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Why taking Probiotic Supplements may not solve all your gut issues

written by Vin Kutty

comments 143 comments

probiotic supplements

Probiotics are popular. People who don’t follow probiotic research are quick to dismiss these pills – they’d be making a mistake. Probiotics are POWERFUL! But taking these pills alone won’t fix all your gut issues. For that, you’ll also need to make other lifestyle changes.

probiotic supplements
A lesson for grown-ups: kids naturally know where to get their probiotics.

While playing in the backyard several years ago, my very young daughter picked up a roly-poly pill bug. She quickly ate half of it and offered me the other half.

We’d been trying to teach her to share.

‘Aye-aye-ugh…thank you, sweetie,’ I replied, trying to hide my horror. The suburban father in me was disgusted. But the geek in me was quite pleased about the introduction of new probiotic strains into her gut.

How was I going to explain it to my wife? This, a day after the same child was caught swirling her hands in the toilet bowl. The kid was under my watch during both incidents.

This brings me to why I don’t regularly take probiotic supplements. Yes, sometimes, this blog strays from talking about Omega-3 and fish oil supplements.

It’s not because I don’t think probiotics are not important. Quite the opposite – they are desperately important.

The importance of a healthy gut flora

I take probiotics. But not every day. We’ll soon get to the reasons why…

But there’s more to it than eating a cup of Activia and hoping you’ll poop regularly. If you take probiotics just for being regular or to boost immunity (whatever that means!), you’re missing the big picture.

There is a flood of new research proving that your ‘microbiome’ or the trillions of bacteria that live in your gut have an effect on not just your gut health, but also several other aspects of health*

These critters control us more than we ever thought possible.

The problem with relying exclusively on probiotic supplements

There are over a thousand species or strains of bacteria in a healthy gut.

‘Potent’ probiotic supplements have, what, a dozen species? What about the other 99% of species?

I’m guessing that if you took every probiotic supplement known to mankind, that you’ll get to about 100 different species. That’s great…what about the other 95%?

We don’t know enough about each probiotic strain to know what each one does.

Exceptions are products like CardioViva, a Lactobacillus shown to help your heart, and products like Align or Culturelle. Or even probiotics for mood, like this Mood Probiotic.* These are  proprietary strains used for very specific health goals, with research behind them. This is where the future of probiotic supplementation is going. There are proprietary (or patented) bugs for colic, mood,  weight loss etc.

The bugs in a healthy gut are mostly environment-sourced. That is a nice way to say dirt. In this list of top gut bacteria, Lactobacillus and Bifidobacteria are only part of the microbiome, not the entirety.

My point is: the number and variety of healthy bacteria in your gut are extremely important.

Sure, probiotic pills mayhelp, but unless you’re taking one of the patented strains listed above, you cannot quantify the benefits.*

If you really want to improve your health and have a thriving gut population of probiotics, you will need to upgrade not just your probiotic supplement, but also your diet, lifestyle and your attitude towards dirt.

The two key things about your gut flora are:

  1. The number of healthy microbes in your gut
  2. The variety of healthy microbes in your gut

But before we jump in, while you read all this, keep in mind that we’ve just emerged from the dark ages of probiotics. There has only been focused research on this for a couple of decades. And US consumers have only been aware of it for a decade or so.

What we know about the benefits of having a healthy gut microbiome is miniscule. I suspect it will be a fairly common occurrence in our great-grandchildren’s time to get poop transplants. Fecal banks. Seriously. Take a little poop from a healthy person and delicately welcome it into ones hind quarters to make an incomplete person whole. Sound crazy? It’s already being done. It’s been effective and safe. (Update: fecal banks already exist! OpenBiome)

Want to lose weight? Skinny and obese people have different sets of bugs in their gut. Can transferring bacteria from a skinny person’s colon into an obese person (fecal transplant) make them skinny? Don’t know.

Poop pills are also not science fiction. It’s also already been done. And has helped some people with irritable bowel syndrome and colitis. We won’t be selling those. Sorry. I know…

The point I’m trying to make (besides using shock to expand our view of the role of probiotics) is that we’re at the leading edge of this probiotic revolution. There are brave pill poppers out there, yet there is a lot we don’t understand.

Back to discussing the key factors in probiotics:

The number of Probiotic Bacteria

No, I’m not talking about the bug count on the bottles.

10 years ago, it was impressive to have 1 million acidophilus bugs per pill. Then the cool kids started selling 1 billion. Then 10 billion. Now 100 billion doesn’t get much attention.

This is a marketing rat race and it’s mostly bullshit.

Whether you’re welcoming these bugs into a place that’s hospitable to them and whether you eat foods they need is what matters.

It’s easy (and normal) for the 100 billion to become 10 billion while the bottle is on the shelf. And then for it to become 1 million after the bugs have been thrashed by your stomach acid. So don’t fall for the numbers nonsense.

A healthy gut has hundreds of trillions of thriving bacteria. One pill isn’t going to do a damn thing to the total number. If you look at your body as a total number of cells. We are outnumbered. There are more bacterial cells in your body than human cells. You’re 5% human and 95% bacteria. You’re a giant lump of bacteria wearing a human suit. Sorry – I calls it as I reads it.

What affects the number of bacteria in your gut?

Antibiotic overuse and a diet low in soluble fiber are the two main reasons for reduced gut flora.

Antibiotic overuse. Sure, they save lives. But rampant and often unnecessary antibiotic use is the #1 killer of healthy gut microbiomes. Antibiotics are indiscriminate, killing both good and bad bacteria.

This becomes a vicious cycle because a compromised bacterial community allows you to get infected by antibiotic-requiring harmful bacteria. And yes, they are a community. Good guys join hands and fight the bad guys. Example: think of a probiotic-compromised child born via C-section and exclusively bottle fed. He or she invariably gets an ear infection and gets regular doses of antibiotics. It could take the child several years (if ever!) to recuperate a full gut flora.

We worry about creating resistant bacteria with excess antibiotic use. But the bigger risk may be that we’re permanently altering our protective gut flora with each antibiotic treatment.

One course of a gut-blastin’ antibiotic like Cipro can wipe out a third of your bacterial community.

