More On Gut Bugs And The ‘Not-Yogurt’

I had additional thoughts when I wrote the previous post about the Undoctored advice from Dr. William Davis that solved my health annoyances. I didn’t include them because the post was already lengthy. But since the post sparked quite a few comments here and on Twitter, here are those additional thoughts in no particular order.

Technically, it’s not yogurt.

Someone here or on Twitter asked if it’s possible to buy the L. reuteri yogurt in stores. No, because as Dr. Davis explains in this post, it’s not technically yogurt and can’t be labeled as such:

To call something “yogurt,” by (semi-arbitrary) FDA guidelines, it must be fermented by the microorganisms Lactobacillus bulgaricus and Streptococcus thermophilus (unspecified strains). It can contain other fermenting species such as Lactobacillus acidophilus or Bifidobacteria species, but it must contains the first two species in order to be labeled “yogurt.” So our L. reuteri “yogurt,” if this were being sold commercially, could not be labeled as such because it was not fermented with Lactobacillus bulgaricus or Streptococcus thermophilus.

You won’t find it in stores, but trust me, once you make a batch you’ll wonder why you ever thought it would be difficult.

There are benefits besides battling fungal overgrowth.

I was motivated to try the not-technically-yogurt as a means of beating back a fungal overgrowth that was causing those health annoyances. Mission accomplished. But I’ve noticed other benefits as well. My sleep is deep and restful. I have long, complex, vivid dreams. I feel fully awake sooner after getting out of bed, and don’t require as much coffee to feel human. I’ve had occasional bouts of insomnia my entire adult life, and I still get them now and then. But I don’t feel as exhausted when I don’t sleep well.

When I do sleep well, I feel amazingly awake during the day. Like AWAKE! awake, very clear-headed and energetic.

Dr. Davis mentioned in his post that people eating the yogurt have reported a number of benefits: smoother skin (including fewer wrinkles), increased muscle mass, a rise in testosterone, weight loss, etc.

I don’t know what accomplished what.

If I’d been conducting N=1 experiments, I suppose I would have started with the CandiBactin and tracked my results, then tried the yogurt without the CandiBactin and tracked them again. I began taking the CandiBactin and making the yogurt at the same time, so I can’t say how much either had to do with the improvements. I can say it was a very effective combination.

I’ve been reminded of why I need to seed and feed the good gut bacteria.

We had a chapter on feeding the good gut bugs in the Fat Head Kids book and film. (The book of course goes into more detail than the film.) I shouldn’t have needed reminding. But I guess I did … and it turns out drinking Kombucha now and then isn’t enough.

Dr. Davis told me on the phone he’s not very popular in low-carb and keto circles these days because he insists we need to eat foods that feed the gut bacteria. That means fibers – which doesn’t go over well with the We Don’t Need No Stinkin’ Fibers! people, some of whom now consider him a heretic. That’s a shame, because he promotes low-carb diets and even ketogenic diets. He just doesn’t want us to go zero-carb and stay there for months on end.  He believes that can lead to gut dysbiosis.

If you’re on an all-animal-foods diet devoid of fibers and are experiencing nothing but benefits, good for you. I hope the benefits keep on keeping on.

But I noticed several people here and on Twitter commented that they’ve experienced symptoms similar to mine. So perhaps the points Dr. Davis makes in this video are worth considering:

Keep in mind, he didn’t form his opinions just by reading research. He’s been actively treating and counseling people for years. On the phone, he told me he’s seen the same pattern over and over: overweight person goes strict low-carb or keto, and everything improves. Weight goes down, energy goes up, labs move in the right direction. Then a year or two or three later, things start slowly going south again. The weight starts creeping back on, the labs move in the wrong direction, and health problems begin to appear – like, say, mysterious itchy patches on the skin, or something that feels like a prostate-colon-whatever infection. Dr. Davis believes the backsliding is the result of inadvertently starving out the good gut bugs.

After seeing how quickly my health annoyances began to fade after following his advice, I plan to be much more vigilant about seeding and feeding the good gut bugs.

It’s not necessary to significantly increase the carbs, by the way. Like I said in my previous post, I feed the gut bugs by stirring the prebiotic mix from Gut Garden into my yogurt shake. Back when I first tried the prebiotic mix, I simply stirred it into water and drank it. I tested my blood-sugar reaction afterwards a couple of times and found my glucose level barely budged. Seems likely you could stay in ketosis if that’s your goal.

As I wrote in the previous post, my cholesterol and triglycerides were higher than usual when I had them tested some months ago. I forgot to mention I also got a fasting insulin test: 10.5 uIU/mL, which is considered moderately insulin resist, and much higher than I’d like, regardless of how it’s classified. I don’t know if that’s gone up recently because I’ve never had the test before.

After I’ve continued this program for another couple of months, I plan to get all those lab tests done again. I’ll let you know the results.

If you enjoy my posts, please consider a small donation to the Fat Head Kids GoFundMe campaign.

97 thoughts on “More On Gut Bugs And The ‘Not-Yogurt’

  1. Dan

    Great posts on gut health. Any input, comments, or experience with the so-called ‘elimination’ diets? I’m considering using them to address stubborn lower GI issues.

    1. Tom Naughton Post author

      I’ve never tried one, but have read they can be useful for getting rid of candida overgrowth.

