Gut Hacking: A Guru-Free Zone

Just a quick follow-up to the last post.

I want to make sure no one takes away the idea that I’m recommending people “put the brakes” on any experimentation, or that they should be worried about dumping a couple tablespoons of a granulated whole food into a glass of water. In fact, the intention is exactly the opposite — my hope is that people don’t become complacent with one solution, or narrowly define microbiome experimentation to just one intervention. I think there is tremendous value in having many people trying many different things. There’s no other way we’ll get to the bottom of all this.

The evolving thoughts I post on this blog are a product of the research I do to primarily figure out what I, personally, should be doing in this area of health. They are not, and are never intended to be, a prescription to others. The reason I post them is because:

1) It’s a good way to document and organize the research I come across and the ideas synthesized from them.

2) It has the side effect of exposing others to new ideas and information, and putting their own experimentation into perspective.

3) The comments and reactions help to refine, expand on, or challenge the conclusions I come to.

The reason this area of health research fascinates me so much is that, besides its tremendous potential for understanding disease and improving health, it is an area of health that is extremely amenable to personal experimentation and do-it-yourself therapy. If the hypothesis that diet is the primary modulator of the gut microbiota is correct, and that the gut microbiota do hold potential to address health and disease, then people who like to make a lot of money from sick people are going to be disappointed.

If any sort of broad guidelines or recommendations do emerge on any of this — and I hope they eventually do — it will be the product of collective experimentation and conversation. As such, I think we can do without gurus or “experts.” I think we have enough of those. Using other people’s struggle and search for health as a platform for self promotion has never much appealed to me. I hope that, as we continue to explore the other 90% of ourselves, the crowdsourced aspect of this remains front and center.

— Heisenbug


29 thoughts on “Gut Hacking: A Guru-Free Zone

  1. OK, This is an excerpt from DRBGs comment in your last post. I had also seen this posted on another blog before but man it sure gives me a smack my simple country girl forehead moment.

    “In the wheat, oat and potato group. 62 genes were activated that increased inflammation, oxidative stress and the stress response. Worsened blood sugar balance and generally amplified all of the forces in the body that lead to obesity, heart disease, cancer,diabetes and Alzheimers disease ! It was 100% effect. No good genes were turned on”

    Accept.. potato starch in modified form does not raise blood sugar but what about all that other nasty stuff tatos cause plus 100% 0 good effects. Does processing remove that all king of nasty. Could that explain some of the side effects (stiff neck).? Need some input from a scientific mind. Think I’ll go outside and chew on a piece of straw and do some figurin. HELP

    • As usual you have to read the actual study. The extended quote from Hyman (namely genes turning “on” or “off”) sounds too black-and-white; some of it is more like “up-/down-regulation”. Looking at the tables some of the results were rather marginal if you ask me. And was it potato and/or wheat and/or oats? Dr BG ascribes the difference to prebiotics in rye. But what about oats? Similar I thought.

      Anyway, the authors are not sure:

      “The mechanisms by which the oat-wheat-potato diet induces gene expression of numerous manifestations of metabolic and oxidative stress and immune activation are unclear. One explanation could be the repeated mild postprandial hypoglycemia that follows the initial hyperglycemia induced by carbohydrates with a high-glycemic or insulinemic index (15). We also found that ingestion of wheat bread is followed by initial hyperinsulinemia and a subsequent transient drop in glycemia below fasting levels, which was not seen after the rye bread meals (14). Hypoglycemia results in activation of counterregulatory stress hormones such as cortisol, glucagons, and catecholamines, which restores its consequent restoration of fasting glucose concentrations and increased nonesterified fatty acid concentrations (15).”


      “It is possible that the changes in SAT gene expression might have indirectly influenced insulin secretion in the pancreas, but the mechanisms are unclear. It is unlikely that differences in intakes of protein, saturated fat, carbohydrate, and fiber in the rye-pasta and wheat-oat-potato groups differentially affected early insulin secretion (17). It is nonetheless possible that differences in macronutrient and micronutrient intakes contributed to the different patterns of changes in gene expression.”