If you have to take antibiotics, make sure you take a variety of probiotics (separate the dosing) to keep side effects to a minimum.  I take this yeast product.

Diet. Gut bacteria use soluble fiber in your diet as a food source. This is the kind of fiber that you really want, not the physically abrasive insoluble kind marketed on breakfast cereal boxes that does very little besides increase stool volume.

Soluble fiber is found in veggies, fruits and beans. They’re also found in unrefined grains, but you get more bad than good with grains. Since most of us don’t eat enough veggies, we starve our gut bacteria. Same goes for the extreme low-carb folks who eat nothing but animal protein and fats – you may be skinny and non-diabetic for the first time in a decade, but your gut flora is starving.

We’ll get to specific foods for your gut later.

What affects the variety of bacteria in your gut?

The variety and diversity of your gut flora is key. Having the right type of friendly bacteria is important not just because of the push and pull of friend versus foe, but because good bacteria secrete butyrates and other fatty acids that keep your colon healthy.

People with IBS have 25% fewer types of bacteria in their gut. We’re talking variety, not total numbers. They’re missing 250 of the 1000 or so types of bacteria. Turns out that folks with colitis and Cronh’s have similar limited bacterial ‘signatures.’

Antibiotic use. Besides cutting down the number of friendly flora, antibiotics wipe out, sometimes permanently, many species of bacteria.

Dirt-phobia and germophobia. This is a big one. I know people who douse their children with antibacterial hand sanitizing goop every few hours. It’s done with good intentions but if only they knew the harm they’re inflicting.

Toddlers and preschoolers need to get grubby and dirty. They check to see if everything is al dente. This is the natural process of gut colonization.

Of course, never to leave a fear untapped, marketers have taken germophobia to new heights. Heck, they sell Triclosan-laced antibacterial toothpaste and kitchenware! I give up.

Exposure to nature. Children living on farms have far less allergies and asthma than city kids. Children exposed to dirt (and the organisms within) and farm animals during their early years even get some immunity from Type 1 Diabetes.

A century or two ago, most of us lived on farms and rural areas full of dirt and bacteria. Showers were scarce and everyone may have walked around with clothespins on their noses but allergies, Crohn’s and type 1 diabetes were rare.

Nature is where we get a lot of our good bacteria – soil based organisms or SBOs – it’s cleaner sounding than saying ‘Bugs From Dirt.’

A ‘soil-based’ bacteria commonly found on fruits and vegetables, Mycobacterium vaccae, has been shown to improve cognitive function and diminish anxiety-like behavior…at least in animals.

I know some people who eat their backyard veggies ‘lightly washed,’ just to get some bugs. For the less daring (nutty?), I suggest a product called Prescript-Assist, a supplement of soil based bacteria. I occasionally take it and even sprinkle it over my kids’ dinners. Even it contains only about 29 species. [Addendum: the company that makes it has changed hands and the product may have changed since this writing.]

Our manicured and sterile suburbs and homes in middle-class and upper middle-class America are dangerously empty of dirt.

So munch away, my dear, on roly polies. We won’t tell mommy.

If you’re lucky, you may still have the bacteria that your mother gave you during childbirth and breast feeding. Or the bugs that you swallowed from your own roly-poly-eatin’ days.

Other factors like high-sugar diets, chronic stress and early childhood conditions like C-section birth and bottle feeding also affect the variety gut flora.

If probiotics are so great, should you take one daily?

There is nothing wrong with supplementing with probiotic pills. In fact, it may be a great idea. Many of the bugs in probiotic supplements are transient – they are gone from your body in a few weeks. While they do a lot of good during their stay, supplements, simply by themselves are inadequate.

There is even some emerging evidence that suggests cells from dead bacteria may have an influence on our bodies.

I’m constantly trying to increase the variety and quantity of my gut flora. I use supplements as part of a ‘recolonization program,’ especially if I’m forced to take an antibiotic. I recently had to take Cipro after picking up a charming respiratory tract infection while camping in the Amazon jungle.

My gut recolonization plan:

  1. Take Prescript Assist, InnovixLabs Multi-Strain Probiotic and about a dozen different brands of supplements. Once I’ve reintroduced these bugs to my gut, I take them intermittently instead of daily.
  2. Fermented foods. Fermentation often takes place in low-oxygen environments like our gut. These anaerobic bugs are not often found in supplements. I consume several different types of sauerkraut, kimchi, kefir, kombucha. I love this Hot Pink Jalapeno Garlic Kraut. I make yogurt at home – the stuff in grocery stores don’t interest me because they’re sweetened, too low in fat, underfermented (still milky with too few bugs) and too high in lactose.
  3. Soluble fiber and Resistant starch. This is really important. I gradually increase the prebiotic content in my diet by eating more soluble fiber and resistant starch. These are what gut flora thrive on. A little bit of prebiotics can make a huge difference in the number and the ratio of good vs bad bacteria in your gut. You could try prebiotic supplements (fertilizers for probiotics) like Inulin FOS or Arabinogalactan, oligofructose etc., in very small doses at first. I prefer food to supplements, but InnovixLabs Broad Spectrum Prebiotic contains one of the widest varieties of prebiotic fibers.  Raw onions, garlic, leeks and jerusalem artichokes are good sources of prebiotics. Phenolics in coffee, chocolate, and tea are good prebiotics too.

Don’t fall for products that claim to be both pre and pro-biotic. This is like a shampoo with a built-in conditioner. For prebiotics to work, you need teaspoon quantities of it. Fairy-dusting is a marketing gimmick.

If you have a yeast or pathogenic infection, you’ll need to work with an Integrative Medicine MD near you to address that first. Complete that treatment before you attempt probiotics or prebiotic fiber.

The real reason I don’t take probiotic supplements every day…

 …is that once you have ‘recolonized’ your gut with probiotics, eating soluble or prebiotic fiber to feed and grow your probiotic flora may be much better than continuing to take more probiotics. This is a far healthier, cheaper and tastier approach to maintaining gut health.