  2. Alec

    I have my first batch of L. reuteri dairy fermentation product coming out of the water bath tomorrow morning. Fingers crossed.

  3. smgj

    I have done elimination. Not primarily for candida, but mostly for trying to find the root of stubborn intolerances. Of course, as a side effect it also battels candida (at least the one I did that also restricted “all things starchy” and sugary). The one I did was basically a low carb paleo diet, where I also eliminated certain foods that I suspected to be triggers for me, personally. No coffee or tea. No additives. No sugars, no dairy (except maybe butter)

    Thus, you start out with your (low starch) veggies and your protein + some fat from either lard/goose fat, cocoa, olive (if you have a lenient doc) or cleared butter (if you do seem to tolerate dairy). I had a small allowance of fruits – no more than a handful twice daily – but keep away from the most sugary ones like grapes, and no dried fruits (because of sugars). No legumes. Some may have eggs, some may not.

    After doing this at least 3 weeks – and hopefully clearing out any issues – this is your baseline, your “safe diet”. If you still have trouble you’ll work to find a baseline by either giving it time, or by eliminating suspects.

    If you have a baseline you may enter the challenge phase. Here you add a candidate foodstuff for at least three meals for three days (or shorter if you have an adverse reaction). You’re supposed to eat a “substantial amount” of the food that you investigate – like you feast on it.
    So, if “green tea” is on trial I’d drink 1-2 cups in the morning, midday and in the evening. If everything seems ok, I do the same for three days. Then I’ll go back to the baseline diet for a day (without the tea) before doing f.ex sweet potato (or cow’s milk or goat’s milk).
    If you have a reaction to standard dairy – you may do another trial using only lactose free. And so on – to pinpoint the issue. Your “adverse reaction” may be gastrointestinal – or not. I got a sinus reaction and bloated skin from flours… or you may get headache or eczema.

    It is critical to wait until any reaction clears out and to go back to the baseline between each challenge – and NOT TO ADD eliminated suspects back into the baseline until you’ve done all the challenges you need to. This is the most difficult for people to do correctly. (If you add the eliminated suspects back in you may have a late reaction or a snowball effect you that you won’t be able to trace….)

    An elimination may be hard, long winded and end up inconclusive – bout you’ll learn a lot on how your body react to certain foods. Often it roots out FODMAP issues (if you have onions on trial and notice the same reaction for onions and beans and other FODMAP correlated stuff you have a CLUE staring you in the eye).

    I found that my body tolerate long-fibered starches well – and thrive on them in addition to other veggies. So, full keto is not necessary for me – but that I must be careful with the starch and sugary stuff because I have a huge sweet tooth.

    The downside of the elimination is that it won’t tell you about any long-term effects. Anyways, I believe that we of northern European descent are adapted to seasonal diets. Thus, it may be better to think of a diet more of a pendulum more than a target to hit.

    (I believe that this is the explanation for most of us feeling better after CHANGING our diet – no matter what we change from or to… Most new keo/LCHF/paleo/5:2/vegans do for quite a time, then the new diet starts to fail. It may even be an explanation that what we need fluctuate during the season/life. Having said that – I do believe that some diets start out a lot closer to our bodies’ needs than others – so I’m not going vegan … )

    Sorry – that was a long one. In short: doing an elemination was really useful for me.

    1. Tom Naughton Post author

      A long comment, but illuminating as well, so thanks.

      Paul Jaminet wrote in “Perfect Health Diet” that people usually feel GREAT! after switching to some new “healthy” restrictive diet — because the new diet eliminates foods that were causing problems, and provides nutrients that were previously insufficient. Than after months or years on that diet, new problems emerge because the diet is insufficient in some nutrients and provides too much of others. So the dieter switches to a new “miracle” diet and feels GREAT! Lather, rinse, repeat.

      1. Kathy from Maine

        Another type of elimination diet is based on the ELISA IgG test (a simple blood test for 184 foods) that determines what is causing inflammation for you personally. I had it done, and then had to do an elimination diet of all the foods that caused a reaction for me. The scale is basically less than 0.199 is ranked 0 (no reaction), 0.200 – .299 is ranked 1 (mild reaction), 0.300 – 0.399 is ranked 2 (moderate reaction), and anything over 0.400 is a 3 (high reaction, causes the most inflammation).

        I had no foods in the highest category of 3, only seven foods in the moderate category of 2 (blue cheese, cocoa, egg whites and yolks, lettuce, nutmeg, and tomato), and quite a few foods in the mild category of 1 (including dairy even yogurt, chicken, peas, corn, pineapple, rice, walnuts, and gluten).

        The doc wanted me to eliminate everything in categories 1 and 2 for three full months. I did, and lost 15 pounds. Then I started adding things back in, and well, the rest is history. What was crazy about it was that I was eating closer to 80 or 90 carbs daily, with one or two servings of potatoes and one or two bananas per day! I was also taking 3 different probiotics per day (VSL #3, Mark Sisson’s Primal Probiotics, and another one I can’t remember the name of) and also digestive enzymes every time I ate something.