      Interesting study, but I think the sudy design is flawed. Look at the intervention. What exactly are they testing? Too many variables is what I see.

      • Thanks for adding clarity. I am disappointed that they grouped wheat, oats and potatoes. What if the results are related only to wheat? or potatoes? The results don’t necessarily apply to each carbohydrate source and it is impossible to separate them out.

        All of the test subjects had metabolic syndrome. That suggests that many/most may have had damaged gut function. How many had an immune response to wheat, potato or oats? Could that account for some of the genes that were up-regulated? Would they get the same results with subjects with healthy gut function?

        Also I noticed that they gave the wheat-oat-potato group dehydrated mashed potatoes. I imagine those would be high in resistant starch. Just as the rye is higher in soluble fiber. It is going to take more study to tease out what affects their results in detail, if they can.

        I find it fascinating how looking through the gut-biome lense affects how I look at study results.

  2. Thanks Michael
    I guess what also stands out to me is” 100% effect No good genes were turned on”. None , zip, zero ziltch… You would think 1 little gene could find something positive in the wheat, oats or tats. I’m just a hammer hits nail kind of person. Not is it causation vs. correlation. I want good genes turned on and to look good in jeans:-) . Pastrami and rye back on the menu! Always with a side of asparagus

    • You just might find something positive in the wheat, oats or tats. But you’d never know which from this study.
      “Pastrami and rye back on the menu! Always with a side of asparagus.”
      Agree, +1

      • Michael
        Nooo…last bowl of oatmeal I had had me white knuckling it down the freeway to BassPro Shop. The insulin was dropping the BS faster than the oats raised it (pre-lc) . If I saw some roadkill on the side of the road I would have been tempted. Thank god I made it. The fried alligator was the quickest thing they could bring me. Positive side îs I probably would never have tasted alligator if I didn’t need it to save my life that day and it was pretty dang good!

    • Bea – just a caution. Most rye breads are at least 50% wheat flour. You can get 100% rye bread, but is is very different. Same with 100% rye crackers – like Wasa. I thought I would bake some sourdough rye. I have a starter going.

  3. Yes, yes, yes. Ultimately we are responsible for dealing with our own health issues as best we can using the available knowledge. Just to add my n=1 ( or 3 including my husband and daughter). Since starting the RS (jumped in with Potato starch/plantain flour/food sources) and incorporating a variety of other starches I personally developed incredibly achy joints, inconsistent and sometimes restless sleep (even if I do a bolus in a..m.) and, most dramatically, intense and widespread eczema which I have never, ever had (never even had acne, skin issues were one of the few things I haven’t struggled with).

    I have been playing with diet and supplements long enough to know how to get back to a better place (fasting and a slow reintroduction of the different elements) and the process is beginning to make it clear that the potato starch was the main culprit. The eczema is calming down (I was literally scratching my skin raw and bloody) and I am feeling better though I still can’t sleep. I find the plantain starch doesn’t bother me, but it doesn’t give me amazing results like others have reported though it has improved my insulin resistance (PCOS) , food cravings and had increased my sensitivity to adderall which is prescribed for ADD and narcolepsy (though that effect has been altered because I had to change rx to generic which is considerably less potent for me, hoping to get off of it altogether). My husband and daughter tolerate the potato starch just fine but it hasn’t impacted their health in an immediately obvious way yet (though admittedly they were already seemingly healthy).

    What I have noticed is that, after being AI paleo and consequently very low carb because of an inability to tolerate almost any starch – an approach that helped for a while until it didn’t and new symptoms began cropping up like sudden weight gain and other “seemingly” random things – to now being able to eat garlic, onions, rice, beans, lentils, and more exotic roots and things that grow in the dirt (no potatoes though) and feeling ok when I do (in the past it would have been painful in many ways).