After all, what’s the point of taking probiotic pills if you’re not feeding your gut flora with the right kinds of food? Think of them as a pet you have to feed. A few grams of prebiotic fiber can help your gut microflora both multiply and diversify more than probiotic supplements alone. In another 10 years, prebiotic fiber may be viewed as far more important than probiotic supplements.

Fido or Bifido – both need to be fed.

Care and Feeding of Bowel Bugs

Start eating foods rich in soluble fiber: brussel sprouts, avocado, yams, potatoes, oranges, sweet potato, asparagus, nuts, apples, turnips, plantains, taro, and broccoli.

You can get soluble fiber from beans, but make sure the beans are soaked overnight before you cook them.

Here is an easy way to cheat: InnovixLabs Broad Spectrum Prebiotic contains over a dozen different types of soluble fiber that you won’t digest, but will make your gut flora very happy. Different fibers for different bugs, in different sections of the gut. Note that feeding just one type of bug will help sustain a community of bugs that depend on the waste of the first bug as a food source. Start with just half teaspoon a day and work up to a couple of tablespoons per day…or else you’ll end up with what my roly-poly eater calls butt-burps.

The cell lining of your colon is built to thrive on the butyrates secreted by probiotics. Any left over butyrates help heal the gut.

Oh, and if you want find out what’s in your gut, check out the American Gut Project.


Probiotics are great. But Eating fermented foods and feeding your gut bacteria soluble fiber are just as important as taking probiotic supplements.*

Source: Benjamin Arthur (NPR)


*These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure, or prevent any disease.


Join the conversation

  1. Some probiotic supplements do work. For example, Natures Sunshine’s “Probiotic Eleven” is a high quality product containing 11 strains of live flora. It may be only 11 strains but they are the important ones that contribute significantly. Adding these 11 strains is better than where you were before. It’s a very popular product because it works and makes a noticeable difference. Theoretically it may not make sense to take a few strains but I recommend trying it for yourself, this brand preferably.


    • Hi Brandon – that’s quite a testimonial!

      Actually, all probiotic supplements work to varying degrees. At the very least, they introduce that bacteria to your gut. There is definitely a place and time for probiotic supplements. Perfect example is during antibiotic treatment – taking probiotics during a course of antibiotics can dramatically reduce side effects like antibiotic-associated diarrhea. This side effect is experienced by about a third of antibiotic users who do not take it with probiotics, while only about a tenth of the people who take antibiotics WITH probiotics experience this distress. I think this alone is worth the price of a good product. If I were to randomly pick products, I would go with Prescript-Assist first then others like Garden of Life Primal Defense or RenewLife Ultimate Flora.

      You should then continue for a little while after the antibiotic therapy to boost bacterial diversity. Then there are several other cases where specific strains of bacteria have been shown to boost or produce specific health effects – like CardioViva, Align, Culturelle.

      • Sure would agree with Culturelle, but I took it within 1 hr = anaphalaxis EPIPEN to the rescue. Checked by Allergist yes allergic anaphalactic reaction. He stated could not tell what I had reaction to because they didn’t list proprietary blend. Called the company, they said sorry for the reaction but could not give me ingredients. Well doesn’t sound like a reputable company to me, especially with a documented problem by a certified doctor with over 45 years experience in allergies. Too bad they have to add dyes and other crap that more people than not are allergic to. Proves my point they are not in it to help people.

        • Wow – Laurie! So sorry to hear about that. There must have been some protein in there that you’re seriously allergic to. This is one of the problems with ‘proprietary’ blends. To keep competitors from knocking the product off, they wont share any pertinent information and sadly, this is the price to pay. Then again, even if they had declared all the ingredients, it is hard to tell if a odd strain of bacteria was cultured in something that you could be allergic to. There are so many factors that go into making these proprietary blends that unless you take it and have no reaction, there is no way to know if it is safe or not. Fortunately, you can take other probiotic formulas (hopefully) and eliminate things like gluten and sugars from your diet. You can even take some of the prebiotic fibers mentioned in the article and eat starchy root vegetables.

    • Hi Aaron – the key reasons why I recommend Prescript-Assist is that it contains almost 30 species of soil based bacteria and that the combination of these bacteria has been studied and shown to impart health benefits. I didn’t notice anything different when I took it, but then again, I was trying to recolonize by gut after antibiotic treatment. As far as the leonardite (fulvic), I did not know that it was a prebiotic until I bought the product. Need to research that more. Leonardite is basically ‘dirt’ and is probably what gives the product the almost charcoal like appearance. Frankly, I dont think there is enough of it in these pills to reduce any heavy metal load. I am not particularly concerned about it either way because once I finish a bottle, I don’t continue taking it.

      • Hi Vin,
        Glad I found your blog! I’m in the middle of my 2nd diverticulitis flare up in 3 months, after having only 1 prior. Clearly something is amiss in the boiler room. I’m taking Augmentin as the antibiotic du jour to treat the inflammation, it seems to be working ok. 2 questions: did you take prescription assist while you were taking your antibiotic? And, if you were diagnosed with Diverticulosis, would you consider daily use of Prescript Assist as well as changes to your diet? I am looking to avoid bowel resection surgery at all costs.
        Thanks for a great blog.

        • Hi Patrick – no, I did not take any probiotics while I took antibiotics. It is sometimes advised that you take probiotics along with antibiotic treatment. There is some evidence that taking probiotics along with antibiotics cam help reduce digestive distress caused by antibiotics.

          As for what I’d do if I were diagnosed with diverticulosis…well, this is not medical advice. This is just what I’d do: I would consider it a friendly warning. I’d dramatically change my diet to include at least 25 different vegetables every week (no particular reason behind the number 25 but it’s what I’ve told hundreds of people over the years). I’d quit sugar and processed foods (anything with flour) cold turkey. I’d ‘seed’ my gut with a few good probiotics: Prescript-Assist, Equilibrium, InnovixLabs Multi-Strain, and possibly others. I’d begin to eat a lot of prebiotic-fiber-rich foods. I’d also take prebiotic supplement – our sister company has a good one:

          Diet and prebiotic fibers may be far more important than probiotics. I’m not sure how much this will reverse the condition, but it’s possible that eating this way could have prevented it.