        Was it the foods I eliminated, or the fact that I was taking probiotics and digestive enzymes regularly that allowed me to lose the weight? Hard to say. My new yogurt maker came yesterday, and I’ll do my first batch of not-technically-yogurt tomorrow. I’m hoping that if I get back on all the probiotics, the digestive enzymes, and the super not-technically-yogurt, I’ll see some improvements in many areas.

        1. Tom Naughton Post author

          I think when you consider the effects of good (or bad) gut bugs, it’s clear that gaining and losing weight is much more complicated than just “the fewer carbs you eat, the more weight you lose.”

          Now I’m thinking of having that same test run. We have an Any Lab Test Now facility here, so I’ll check if they offer it.

    1. Tom Naughton Post author

      Never had labneh. If you want your yogurt really thick like that, you’d need to strain it.

  4. Michael

    Hey Tom, great post! By now I found out that a keto diet (nearly zero carb) suits me very well and I’ve learned a thing or two about low to zero carb diets. However, I know nothing of ‘feeding gut bacteria’ (yet) and your post made me look into some probiotics. Appearantly here in The Netherlands there’s a plethora of options when it comes to probiotics. “Contains 200 million living organisms!” “5 billion different bacteria to feed your gut” “Extracted from lactic acid” “Packed with healthy resistant starch” Etc… From your experience, is there a way of reasoning which may suit best? What even is the actual difference, are all of them the same? Or should I just give the good old trial-and-error method a go here?

    1. Tom Naughton Post author

      I”m afraid it’s a trial-and-error process for most of us. All you can do is read reviews, gather some ideas, and then see what works for you.

    2. Don

      This is my opinion, but I have cons to believe that focusing on prebiotics makes the most sense for me. The gut biome is so complex that simply adding a few strains in comparatively tiny amounts seems inadequate to me. I do make and eat L. Reuteri 6475 yogurt daily, but focus on eating a wide variety of prebiotic foods. That goes g mean that I don’t eat probiotic foods as well, but I consider most probiotic supplements to be if limited usefulness. I think the body will find it’s ideal gut equilibrium if supplied with the necessary precursors.

  5. Firebird7479

    As I mentioned in your last post, I, too have had urination problems that include stinging and burning. Tests are all negative. I had gone through physical therapy for what my D.O. felt was a pelvic floor issue. The exercises seem to have helped but the problem has come back. Typically I go to the bathroom every 2-3 hours. Sometimes I make it through the night (as I did last night) but mostly I sleep through the night.

    Two years ago I started having issues with choking and swallowing food. Woke up one morning and started gagging on vitamins. What use to be an easy task of taking all my supplements and downing them with a sip of water at the end became a routine that required 2 16oz glasses of water to get everything down. I was gagging on eggs, chicken, other meats where the last bite would sit in the back of my mouth at the top of my throat. An ENT thought it was “Silent Reflux” and gave me antacids which made things worse. I went to a G.I. He gave me samples of an antacid after checking my B-12 and Potassium levels (not to see if there as a deficiency but because the antacid would MAKE ME Deficient). In the meantime, I am drinking protein shakes, eating Quest Bars (they melt in the mouth) and baby food.

    They performed a gastrophagy and find no issues with gut bacteria. A month later they perform a manometry to see if there is an issue with swallowing. Nothing. Eventually the situation cleared up on it’s own — mainly because I was using some of the herbs in the CandiBactin, but on an individual basis. Additionally, I cook liberally with cumin which seems to really have helped with those issues.

    I’ve been reading a lot lately about many issues that they believe is tied to guy health. One of the things they said had to do with sleep — melatonin is processed in the gut. I know when I take even the lowest recommended dosage, while I sleep sounder I still wake up in the middle of the night and have a hangover most of the day. I am wondering if working on gut health will change that. Also, I have had a bad back since I was 12 and a few people think that this is wrecking my sleep to a point where nothing can help fix that.

    I’ve done some research in the past couple of days to see how I can make homemade yogurt. I found I can make it in my pressure cooker even though it has no yogurt making function. But I want to make Skyr, which is an Icelandic Yogurt — creamier, smoother with less tang to it. I’ve tried the brand that Aldi carries and I love it. My concern would be if adding the L. Reuteri to it would ruin it.

    1. James Eastwood

      I don’t know very much, but fo years I avoided melatonin becauce it didn’t make me sleep, and I had the hang over. Read that you really need only a tiny dose to aid with sleep. I now take a half of 300mcg tablet and it works very well, and no hang-over It really works for me if I wake in the night and can not go back to sleep. 70 plus years of vitamin B12 deficiency systoms have resolved since making and eating Dr. Davis’ yogurt for three months.

      1. Firebird7479

        I was taking 300 mcg of Life Extension’s melatonin. I stopped three weeks ago. My sleep is the same but the hangover is gone.

        I was never deficient in B-12. The G.I. checked my B-12 levels before giving me a new antacid to take because one of the side effects of the medication is to cause a deficiency. My levels were very high, actually.

    2. Emi11n

      I think that will depend on the conditions in which skyr is made. My understanding is that the l. Reuteri “yogurt” requires lower temperatures than regular yogurt-making bacteria, so you run the risk of one strain out-competing the other depending on which one likes the conditions better. As Dr Davis says, it’s not about yogurt, it’s about maximizing bacterial counts, and that’s what his recommended methods are designed to do. So if you fool around with other strains, temperatures or fermentation time you may be slashing your expected benefit. He recommends these specific strains because of their scientifically demonstrated benefits, so other bacteria may not give you the same results. This is just a homemade probiotic.