    There is more to my own story but my point is that the experiences shared here and elsewhere (thanks Tim, Terri @, Heisenbug and many others. Your feedback has been invaluable in informing my own understanding of my unique situation and that of my family. Right now the things that seem most clear to me are: find what works for you through reasonable experimentation (if you can be organized and methodical so much the better, but if that is not your nature just do your best) and, as much as possible, increase the diversity because that is probably the only way to figure out what specific species need feeding in your very particular system. No one can do this for me, but there are some really helpful people out there posting their info. free of $ so that we all may learn. And, as a special education teacher may I add, hopefuly in a safe space where we can communicate what we’re learning and what we do and don’t understand in an effort to learn more without being pounced on or ridiculed – we’re all just trying to figure out what is best for us. God knows our government, food industrial /healthcare complex and pharmaceutical industry aren’t interested in helping us and our children be healthy and truly well.

    So, there’s my 2 bits and I hope it helps.

    • Jlowbug, I’m with you all the way. My intuition tells me concentrating on one RS source is not the way to go. Trying to get as much diversity as possible is the way to go, because only doing it this way will we learn what works for us and what not. Continuing on regardless of what our gut is trying to tell us, to my mind, only makes things worse. Something we definitely DONT want.
      By the way, I have recently found a new way to get RS. I take half a green plantain, slice it and put it in a blender. Add half a can of cocunut milk and blend. It makes one THICK smoothie, jummmmmy!! 🙂

      • Great idea and it sounds pretty good. I’m getting used to drinking down thick, chalky, glpppy, grainy, sour . . . stuff although that actually sounds kinda tasty. For a while I couldn’t tolerate coconut products very well so I haven’t been consuming them for a while but maybe it’s time to try them out again. That has to be better than the plantain flour from Berry Farms which literally tastes like very old gym socks (at least how I imagine them tasting).

      • If you can’t tolerate coconut milk and you can tolerate your homemade yoghurt, you could try it with that. I use coconut milk because I can’t tolerate dairy.

      • I, too have trouble with canned coconut milk, but I can tolerate raw coconut oil. I have often thought of trying fresh coconut to see if it sits well with me. If it does then the cooked coconut milk products are what disagrees with me. So many people drink fresh young Thai coconut milk, I want to experiment with that type too, some day.

  4. Greetings Mr. H,

    Very interesting post last time. Thank you for it. My two take-aways were:

    1) Keeping a low gut pH is pretty important, but the “how” was left somewhat tautological… feed the “good” bacteria well and they will lower it themselves(?) except the “bad” bacteria feed on RS better than the “good” bacteria.

    2) If bacteriodetes can switch between RS and mucan, might swamping them with RS cause them not to feed on mucan? I guess we’d need research to confirm whether they are either-or, but if they are that might explain why RS helps with bowel problems. Of course, it also means once you’re on RS, and have grown a sizable bacteriodetes population, be very careful not to stop. They won’t appreciate it — Attica! Attica! 🙂 It seems all one can do to mitigate is keep the pH down, i.e. see 1) above.

    As for the ‘keep experimenting,’ tomorrow begins our final week of the family science project. After reading the last post, I’m really glad we took your suggestion and have my wife mixing her PS with kefir. She lets it sit for ~5 min in the interest of letting the bifidobacteria attach to as much of the RS as possible. Having said that, 2T RS in 1/2 cup of kefir is probably a lot more RS than the bifido could ever attach to, especially in 5 min at 40 degF, but it will be interesting if that bit of head-start makes a marked difference. At the risk of exposing researcher bias, here’s to hoping it does. 🙂

    I’m also curious if my son taking psyllium husk along side his PS will end up making a positive difference. Perhaps psyllium will help to lower gut pH, keeping bacteriodetes in check despite all the RS floating around. Thanks goes to Grace for the psyllium husk suggestion.


    • Hi Allan. 1) pH is a function of amount and diversity of fiber. A lower pH seems to allow beneficial microbes to compete effectively for RS and other substrates. A higher pH gives the edge to more alkaline-adapted microbes. Does that make sense? 2) Yes, that’s sort of the theory but quite speculative. Obviously providing some fiber is better than leaving it all to mucin degradation. But is it optimal? That’s the question.

      Very excited to see the results of the experiment. Thanks for doing it.

      • Does that make sense?