  2. Great article Vin. I do most of the things here (including Prescript Assist), but haven’t delved into resistant starch yet, although I’ve recently been reading about it. Do you just stir this into a liquid or mix into foods or?


    • Hi Mark – from past exchanges, I know you are low-car/paleo, so I strongly think you should look into resistant starch. Low carb or ketogenic diets are amazingly effective at many thing, but one of the drawbacks is the starvation of gut flora. You could always take the onion, garlic, leeks and jerusalem artichoke, green plantain chips route to get soluble fiber and resistant starch, which may be a lot more fun, but Bob’s Red Mill unmodified potato starch is about 70% resistant starch. So you won’t digest that 70% and it won’t add much carbs to your diet but your gut bacteria will be thrilled. My only suggestion is to start reeeeeal slow. Half teaspoon per day for a week and then go to up by half teaspoon every week or so. Otherwise you’ll be bloated and gassy. It’s virtually tasteless. I take 2 tablespoons daily, blended into my smoothie and no issues. I haven’t seen any research on this, but I suspect that soluble fibers and resistant starch from different food sources may benefit some types of bacteria than others. So I suspect it is best to get a wide variety of soluble fibers from different foods.

  3. Hi, Vin,

    This is another wonderful article that provides valuable information in an emerging area … probiotics. I have about a million questions, so I won’t start here. Rather, I’ll save them for another time and another place.

    Suffice it to say that I have followed your advice and recommendations.

    Nice work, and thank you!


  4. Hi Vin,

    Very interesting ! You mention sprinkling Prescript-Assist over your kids’ dinners. But won’t opening up the capsules expose the contents to stomach acids and the bugs can’t survive long enough to set up shop in the intestines ?



    • Hi DPK – the Prescript-Assist capsule is not enteric coated. So once you swallow the pill, the capsule will dissolve in your stomach in about 10 minutes and be exposed to stomach acids. So I am not risking the survival of the probiotics by opening the capsule. All probiotics have to run the gauntlet of stomach acids…at least if you were to rely on natural foods and dirt to get your bugs. There are some probiotic supplements that are stomach acid resistant – if you are concerned, you may want to look into these, but the downside may be that these strains may not have proven research behind them.

      • Vin,

        Just started a batch of the hot pink jalapeno garlic kraut. I’m on a low salt diet. This recipe calls for 1 tablespoon salt. Once I’ve finished the batch, will my blood pressure be off the chart ?

        This what I use in my “fermentation” … I call it pickling, however.
        * water & white vinegar (2 cups water/1 cup vinegar)
        * salt (1-2 teaspoons)
        * sugar (1/4 cup)

        Everything then can be eaten in 2-3 days instead of the weeks it would take for the traditional lacto-fermentation method. Example, per the recipe, the hot pink kraut takes about 3 weeks before you can eat.

        My question: is the method I’ve been using, with vinegar to speed things up (cheating ?), giving me the beneficial bacteria you recommend ?



        • Hi DPK – my opinion on salt is that it’s been unfairly vilified, like saturated fats. If your blood pressure is bad (usually due to other dietary reasons), salt will nudge it up a little…but salt isn’t the root cause of the problem. Your body needs a little salt every day. Without it, you’ll stress out your adrenal gland and cause several other problems. Of course, if your doctor put you on a low-salt diet, you should remain on it until you’ve checked with him/her.

          The two to three week process is what is required to grow the good bugs on the kraut. Without the traditional method, you’re just eating sour veggies. Not that anything is wrong with sour veggies.

          • I added about 3 teaspoons of white vinegar to the salted kraut for added tartness. I’ve read this can kill the beneficial lacto bacteria I’m trying to grow due to the vinegar’s low pH level, around 2-3. True/Untrue ? And if untrue, at what stage of fermentation is it safe to add vinegar ?

            Is there an acidity threshold above which these bacteria simply will not grow/survive ?

            Again, many, many thanks for taking my questions.


            • Hi DPK – I am far from a fermentation expert! My experience is limited. But I know that acids certainly can kill some of the probiotic bacteria. You also have to think about the ultimate acid test, which is your stomach. Only about 30% of probiotics survive the stomach. So you may just be ‘pre-killing’ the acid-sensitive ones with your vinegar. Then again, even the ones that survive stomach acid may not make it thru your lower-acid but longer-immersion process. Generally, if you’re trying to grow bugs, killing them with vinegar seems counter-productive to me. Just my 2 cents. You may want to bounce this off someone who knows REALLY veggie fermentation.

              • Vin,

                When juicing, the manual advises to drink the juice immediately, within 15 minutes of juicing, to keep the extracted nutrients from degrading. Or if the juice can’t be consumed immediately then it has to be stored in a glass container, completely covered and refrigerate to prevent exposure to air/heat which will destroy the nutrients. Even then, it can only be kept for no more than a few hours.

                Your opinion please. I’m thinking stomach acids are probably more powerful than either air or heat and if the juice can survive the harsh stomach environment then surely leaving it exposed beyond the 15 minutes recommendation won’t harm it.

                I no longer juice, prefer smoothies instead. Does the same advice apply to smoothies ? I like sipping my smoothies slowly, not gulping it down in a hurry. I take them to work for b-fast so by the time I finish, it will have been a couple hours from the time I started making the smoothie. Am I doing this all wrong and destroying all the nutrients ?



                • Hi DPK – there is some truth to nutrients in foods degrading with time and processing. But this is a matter of perspective. If you want fresh, then pluck the fruits right from the trees. Fruits and veggies are already old when you get them from the grocery store. Let’s accept that. Ideally, we all should walk 10 miles a day while harvesting perfectly ripened berries, stealing eggs and hunting deer. That’s what our bodies were built for. But we haven’t lived that way for several thousand years.

                  So, yes, you do lose a few nutrients when you let it sit around. But don’t beat yourself up about it. It takes me an hour or two get through my smoothie too. No big deal. Diet wise, if you’re avoiding sugar, vegetable oils and refined grains, you’re 90% there. The other part of health that everyone ignores is stress management, adequate sleep and activity.