  6. Firebird7479

    I’ve also expressed my concerns to a few carnivore people about gut health. They believe that by eliminating all plants that there is no need for all that bacteria. Fine. But what happens when you find you can no longer sustain that diet and need to go back to including plants in your diet?

    My friend is a nutritionist and he has declared carnivores as whacked as vegans.

    1. Tom Naughton Post author

      If people like the carnivore diet and are thriving on it, I say carry on. But Jordan Peterson (as well as others) noted that once he went full carnivore, he can no longer eat any plant foods without a severe reaction. Well, yeah, of course. The diet starved away the gut bacteria that help to digest plants. If that’s a trade people are willing to make, okay. I’m not willing to make that trade.

      1. Firebird7479

        I loved the Carnivore Diet when I was on it. It just didn’t work for me and caused more problems than it solved.

      2. JillOz

        hey that is interesting.
        I find so far that meat and vegies works well for me.
        If I don’t have vegies i don’t feel properly full and eat too much meat.

        1. Firebird7479

          Same here. I find the combo of protein, fats and carbs curbs my hunger than just protein/fats alone.

    2. Morgana

      I’m not in complete disagreement with you on this, but would simply add that humans have lived a meat-only existence many times in our history, and if you think about the ice ages, it likely went on for many groups over long periods of time, perhaps even decades or more. Whole generations likely never saw anything but freezing temps where no vegetation would grow. Not all humans were as migratory as we think of today, and even if they were, when the whole Northern hemisphere is hiding under a covering of snow and ice, there really was no feasible distance of migration that made seasonal eating possible.

      While some groups, such as the Inuit, fermented meat foods and ate the stomach content remains of their veg eating prey, and in this way supplemented things like vitamin c and likely fed gut bugs this way, many cultures, like the First Peoples of the Midwest, Plains, and Northern territories spent months during the winter eating little more than fat mixed with berries. Hunting was the only thing they had to supplement their diets for long periods of time. Not a lot of gut diversity there. You can imagine that the ice ages were like that but for much longer periods.

      It occurs to me that it’s far more likely that our environments are too sterile to maintain a diversity of bacterial strains in our microbiota than it is a simple matter of a particular elimination diet starving them out. Anyone, vegan, carnivore, or whatever, gets a healthier microbiome and a heartier immune system simply by working outside in the dirt for several hours per day. Cultural groups today that rely on subsistence farming for survival have healthier microbiomes. Western microbiomes are far less diverse than those of our human counterparts in the rest of the world, and we are inarguably more germ and bacteria-aware (and paranoid) than most other countries. To our detriment, clearly.

      It has also been shown that spending time in hospitals, reduces our diversity of bacteria.

      Our indoor, sedentary, and sterile environments in this culture are undoubtedly contributing to the loss of our gut diversity.

  7. Nathan

    It sure seems the “Carnivore Diet” is just the obverse of vegan. Sure, some people may be able to be healthy on it long term, but not most people. And yes, you may see some really good results short term that make you think that this is THE way for you to eat. But of course these things take time to manifest fully. And lastly, it has become more religion than diet for many (most?) of these people. No objectivity is possible any more. Same could probably be said for just keto. Heck, even LCHF.

    1. Tom Naughton Post author

      I enjoy reading posts by Amber O’Hearn because it’s not like a religion for her. She’s stated that she’s on a carnivore diet because she literally can’t eat plants without developing issues, and she considers that a health condition.

  8. Mike Cortopassi

    Tom, you mention in the previous post you’ve been doing it for a few weeks. How long did it take for your symptoms to start going away? Has your weight gone down?

    I think I’ve read enough to try the yogurt again. It seems I probably screwed up a couple things. 1) Trying to do it in an Instant Pot, which is probably too high of a temp and 2) I did not add any potato starch or inulin to feed the bacteria. I did add sugar, though.


    1. Tom Naughton Post author

      Symptom begin to improve after maybe a week, and felt pretty much gone by three weeks. I’ve dropped four pounds so far.

    2. Firebird7479

      There are videos on YouTube that show how to make yogurt in an instant pot. They say the temp needs to get to 185-190 then cooled to 110 before adding the cultures. I’ve never made it myself. I’m just going by what they recommend in the videos.

      1. Mark

        that would be temperature of milk before adding culture. there are some sites that say not really required to heat up to pasteurize as milk is usually pasteurized already. But probably good idea if you are using raw milk.

  9. Stephen Blackbourn

    After reading your earlier post, I decided to try that “Yogurt” recipe. Unfortunately, despite giving it a few extra hours in the incubator (105F), it hasn’t set and doesn’t taste sour like I think it should. I’ll leave it a few days and hope for the best. Any thoughts?

    1. Tom Naughton Post author

      Only thing I can think of is either the pills were somehow damaged in a way that killed the bacteria, or the bacteria didn’t like whatever starch you fed them. What kind did you use?

      1. Stephen Blackbourn

        Inulin. A little past the “Best before” date but it appeared to be ok. Will get some fresh and try again.

        1. Tom Naughton Post author

          I’m thinking some raw potato starch might help. The Gut Garden mix is mostly raw potato starch.