        As to results, sure. I never argue with results. As to mechanism… well, not really. 🙂

        Eat more fiber because it feeds beneficial bacteria, which lower the pH, which helps beneficial bacteria. And by the way, bacteriodetes is the most efficient consumer of RS fiber, and they prefer a high pH, and they aren’t always beneficial.

        What’s that mean?

        I infer the answer is we don’t know exactly so aim for diversity and be wary about over-dosing on “teh RS,” and taking it alongside bifido is highly suggested, and be wary about quitting cold turkey. Bacteriodetes has a nasty plan B which a lot of other bacteria do not. Three caveats. I can live with that, but it makes for a pretty interesting/important footnote. Yes?

  5. I am experimenting by adding 2T RS and 2T soluble fiber to the the kefir when I make it, and give it at least 24 hours at room temperature before I eat it. We will see; I am on my third day and haven’t had any acute negative effects.

    • 24hrs at room temp seems a very long time to me.

      For comparison sake, yogurt is fermented around 12-18 hrs. In my own experience and to my own taste, 12 hours is still pretty sweet, 14 is just right, and >16 is too sour.

      Then again 2T RS might still be way more than the residual bifido in kefir could digest in 24 hours, I have no idea. But I do think you are well past the point of diminishing marginal returns. The point of RS is to feed the bifido in your gut. It seems you are attempting to consume more bifido directly, more or less a home-made probiotic. Unless you are really worried about bacteriodetes, that approach seems too indirect to me, and if you are really worried about bacteriodetes, I think you need to do research to know how much RS to use to make sure it is completely digested in the kefir before consuming it.

      To be clear, I don’t think it’s a matter of negative effects, as you’ve mentioned. I think it’s a question of what effects are you trying to achieve. If it’s kick-start the bifido in vitro a little bit before subjecting them to the rigors of the GI tract, 2-4 hours at room temp seems plenty to me. But then again, I don’t know except 12-14 makes complete yogurt.

      • Well, I think it depends on temperature. It is 65 degrees in my house right now. I don’t mind the more sour taste, I just don’t want to starve the bacteria. It may need to be a shorter time in the summer.

        I am not attempting to get the RS completely digested, just give the bifido time to bind to the RS before consumption to favor the bifido over bacteriodetes. Thus starting the chain required to produce the short chain fatty acids in the large intestine.

      • Fair enough, Tate. I think you could probably get all the same benefit in an hour or two, but hey, if it works for you, excellent. I won’t argue with that.

      • You are probably right. But it takes 24 hrs to make the kefir, and I just add the other ingredients when I add the milk. It isn’t at least 24 hrs, that is just how long I am letting things go. Also, I am not sure on the results yet as I have just started the experiment. I am five days into it, and if anything else, it taste good.

      • Oh wait, I thought you were adding the RS to the already completed and ready to drink kefir. You’re adding it to the milk & kefir grains? That’s a whole different ball of wax. One on which I have no opinion; except to say, sure it couldn’t hurt. 🙂

      • If I have it correctly, I could add RS to homemade yoghurt and let it sit for a while for the Bifido to bind to the yoghurt so that the Bacteroidetes don’t get the bulk of the RS.

      • I haven’t had a problem keeping it suspended, but even if it fell to the bottom of the solution, it shouldn’t stop the bacteria from getting to it.

      • Yes, JO TB, that is the speculation/working assumption. Though, this also presumes your yogurt has bifido in the culture, usually referred to as “L. Bifidus.” Most do, but not all. It’s worth double-checking. Also, I’d add it to the yogurt, not the milk, because…

        One thing I didn’t think to ask Tate, when adding potato starch to milk and kefir grains, hows do you keep the starch powder suspended? It sinks to the bottom of a glass of water pretty quickly.

  6. Hi All

    Talking about personal experimentation; I was thinking about eating raw, organic carrots without washing them. Companies are selling SBO in a pill. So would it not be better to get the SBO from edible raw organic vegs and fruits?

    Any thoughts?

    • Wouldn’t hurt, but probably depends on the soil it was grown in. Microbial diversity is a real toss up. Organic doesn’t necessarily mean good soil. Best bet is probably farmers markets/small family farms. More attention to soil quality.

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