  5. Vin,

    Vin, I am currently taking your smoothie concoction, consisting of AROY-D 100% Coconut Milk, Great Lakes Gelatin, Rapunzel Pure Organic Cocoa Powder, and Bob’s Red Mill Potato Starch. All of these ingredients are available on Amazon. I add a teaspoon of flax seed to that, as well as some strawberries and raspberries. The taste is a bit chalky, in my opinion, so I wonder what I can do to sweeten it? Agave?

    I am also experimenting with Jarrow Formulas Jarro-Dophilus EPS, a probiotic supplement.

    What is your view of this approach, taken together?



    • Hi RWM – let’s talk about the chalky taste first. My suggestion is to make the smoothie everyday for the next few days but leave out one ingredient and see if that elimination gets rid of the graininess. It is possible that you are adding too much of one or the other.

      Sweetness. Sounds like you’re still sugar detoxing. If made the right way, this smoothie does not need a sweetener. My suggestion is to add some blueberries as well. Use dark colored berries – these are the best choice of fruits. If it is still not sweet enough for you, try half an apple or banana. Adding sugar or anything to this high-fat smoothie is a bad idea. Fat + sugar = bad things. Keep the sugar low for a 2-3 weeks to let you taste buds reset. It takes a while. Trust me, if you can make it for a few weeks, you’re off the hook. Don’t go near Agave or any of that crap.

      The probiotic you’re taking is fine. No rationale for combing the supplement with the smoothie. Independently, both are OK. The goal of the smoothie is to cut back on sweet breakfasts and to help satiate (no cravings) well past lunch time. Cutting out the sugar in your diet will improve the balance of good vs bad bacteria in your gut.

  6. Do you know if taking birth control pills “sterilizes” your gut system therefore probiotics have to continually be taken ?

    • Hi Char – birth control pills have other issues associated with them, but killing friendly bacteria is not one of the known side effects. So you should be OK from a gut flora perspective.

  7. Vin,

    1. Please clarify. You only take probiotics as part of a ‘recolonization program.” Since many bugs in supplements are transient, how do you increase the number & diversity of bugs if they don’t stick around ? If the SBO’s in Prescript-Assist only hang around a few weeks then wouldn’t you have to take these on a regular basis and not just occasionally ? How long do bugs from fermented food such as the hot pink kraut stay ?

    2. “Don’t fall for products that claim to be both pre and pro-biotic …. For prebiotics to work, you need teaspoon quantities of it.” Prescript- Assist also contains prebiotics is the form of leonardite. Each capsule is slightly less than 1/4 tsp full so how useful is this miniscule amount of prebiotics ?

    3. In terms of resistant starch, is it safe to assume some is better than none at all ? Does, say, taking 1/2 – 3/4 tsp/day provide some nutrients to the bugs or is this amount just a complete waste ?

    4. In reference to the yeast, Nutricology posts this statement on their web site: This product is heat sensitive, and will be shipped Next Day Air, “Signature Required.” If you choose another shipping method during checkout, your completion of the order verifies that you take full responsibility for the condition of the delivered product. Cost $26/50 caps.

    Amazon has the same for half the amount, $12.99/50 caps with no reference to heat sensitivity. Is Amazon doing something wrong ? How can you determine if the yeast’s still active ?



    • Hi DPK – good questions!

      Many bugs are transient in that you stop being able to measure them in large quantities in the stool. That does not mean that they have been completely and 100% cleared from your body. They may be there in small quantities. But they are present in larger quantities, they certainly provide a lot of benefits. Also, the key point I was trying to make with this article is not that I stop consuming all probiotics after my recolonization, but that consuming probiotics from fermented foods, accidentally from nature (read dirt), ingesting soluble fiber from veggies needs to be a daily and constant thing.

      If you interacted with mother earth (read dirt) like we are all designed to, then we would not need SBO supplementation. This is hard for many people to do – I hike a lot, vacation in uncivilized places and play in the backyard with the dogs and kids, but even that is probably not enough. We’re just simply too clean for our own good. My kids are already conditioned to be dirt-phobic. Sad.

      So may be there is a point in taking SBOs as supplements more regularly. Again, the point I was trying to make is to not depend on supplements for your health – they have their place, but they should not be the base of a healthy lifestyle.

      I don’t know how long the bugs from fermented foods stick around. But since we are supposed to be eating that stuff regularly, it probably does not matter.

      The prebiotics in Prescript Assist is probably insignificant.

      Yes, half tsp of resistant starch per day is a good start. Better to go easy with it at first anyway.

      Amazon does not refrigerate many products that probably ought to be refrigerated…like liquid fish oils. This probably reduces the shelf-life of the product or in this case, the number of active bugs. After I posted this article, I got a call from a doctor in Texas, who frequently appears on Dr Oz show, saying she prefers to keep her patients away from all yeast and Saccharomyces. In her opinion, there is no good yeast inside our bodies. ??? Something to ponder…

        • Hi DPK – I don’t have a brand of probiotics that I take regularly for the reasons stated in this article. But I’ve taken several of them – Garden of Life, RenewLife, Natren, Culturelle, Jarrow, Align, and the list goes on. I’ve tried most of them. I did not notice any difference in my health after taking them…but that’s no reason to avoid eating fermented foods or probiotics. Currently, I’m taking Cardioviva. I’m looking into a bug that influences mood/anxiety but I don’t have anything to report on that yet.

          Most of these bugs are transitional – they do a lot of good while they’re in the gut and they’re gone from your system a couple of weeks after you stop taking them. A few may remain, but their numbers become too small to measure. The best thing you can do to protect your good bugs is to not take antibiotics unless your doctor feel you must or have your doctor’s office ‘call it in’ at the first sign of a scratchy throat. Other than that, eat lots of fermented foods regularly. And no, low-fat ‘yogurt’ with sweetened fruit mash on the bottom is not a real fermented food…it’s junk food with a false halo.

  8. Thanks very much for your blog. I have been taking probiotics (Primal Defense) for IBS for a few months, and now I understand why they helped at the beginning but don’t seem to make a difference any longer. Your EPA supplements, by the way, have helped a great deal with my lupus inflammation.