          1. Kathy from Maine

            I had the same problem: thin and sour tasting. Maybe the tablets weren’t crushed enough, and maybe the milk/cream mixture needed to be warmed before adding it (I added the probiotic to the milk/cream right out of the fridge). Also, the inulin had an expiration date of 7/19, so it might not be as effective. I’ll get some potato starch and try it again. If that doesn’t work, I’ll probably return the yogurt maker. I like the idea of making one or two large containers rather than 8 containers with just over a half cup in each, where you run the risk of the concentration not being consistent in each.

            Quick question. Why is it that the VSL#3 probiotic needs to be refrigerated, and the BioGaia does not?

            1. John Lahore

              We had issues with temperature control, normal yogurt makers control between 110° and 115°F and go outside the range on start up variations and kill your starter bugs.
              I had to modify a slow cooker with an industrial temperature controller ($25 on Ebay) to get the narrow temperature range needed by the l-reuteri we now make it at 100°F +/- 1 deg for 36 hours and get wonderful results


      If the BioGaia bacteria were, indeed, killed, it would be dangerous to “leave it a few days,” as other bacteria will move in and take over (spoilage). At that point you would likely have a bacterial soup potent enough to cause you some real problems. If you want to try again, I suggest you throw this batch out and start over, paying particular attention to the 180 degrees pasteurization and making sure that you don’t add the L. Ruteri until the temperature has come down to below about 105- 110.

      One thing you can do to help is to make sure that you have a high quality, calibrated thermometer. Or, as Tom does, a Sous Vide. We have both, but because we prefer to make our batches by the gallon, I use the Instant Pot with a constant high/low monitor of the temperature. Besides, our Sous Vide is nearly always busy cooking steak 🙂

      From what I have heard in other places, sometimes the Instant Pot is not consistent in quality throughout the brand. In other words, if you have one that doesn’t monitor the temperature properly, then it never will, but if you have a “good” one, then the temperature will likely be fine for even this type of yogurt/not yogurt!

      My Instant Pot for the past couple of years has always maintained my incubating yogurt between 105 and 109 degrees F, never going outside those boundaries, and it has done a marvelous job of making yogurt of the traditional type as well as the L. Ruteri. Even though that is a bit higher than recommended for the L. Ruteri, my thought on that is that the bacteria is either dead or alive, and if it’s dead, there’s nothing you can do but throw it out and start over – and if it’s alive (which mine always is) the a few degrees here and there makes no significant difference (keeping in mind that there may be some things I don’t know about this particular strain, so I could be wrong.)

      So far I’ve not had a bad batch, and hope that streak of “luck” continues.

      Very interesting conversation!

    3. Don

      I have been making the L Reuter yogurt for about a year now. I have had only batch failure and so believe the tablets were to blame. Maybe heat damaged in shipping?

      I have tried many different recipes and have settled on the following:

      1/2 Gallon half and half
      4 Tbsp Potato Starch
      10 tablets / Or 2 tablets and heaping Tbsp of last batches yogurt.

      (I use an Anova Sous Vide wand)
      10 Minutes at 195
      Cool to 101
      Add starch and tablets/yogurt
      36 Hours @ 101 degrees

      I get perfect, thick, mild tasting yogurt every time.
      You may get a thinner product of working fro. Tablets but there should be no strong odor or taste! If thin just start another batch using the yogurt as starter.

      1. smgj

        I’d suppose you could leave out the tablets and just re-seed the new batch by adding a couple more tablespoons from the last batch after a while? (When you have a strong culture going.)

        That’s what I did when making sour dough bread (before I had to go GF 🙁 )

        It reminds me of a story about my great grandmother. She had a brother that migrated from Norway to the Midwest. He missed the Norwegian “kefir” very much, so my GGM took a clean cheese cloth, dipped it in the kefir, wrung it, dried it and posted it. IDK if he ever got a kefir going from receiving the cloth, but is should be possible if it was kept dry until it arrived….

      2. Charlie

        Putting resistant starch into the mix is your problem. It basically retards l reuteri (google using potato starch to treat lupus). You should use inulin made from chicory instead

  10. Jan

    Hey, I just wanted to reiterate what you say about how easy it is to make this “not-yogurt”. I have to say that your set up with sous vide LOOKS complicated to those of us who don’t have a sous vide device or the loose change to go out and buy one for precise temperature control. But there are perhaps a dozen ways to incubate yogurt, they all work fine. People have been making yogurt for thousands of years without any fancy devices. You just want to maintain a warm temperature within a specific range for a length of time.

    You can google any of the following methods for details on exactly how: In a container wrapped in a towel and placed inyour preheated oven (turn the oven OFF) , in a food dehydrator, in an electric pressure cooker with a yogurt function (or one without a yogurt function following directions you find on the internet), in a pre-heated crockpot, in a Styrofoam cooler filled with warm water, in a pre-heated vacuum thermos bottle, on a heating pad or seedling mat, in a microwave with a cup of heated water to warm up the interior (before you put the yogurt mixture in), in a yogurt maker, etc.

    Whatever is convenient for you will work, though you may have to reheat your incubation chamber occasionally if you go the full 36 hours. It doesn’t have to be fancy and you don’t have to run out and buy equipment.

