rebound hypothesis. The only other "drug" I use is my morning coffee, and most headache specialists counsel against coffee. So, 4 months no triptans or coffee. All I can say is that at the end of that four months I felt worse! Went back to coffee, but let the triptan scrip lapse.

    2. I used to get loads of headaches. Fixing my gut has helped enormously. I don't get them anymore, unless I have taken too much prebiotic fiber and am vaguely detoxing. You might not want to go there, but it was coffee enemas in particular that helped.
      I once heard that Traditional Chinese Medicine considers headaches to be the result of slow transit times, or poo in the brain! Migraines are probably a different matter, but if it is more headaches, you never know! Worth a try.
      Coffee enemas have an incredible effect on the entire system, clears the liver, helps the body make glutathione, etc, etc. Start off with a small amount of coffee.

    3. Anonymous--it is good to hear that your headaches have gone away with better gut function. I to was interested in coffee enemas. Gerson himself purportedly fixed his migraines with them. I tried it 4 or 5 times. Honestly didn't notice any difference in how I felt. I do suspect, however, that improving gut function is a least a part of the solution.

    4. Kate, have you tracked your headaches against cycle day?

    5. Jin, Before menopause (It's been about 4 years now), I felt my worst time for headaches was about day 4-12 or so. Now there is obviously no longer any correlation. However, and I believe this is common among people with migraines, I am more likely to have a bad headache after a stressful few days. I call it the stress hormone hangover.

    6. @Kate

      Have you tried to replace potato starch with a whole, raw potato?

      Also, do you eat some honey, and garlic sometimes? If, with what results?

    7. Gemma, I think I'll try the raw potato next. I have been eating honey for the last few weeks as an experiment. Raw, wildflower honey, maybe 2 tablespoons a day. If there are any results from that they are too subtle to notice. I do use a fair amount of garlic in cooking, but have never tried taking it therapeutically.

    8. @Kate

      I used to have headaches for many years. Never went to a doc for any diagnose, as I knew the probably outcome would be some kind of triptans etc. and I did not want that. So I just used some ibuprofen, which obviously caused the rebound, I realised what was happening, so I stopped with that and tried to survive (more coffee, less coffee, no wine, no glutamate, ice cold water on my head, more sleep, etc.). No effect. I have missed a lot of life because of that, I think. The only best headache-free phase was during the pregnancies. I used to think that it was hormone related, now I think, retrospectively, that my body was maybe simply more tolerant. I did not realize that I was simply not eating right.

      Anyway, in spring 2013 I decided for a gluten free diet and low/no easily digestible sugars (another story, the diet I am on now is different) and since then, NO headache never ever. Maybe I just was lucky that it worked.
      I have been thinking what could be missing in your case to have the gut healed, that is why I have proposed the above.

      I have heard of a woman who did a long water-only fast, and then as the first food item she ate was a clove of garlic. Migraine cured forever in her case.
      Any chance you could get honeydew honey, not floral? Might be even more therapeutic. Here I am thinking of neuroprotective effects of exogenous kynurenic acid (KYNA).
      And we have been talking of possible magic hidden in a raw potato (or juice only, perhaps) before. Well, KYNA again, among others.

      Here a possible link:
      Kynurenine Metabolites and Migraine: Experimental Studies and Therapeutic Perspectives

    9. Makes me wonder if low progesterone is playing a role.

    10. Sure, progesteron/estrogen ratio, and the glutamate levels. Many papers on that... But we need to count the microbes in, too.

    11. Thanks Gemma, that's very interesting. I've got a couple days of raw potato going, I'll let you know how it works out. I had never heard of honeydew honey, had to google. I'll see if I can get some.

      The fasting is interesting as well. I've read some anecdotal accounts of fasting migraine cures as well. I did venture there a bit a couple years ago. Was never able to last more than 48 hours, ha ha. And no obvious benefits. HOwever, I remember when I was 50, and did the recommended colonoscopy,, I woke up the day of the procedure after emptying myself out the night before and my head felt perfectly clear. Didn't last beyond that day, alas. Maybe a longer fast could reproduce that.

    12. @Kate

      "Maybe a longer fast could reproduce that."

      Could be. I think it depends a lot what you start eating afterwards, otherwise the unwanted bugs repopulate very fast.

      What about oil pulling - have you tried?

      Sometimes it is good to use more weapons at once.

    13. Yes, Tim has pretty much convinced me to oil pull. I have the sesame oil and have done it here and there. Have to figure out a good time to make it habitual.

    14. KATE your bacteria may be good but l@@@@@@K at the OAT ---OAT testing ..... what about the other thing living in your gut yeast/fungi sample report I had BAD heachaches then later got crohns and colitis ......became gluten intolerant and the end starch.. I didnt fall for the BS from gut docs or general docs...... in the end I was overloaded with fungi.... something NO doc checks for --dont even say the word... today I havent had a headache in forever , randomly eat some grain , dairy (no soy) and the best part no crohns or colitis Im 42 as I got older in my mild 30's up to 38 the headaches got worse---- now the last time I had one I had a glass of wine (yeast)

  8. Hi, Kate - I have been doing about 2TBS of potato starch since the very beginning. I used to be constipated or diarrhea, now just normal every single day. I eat low carb without much fiber when you add it up. According to some that makes me a pariah, but everybody applauded me when I went low carb. Such a strange community! The potato starch hack is the only thing I've done that really made a noticeable difference.

    Thank you, Tim!!!

    Keep up the good work, just report what you see and let us decide how to implement it. I hope you have lots more American Gut reports to show us. I sent mine in 3 weeks ago.