    • Hi Ernestine – glad to hear that the EPA supplements are helping. IBS is a complex situation. You will have to try a lot of different things and it may be the combination of efforts that finally pays off. I suggest complete gluten elimination, lots of fermented foods, fructose elimination and a high-veggie paleo type diet. A gluten-free zone-type diet may help too. This article is not about IBS, but to let you know how interconnected these gut and autoimmune conditions are:

  9. Vin..
    trying hard to get my flora back!!destroyed from antibiotics 12 years just finally realizing the bowel control.. thankfully no pain.. am now making kefir at home with 2%milk and the “bunnies”..leave 2 -3 days to this productive?..trying to do a dairy free diet but is this o.k.? will try the potato starch..use milled flax seed and protein powder in smoothies.. are you saying vinegar and honey are not helpful? I am desperate and willing to try almost anything. I have learned much from all the comments.

    • Hi Linda – if you’re dairy-sensitive, then kefir may be a mixed bag. If you don’t know whether you’re dairy-sensitive, go without it for a few weeks/months and see what happens when you reintroduce. If you’re fine, then kefir away. But what kefirs provide is just a tiny slice of bug diversity that your gut needs. Try a whole bunch of other fermented foods. You have a lot of options. You should also try some probiotic products like Prescript Assist since it contains bacteria that you would otherwise not find in foods. Humans are meant to eat like our hunter-gatherer ancestors – they were in constant contact with soil and nature. The fruits and veggies they ate probably were unwashed and covered with bacteria..and they didn’t constantly wash their hands like we do. When it comes to your gut, think about the variety and diversity of bacteria. A healthy gut has thousands of different bacteria, compared to kefir with, what, a dozen? Another thing you need to do is eat a lot more of the veggies listed in this article. The soluble fiber feeds the good bugs and that helps them out-compete the bad ones. More here

      BTW, if you’ve gone 12 years without an antibiotic, you’re doing better than the rest of us!

  10. Hi Vin,

    Chance upon your blog and have benefitted immensely over the last 30 mins reading your articles. I have been given many doses of antibiotics over the past 3 years and was wondering if there’s anything I can do to rejuvenate my gut flora. Although I have not developed anything like IBS or Crohns, I am quite certain that my gut flora needs a boost.

    Will taking Prescipt Assist, increasing intake of soluble fibre and taking fermented foods help? Or would I need something more potent? I did try the raw veggies and fruits smoothie for a few months but that gave me bad breath! So I’m reluctant to try it again. As for fermented foods, I usually buy my kimchi and sauerkraut from the supermarket but I’m really not sure what is really fermented and what is not anymore.

    • Hi SPK – well since damage is done, the best you can do it increase the diversity of your gut flora (microbiome). Taking BILLIONS of one species is not going to do the trick. You need to continue doing a lot of the things you already are – several types of supplements, several types of fermented foods from several varieties, and try to lose your dirt-phobia if you have one. Spent some time in farms, swim in lakes and oceans instead of chlorinated swimming pools, get rid of all household products that contain antimicrobials. Get rid of your Neti-pots, Summers Eve, Listerine and Colon cleanses. All of these disturb your natural flora. I don’t know a single person who needs their colon cleansed. It’s like we’re at war!

      And of course, only take antibiotics when your doctor feels you must. Eat all the prebiotic containing foods mentioned above. An occasional raw veggie and fruit smoothie is OK. Fermented foods from mass market supermarkets may not contain much (or any) probiotics. You may need to go to a farmer’s market or get it from health food stores or order stuff online.

      • Hi Vin,

        Thanks you for the suggestions. Will look into fermented products online. Do you mean that I should take a variety of probiotic supplements too? Are there particular brands or types of supplements that you would recommend besides prescript assist and the prebiotic supplements you have already mentioned?

        Thanks a million for your insight. Finally I feel that there is a good chance of fixing things.

        • Hi SPK – there are dozens and dozens of probiotic supplements out there. You will have to sort thru them to see which product can get you a wide variety of species. It may get tedious, expensive and may even be useless, but it’s one of many tactics to get your microbiome closer to its pre-antibiotic diversity. We have to accept that with each antibiotic therapy, a few of the species in our bodies may go extinct – as in gone, gone, you ain’t getting it back. We don’t know which ones we lose and if all this effort ever puts things right again. You may want to consider reading this book:

          I’ve only known about the importance of probiotics for about a dozen years and really grasped the enormity of it all in the last couple of years. So we’re all coming at this with lots of mistakes in our recent past. You’re in good company.

    • Hi Mike – not ALL vegetable oils. Olive oil and coconut oil are fine. If you want to cook with coconut oil, you’ll have to look for expeller pressed, not extra virgin. I also use a lot of butter made from grass-fed cows.

      • Hi Vin,
        you mentioned is better to look for expeller pressed coconut oil. What about cold-pressed coconut oil?
        From what i read, Expeller-Pressed Coconut Oil, the pressure and friction in the expeller can lead to temperatures of around 99°C. Whereas cold pressed is below 60°C.


        • Hi Jasica – makes no difference to coconut oil because the fatty acids are saturated – a little bit of heat will not alter the nature of the oil. What most people find difficult to handle is the strong flavor of coconut oil. It overpowers the flavors of other foods it is mixed with. So, many people prefer deodorized coconut oil. Deodorizing requires a little more process of the oil, but fortunately, coconut oil is not delicate like many other oils.

  11. Greetings:

    I’m curious why the title of the article is “Why I don’t take Probiotic Supplements” when during the article you mention that you occasionally take Prescript Assist, and give it to your children. Then during the article (perhaps for effect?) you mention that PA has “only about 20” strains of bacteria, when on the bottle it says it contains 29 (and not in small print on the back…there’s a huge “29” on the front of the bottle). Just curious what your thought process was in titling an article this way, where you show that probiotics are useful, albeit less than the mainstream perception suggests.

    • Good catch, Reis. That was a typo! I meant to say ‘only about 30’ which, I suppose, is not a shabby number for a probiotic supplement.

      My goal in writing this was to convey that our microbiome is far more complex and important than just digestive regularity or immune health related benefits. And that taking one probiotic supplement and considering the case closed is flawed. We need to coddle our microbiome and that requires a paradigm shift.