    I never have to strain this yogurt. It’s very thick, with very little whey, I just stir that back in for a smooth, creamy texture. I make mine in my Instant Pot.

  11. Kathy from Maine

    I have my first batch going right now. I’m hoping it turns out right. I crushed the 10 probiotic tablets and then added the inulin until it looked like powder. Then I added 2 Tbsp of your liquid (I did half whole milk and half heavy cream) into the powder to make a slurry. Sure looked like a slurry to me. Then I added that to the rest of the liquid, stirred, and poured it into the individual glass containers. As I was pouring out the last couple, I saw that there was a bunch of undissolved powder in the bottom! DANG. I poured it all back into the large bowl and whisked until my arm about fell off. Then poured it in again. This time it seemed better.

    The yogurt maker itself is a bit odd. The box says it can make yogurt in 6 to 8 hours. The instructions that came with it say 10 to 12 hours. The instructions I got off the Undoctored site says 24 to 48 hours, but then one guy (who seems to have done this many, many times and has been successful) says he ferments it for 12 to 14 hours.

    I added some warm water to make a water bath, which is supposed to keep the temp more even. Then I set the unit to 110 degrees for 24 hours.

    How long do you really need to let it ferment? How do you know when it’s done? How do I know if it’s too hot? Check the water bath, or open one of the jars to take the temp of the actual “yogurt”?

    1. Tom Naughton Post author

      The 6-8 hours figure likely depends on incubating at a high temperature. Dr. Davis says the bacteria will be killed off at 115 degrees and suggests 100 degrees to be on the safe side. Can it fully incubate in 14 hours? Maybe. I don’t see a downside of incubating the full 36, however.

      1. Kathy in OK

        I have my thermostat set at 98 and run for 36 – 40 hours. Bob Niland says he runs 48 hours just because it’s more convenient, like 9am to 9am two days later. The longer it incubates, the higher the CFU count, which is what we’re after in the first place.

        1. Tom Naughton Post author

          Good to know. I wait until 9:00 PM to start incubating so it will be ready at 9:00 AM. If 48 hours is better, it would more convenient to start in the morning.

  12. mrfreddy


    I have kinda minor versions of the problems you mentioned. The most annoying is a recent weight gain – I am usually closer to 190 pounds, but for the past several months I’ve been mostly just over 200. I attributed it to too much booze and too many cheats, but who knows, it could be a gut bug issue. I think I’ll give this un-yogurt thing a try- why not, right?

    Along with this stuff, are you still eating tiger nuts? I was doing that for awhile, for gut health reasons, but I kinda fell out of it.

    1. Tom Naughton Post author

      I ran out of them and didn’t order more. Now that I’m convinced (again) of the need to feed the gut bugs, I’ll probably order more — although stirring the resistant starch into a shake is much more convenient.

  13. Kimberly

    Hi Tom,

    I like Dr. Davis as well, but it appears that Jimmy Moore is one of the many from the keto community that has turned on him. Have you talked to Jimmy recently about this?

    1. Tom Naughton Post author

      Not about this specifically, no. What do you mean by “turned on him”? I haven’t seen anything in that regard.

      Wait, never mind … Google search pulled up a “Jimmy Rants” episode directed at Dr. Davis.

      I haven’t seen anything convincing that a ketogenic diet causes colon cancer either. But I’m not ingesting fibers that feed the gut bacteria to avoid colon cancer; I’m doing it because the fungal overgrowth or whatever convinced me feeding the good bacteria is essential for my overall health.

  14. Sean

    Richard Nikoley did some writing on potato starch, ketosis and gut flora a couple years ago at his blog. Jimmy Moore didn’t take it well but I find potato starch/water cocktails really help with flora.

  15. Dee

    If one’s ELISA test is positive for whey and casein and there are highly negative reactions to both, is it possible to use coconut milk to make the un-yogurt recipe?

    I’ve been battling gut issues, including SIBO, low energy, and weight gain for what seems like forever and restricted my diet to meat, leafy greens, 80% dark chocolate, dandy coffee blend, and coconut milk for years now – any deviations, especially fruit or starchy vegetables, are disastrous.

    1. Tom Naughton Post author

      Dr. Davis lists coconut milk as one of the possible substitutes for cream. Let us know if that works.

    2. smgj

      I’m not sure of which bacteria strains you’d get, but if you’re up for it there are other natural ferments as well. I’ve done kombucha (I like it, but I’ve not looked into if it has any health benefits) and the Russian wild fermented cabbage (lactofermentation – delicious)
      and wild fermented salsa (also very delicious)

      The great thing about fermented veggies is that if you’re really trying to keep your carbs down, the fermentation will help – and (probably, if done correctly) add beneficial gut bacteria as well. And at the same time – if you have a hard time digesting long-chained starchy things the fermentation will help there too by starting to break down those chains.

      1. Dee

        I have experimented with kombucha and salted cabbage – love the stuff but it does nothing for thr SIBO or weight gain… I know my bacteria are good, had them tested. They’re just living in the wrong location!

        1. Firebird7479

          The only thing kombucha does for me is give me a “soda” treat. There is a brand that flavors them to taste like cola, root beer and Dr. Pepper.