  12. Landed on this page and read your post as I researched (for the 1 millionth time) why I have severe and chronic bad breath. Others with this problem refer to it as fecal bad breath and all cite the same experiences… intermittent but chronic bad breath – enough to drive anyone in “nose shot” away; suffered for years; visited many varieties of traditional doctors (GP, ENT, dentist, Gastroenterologist, etc) to no avail; disparate for solutions; turn to natural remedies; experimentation with probiotics and digestive aids to address the belief that the problem is gut related. I personally am exasperated and am exhausted with western doctors who only evaluate physiology and appear not to acknowledge the “system” that is our bodies. 1) Have you ever encountered anyone suffering in this manner? 2) what would you recommend as a balance regime to begin to address this? 3) I found it quite interesting that low carb diets can exasperate the gut problem because for years I have maintained a pescatarian diet – rarely eating any carbs at all. I choose this primarily because it was easier to digest than meats and carbs. What carbs would you recommend for someone who prefers seafood and veggies? 4) Are there any books you would recommend to help me raise my IQ in this area of microbiome and think my holistically about how to manage my overall health?

    Thank you for this great article.

    • Hi HealthyRuby – have you looked for a functional or integrative medicine MD or practitioner in your area? Try:

      Your question qualifies as a medical inquiry…I’m not a doctor and even if I were, I couldn’t dispense medical advice online. That’s not to say I don’t have strong opinions about your condition.

      I suggest you start with a whole foods only paleo type diet that contains lots of veggies, seafood, meats, eggs, roots and tubers. But it’s the veggies, roots and tubers that are going to give your gut health a boost. Cooked and cooled roots and tubers are great source of probiotic foods (prebiotics). There are lots of tips above for re-colonizing your gut. Get a copy of The Perfect Health Diet by the Jaminets. Once you’ve read that book, read absolutely everything written by Jeff Leach and the Human Food Project.

      A very-low-carb and a microbially unfriendly lifestyle are not going to help you. Toss the Listerine! Fix your diet. Repopulate your gut with friendlies. Give the friendly bugs something to eat – onions, leeks, resistant starch etc – preferably raw…given the issue, eating raw onions may seem like the last thing you want to do, but raw has more probiotic food. You will need a doctor’s help to treat issues with inappropriate microbial/candida overgrowth if present/necessary.

  13. Hi Vin,

    I’ve recently been in and out of doctors with digestive issues. They couldn’t find a thing wrong. I took it upon myself to get better. I’ve been treating myself for a candida infection. I took the candida cleanser program and it REALLY helped. I’ve been taking probiotic supplement called “Probioyic Eleven” from Natures Sunshine. I’m still getting a lot of gas and bloating. Is that from too many probiotics? I’m taking one a day. I want to prevent another Candida Infection and have optimum health. Should I only take probiotics one week a month? I also try eating more fermented foods but I have cut out most sugar.

    • Hi Ross – this is a great question. I’m concerned that sharing what I know about this will be interpreted as practicing medicine online…something that I’m neither qualified nor authorized to do. Having said that, I think you probably went to the wrong doctors. Find a functional medicine MD in your area who specializes in gut health. Go to or to find someone in your area. It sounds like you’ve read up on this a bit…probably why you decided to go after Candida. This is not necessarily a bad idea. You probably did have Candida overgrowth but the key thing I want you to know is that there is a sequence of treatment events that need to happen. Killing the Candida is only a part of it. Someone specialized in treating this will look at the big picture first – you will have your diet analyzed and changed from top to bottom. Speaking of bottom, you will have to send off fecal samples in the mail for a thorough analysis. You will need to get several blood tests done. Once all of this is done, THEN, you may be ready for go on elimination diets, treating Candida, treating other infections, reintroduce probiotic bacteria, eating fermented foods, consuming prebiotics, etc. So having taken matters into your own hands, you’ve kinda done this randomly. I don’t think you’ve made huge mistakes, but the gut is complex and important. It’s worth it to find a good practitioner to help you.
      Watch this for putting probiotics in the right sequence:

  14. @HealthyRuby –

    I think you really need to find a Holistic/Biological Dentist, especially one who specializes in Mercury/Amalgam removal and is IAOMT certified … even if you don’t have mercury fillings. Do a few searches using biological and/or holistic dentist to find one and check out their website, credentials and patient reviews.

    You may have to travel a bit to see one, as they are far and few between, but they are worth it. There is one nearby where I live but his reviews weren’t very good so the one I see is almost 2-hours away. But then I only only see him once every 6-months and it’s worth the long drive. A mainstream dentist will not be able to help you with your specific problem. Good Luck.

  15. Dear Mr. Kutty,

    I have been suffering from a debilitating systemic intestinal fungal infection for just under 4 years now, I have taken a huge number of different natural supplements and altered my diet to combat the problem including different brands of probiotics but only with very few periods of improvement that didn’t last long. The last 1 1/2 years (after a slew of colonics) have added bowel urgency and gut dysbiosis into the mix.

    I briefly took Prescript Assist 6 months ago but I took them with my meals (which I now realise may have been wrong). I recently stopped seeing a holistic practitioner who put me on a 3 month protocol that had only a very mild effect.

    The probiotic he prescribed claims to be high-count and multi-strain at 60billion CFUs consisting of L. Acidophilus, L. Rhamnosus, L. Plantarum, B. Lactis and B. Bifidum.

    I would like to ask you: what probiotic (and prebiotic) regimen would you recommend and how do you think I should take them? Furthermore, do you think taking Hydrochloric Acid Betaine with Pepsin (one of the practitioner’s recommendations) is advisable?

    Thank you in advance,


    • Hi Baret – sounds like you’ve been dealt a difficult situation. Unfortunately, most mainstream doctors are not equipped or trained to handle these situations. I suggest you try the following people:

      Instead of giving you specific brands of probiotics and prebiotics, I suggest you re-read the sections of this article that talk about how to eat the right way so you can gradually alter your microbiome in your favor. I also don’t want to get into practicing internet medicine, for which I am neither qualified nor authorized.