  16. chris c

    So, in a nutshell, they did an excellent job of curing the condition you went in with, but the combination of antibiotics and (presumably) hospital food slaughtered your carefully tended gut biome, and just to be on the safe side they introduced fungus via an improperly sterilised catheter?

    I must admit the thought of being admitted to hospital scares me (last time I was in was to have my gallbladder out on the day Chernobyl blew, and yes I did check afterwards to see if I glowed in the dark). The standard high carb low fat low protein low nutrient diet will undo all the good I have achieved in the last fourteen years.

    I’ll keep a note of this post and the not-yogurt in case I need it in the future, thanks. Now off to eat rump steak and purple sprouting broccoli with a couple of thickly buttered oatcakes and some Chilean Carmenere.

    1. Tom Naughton Post author

      My shoulder/bicep surgery was outpatient, so at least there was no hospital food. Keep in mind I’m only speculating that the fungus was introduced during surgery. The problems began soon after, but that could be coincidence.

      1. chris c

        My mother had an emergency operation (for a blocked bowel caused by adhesions from previous surgery for Crohn’s, which we were told may happen after several years.

        The operation went well but she developed horrendous cellulitis in both legs. MRSA was never mentioned but she was on serious antibiotics for some while.

        A lot of the old folks here get joint replacements and again the operation is usually a success but it is often followed by infection or other complications. We are roughly equidistant between three hospitals and one has a seriously bad reputation while another is head and shoulders above the others.

        Someone made an interesting point, that hospital-borne infections took off after the old Victorian brass fittings were replaced by stainless steel and plastic. Copper is a surface antibacterial. Those old guys knew a bit.

        Whenever I took mother in for outpatient appointments I would monitor her afterwards to see what she had caught this time. Hospitals are full of ill people you know, things get passed around.

        1. Tom Naughton Post author

          Yup. A nurse friend of mine who worked in hospitals said basically the same thing.

  17. Susan Meyer

    I have successfully made the l. reuteri yogurt a few times and enjoy it. How many carbs per half cup when using organic half and half?

  18. wayne gage

    I was under the impression that once a gut bacteria is established it only needs fuel to stay in the gut. I eat pecans for fiber…4 grams of pecans has 3 grams of fiber.

    1. Tom Naughton Post author

      Could be, but I like the stuff and don’t see what it can hurt to keep the reinforcements coming.

      1. Firebird7479

        I read the ingredients in the prebiotic product Dr. Davis recommends. Is it really necessary to have all those going at the same time? It seems to me that potato starch, inulin, glucomannan, acacia, etc. all at once, at 20gms per serving, would be a shock to the system.

        I also looked them up individually for price comparison. Seems that this product is great for convenience but purchased separately would be more cost effective in the long run for those of us on a very strict budget.

  19. John Bafaro

    I got the same sleep/dream results with just potato starch alone when I was experimenting with it a couple of years ago. Think I’ll start it again.

    1. Tom Naughton Post author

      I did too, probably for the same reason: the gut bacteria were happy.

  20. Kathy from Maine

    Hi, Tom! One more question for you regarding the AR and BR formulas for the CandiBactin. I saw a couple comments on the amazon website. One said: “You need to alternate attacks on candida because it grows immune. So, five days on one, then 5 days on the other, with lots of water.”

    Another comment was this: “According to Dr. Mark Hyman, they are herbs for cleaning out bad bacteria or yeast. Take 2 capsules of the BR three times a day for a month for the bacterial overgrowth, and take 2 capsules of the AR three times a day for the yeast.”

    What did Dr. Davis tell you regarding how much, how often, etc.? Does he recommend X number of days on one, and the X number of days on the other? Any thoughts on this? Thanks!

    1. Tom Naughton Post author

      Interesting. Dr. Davis told me to just take the recommended dosage, so that’s what I’ve been doing. I haven’t altered them, but that sounds like a good idea.

  21. egocyte

    Hello Tom.
    What is your view on kefir and tibicos (water kefir) ?
    I make tibicos for the good bacteria it contains. In theory there would be almost no sugar left after 48 hours but I’m not sure because it still has a sweet taste.

      1. egocyte

        I find it interresting because it’s very easy to make, you just need kefir grains (50-100 g), water (1 L), sugar (50 g), a fig and a lemon (or just its juice). The fermentation is dead simple : you let the whole thing sit at room temperature in a jar not hermeticaly closed, and watch it bubble. If you want to keep the bubbles to have a sparkly drink, you filter out the kefir grains and have a second fermentation in a closed bottle (the drink is cloudy, so there are remaining bacteria in it), then in the fridge before drinking. My concern was about the remaining sugar, suposedly you have 80% of sugar transformed in C02 and other components by the end of the fermentation, so you’re left with “only” 10 g/L in the end. I’m wondering if the probiotic effect is not conterbalanced by the sugar.

  22. Brandon

    Tom, thanks for sharing this. I just finished my second batch, which was far superior to the first, just using some of the first yogurt as a starter with no additional crushed probiotics. It thickened much faster and has a much creamier texter. I did, however, use organic milk and the second batch and not the first, so I’m unsure if that may have affected the quality. I use the yogurt setting on the instant pot and it’s really amazingly easy to make. I can’t believe I haven’t played around with making yogurt earlier. I’m excited to see if batches continue to improve and if I notice the positive effects so many here and at the Wheat Belly blog have noticed. Thanks again for sharing!

  23. Patti

    Hi Tom,

    Now that it is November 2019, have you continued to consume the yogurt and Gut Garden resistant starch daily. If so, did your weight return to 200 and have you noticed any other benefits beyond sleep and the resolving of the fungal infection?

    Thank you,

    1. Tom Naughton Post author

      I cut back the yogurt to a few times per week and ran out of the CandiBactin. I figured I was probably rid of the infection by this point. Nope. The symptoms have just started returning, and my weight drifted back up to 210. So I ordered more CandiBactin and will resume eating the yogurt daily again as soon as our next batch is done.

      1. Patti

        It would seem that there were some benefits, however, possibly the course of treatment needs to be longer? It would be interesting to know if after you go back on the CandiBactin if you get the same results the first time you used it.

        I ordered the L. Reuteri and the prebiotic mix you were using to see what kind of benefits I might be able to achieve.

        Thank you for answering.

        1. Patti

          So I purchased the L. Reuteri from BioGastrus and the Gut Garden and made “yogurt” from both products. I used a dehydrator to keep the temperature around 97 degrees for 36 hours. The results were not yogurt but a separation of liquid from a bubbled infused blob which smelled like cheese and the flavors from the tablets. I was going to throw it away but instead I put in the refrigerator. This was two weeks ago. Today I opened it and it smelled only like cheese. I took a taste and I must say it was not bad sort of like a cross between feta and blue cheese. I sent an email to BioGastrus in St. Louis and asked if they have it in powder form instead of the tablets due to the tablets in my opinion have a nasty flavor. The representative said they are working on it for 2020.

          On another note, David Sinclair, author of Lifespan why we age and why we don’t have to, said on the Joe Rogan podcast that he makes his own yogurt from a culture that mimics the gut biome. He did not state the name of the company and I have been trying to locate the name but to no avail. Have you heard of this? Apparently this yogurt also has benefits for weight.

          1. CC

            I just got the same exact cheese result. Crumby like feta w a not unpleasant funkiness to it. I think I will use the whey to try again. Meticulously ran 180 degree heat and cool before adding the crushed tablets and potato starch.

            1. Patti

              Hi Tom,

              I finally received a response from David Sinclair regarding the yogurt starter he uses. I thought you might be interested in knowing about it. The name of the company is Bravo Probiotic Yogurt.


  24. Sandra Percell

    Hi Tom – I am so sorry for all of your recent troubles. Some thoughts for you:

    I take Bio Kult. It was developed by the Dr. who developed the GAPS diet for autism.
    I believe it is enteric coated and they have tested that it actually reaches the gut and has a 2 year shelf life. and is a bit controversial, but he has aggregated some interesting research that others have done regarding the effect of blue-light toxicity on the gut and the hypothalamus and on circadian rhythm and the all important distance between respiratory proteins in the mitochondria which could be very relevant to you as a programmer and blogger who stares at screens all day and into the night. I wear orange uvex glasses while in front of screens in order to block this blue light. 8 bucks at amazon.

    Also, in future please try to use any other antibiotic besides a fluoroquinolone. There’s much more that could’ve happened to you from the fluoride – it blows mitochondria and tendons apart. My sister-in-law was floxxed and suddenly was experiencing ruptured tendons in her shoulder and ankle. And it now has a black box warning on it for causing some huge rate of aortic aneurysms within 2 years – which I personally suspect led to aortic aneurysms in an exboyfriend and my dad. If you ever feel extreme pain in your upper gut below your heart, go immediately to the hospital. My dad did, and they were able to put him into emergency surgery and he survived. My ex didn’t because he was the sort who prided himself on “playing hurt” .

    Here’s Jack’s take on what Cipro does to the body. You can google around “Jack Kruse” and “Floxxed” to see what he recommends to repair the damage.

    Wishing you the best.

      1. Mindyroo

        I followed the Wheatbelly recipe for L reuteri yogurt with organic half and half in an instant pot for 36 hours. My yogurt came out perfect, but I must ask, is it supposed to taste like sour meat?

        1. Tom Naughton Post author

          Heh-heh … it’s an acquired taste. I mix mine up with protein powder, some berries and some stevia.

          1. Donna Armstrong

            In some studies, stevia was found to kill L. reuteri. You can Google and see the details and rebuttals as well. Curiously the only real article stating stevia is harmless to gut bacteria was done by a stevia company and they did not specifically test reuteri most likely – This bacteria is very limited in modern “civilized” humans, especially those not breast fed through many generations.

  25. John Sutherland

    I am confused, I have seen different recipes for make L. Reuteri, seme say 99, 100, some say higher like 110 is needed.
    If I use a higher temperature like 110 will it kill it?  What temperature will maximize the bacteria growth?

    1. Tom Naughton Post author

      Doctor Davis recommends 100 degrees. We incubate ours in a sous vide at that temperature for 36-40 hours.

  26. Robby

    I’m totally shocked that apparently there hasn’t been a single person to test the CFU of 6475 in the yogurt. This has incredible potential, so why wouldnt any of the high profile proponents actually have a CFU test done (Dr. William Davis) ? I would think it’s crucial to have a general idea of the potential CFU count of reutri 6475 in each batch. Has anyone done this yet? If not, I will….

Comments are closed.