      But I will tell you this: fixing the gut will have far-reaching benefits, not just with combating your infection. And fixing your gut involves FAR MORE than just taking probiotics. It is a process that often beings with identifying specific problems via stool test. Then working with a practitioner to address those infections. Healing the gut follows with changing your diet and avoiding toxins and may be gut healing supplements. Then you get into probiotics and prebiotics. If people commit random acts of health and take probiotics and wonder why their health isn’t improving, this may be the reason why. I’m not suggesting you’re doing this, but I’ve seen this a lot. Taking probiotics is just ONE STEP in the process of healing your gut. In the meantime, talk to the people in the links above.

      • Dear Vin an Joy-Ann,

        Thank you for you responses and I will take your words under advisement. Mr. Kutty, I would like to ask about what Joy-Ann said in regards to nuts because there seems to be discrepancies as to whether shelled or unshelled nuts are safe. Could you please clarify?

        Aside from that, I am currently 3 weeks away from the end of my current treatment protocol. If that proves to be fruitless, I have the contact of a conventional gastroenterologist who is said to to be one of the best in Cyprus and cured my friend’s mother from a serious intestinal auto-immune disorder. From my understanding, he is very knowledgeable about these matters as well as probiotics and is generally against antibiotics – a combination that is a bit of a rarity with conventional doctors.

        Mr. Kutty, I will keep the links you sent me for future reference if needed but for the time being, a local doctor seems to be more practical.

        Thank you again for your time and patience,


        • Hi Baret – Joy-Ann gave you a lot of good advice. Some of it could be very useful and others may or may not do much. The magic formula for health is slightly different for everyone. Assuming you have no nut allergies or intolerance, you may be OK with nuts. But if I were you, I’d make nuts part of my elimination diet. Take it out and see how you do when you add back one nut at a time.

          Both the health practitioners I provided links to use Skype and deal with patients around the world.

    • Hi Baret –

      As Mr Kutty stated in my January 5th email response, about the MTHFR gene, you may also have high Histamine levels, and if so, any fermented foods will make you sick and sicker. I’ve already been down this road. And, I’ve seen others go down this same road.

      IMO, the Probiotics strain/species you’re taking seem to be the best, although I can’t speak to the brand, even if I knew it. But, those specific PBs you’re on are low Histamine, not Histamine releasing, which is a very good thing, IMO. Certain PB’s are known to release more Histamine into your system.

      BEFORE you can use prebiotics or fermented foods, such as sauerkraut and AC Vinegar, and so on , you MUST FIRST clean up the yeast/candida/fungus. That MUST be done first…learned the hard way… not a doctor… life experience.

      You need to go on the Yeast-free/Candida diet, along with low Histamine foods only… and STOP the Prescrip Assist, at least for now. The list of ‘Allowable Foods’ is a short list. But, you must stay on it for 42 consecutive days — minimum.

      NO sugar/sugar substitutes or alcohol or yeast/gluten foods, NO fermented foods including Kimchi, soy and yogurt… and NO fungi foods, such as mushrooms are allowed — not even ketchup is allowed as it contains sugar and vinegar… and tomatoes are a high Histamine food and you need low Histamine foods as well as Yeast-Free… NO yeast, gluten white/wheat flour. No white foods, such as rice/potatoes. No nuts as they may contain (not visible) specks of mold.

      Oh, and sorry, no caffeine at all. Don’t go cold turkey with the caffeine like I did. Do it gradually, use less and less over a week’s time to slowly wean yourself off it, as well as eating low Histamine foods only and do this for one-week and then go on the above low Histamine Yeast-free diet along with the Probiotics you are currently taking.

      My holistic doctor had told me before one can use fermented foods containing natural Probiotics (which, no doubt are good for you) one must first clean up the yeast/candida/fungus in their system. After the minimum 42-day clean-up clean-up, you can slowly add the fermented foods back, gradually, little by little.

      Also, stop using products that contain sulfites, proply, parabens, and any form of alcohol, even Cetyl alcohol. IMPORTANT: Anything that touches our skin enters our bloodstream within 20 seconds; sunscreen, body lotions, soap, dish detergent, etc., and, over time, it builds up and causes problems.

      When doing laundry, run all your clothes/all laundry through an extra 10-20 minute cold-water (no soap) rinse cycle to remove excess detergent residue.

      Also, Mr Kutty, you are a life-saver and I appreciate your helpful comments.

      I sense that you feel censored because if big-brother is watching, you can be bullied and chastised, accused of giving medical advice, which is not your intention. Sadly, there are horrible people who like to misconstrue and misinterpret one’s positive intentions and who simply don’t care about others well-being and dislike when good people (like yourself) reach out to help others with your wealth of knowledge… sad but true.

      Hope this helps from someone who learned the hard way. J.A.R.

  16. is it ok if my boyfriend giving omega 3 -1000mg to kids of age 6 and 10. i always told him to buy omega 3 for kids he seems no listening and he is sure they can eat that as well..

    • Hi Janka – 1000 mg of fish oil is fine for kids. Typically 1000 mg of fish oil contains 300 mg of Omega-3…this is a safe dosage.

  17. I was wondering about ‘the empty stomach’ rule. If I take my probiotics 3 hours after eating and half-hour before eating again how could my stomach really be empty?

    I read that it takes more than 3 hrs for a meal to empty from our stomach.

    Also, if I take my probiotics and wait 30 minutes to eat again, aren’t the probiotics in my stomach along with the food?

    I know you addressed this before but I couldn’t find the post/comment.

    Thanks in advance. Joy-Ann

    • Hi Joy-Ann – I don’t recall addressing taking probiotics on an empty stomach. And I’m not sure what this empty stomach rule is. I often tell people to take fish oil with a meal. When I take probiotics, I take it WITH food or it IS food. I’m not aware of any benefit associated with taking probiotic on an empty stomach…I wonder what the logic there is. Taking probiotics with a meal might blunt the acid exposure in the stomach. The acidity of the stomach drops a little temporarily right after a meal and this may help some of the bugs survive into the intestines. Also, if you look at this from an ancestral perspective, we got our probiotics from our mothers, our environment and our food. It is meant to be a constant and dynamic thing. Microbial acquisition was not tied to the full/empty status of the stomach. And don’t think of your microbiome as being just in the gut. Every nook and cranny, inside and outside your body has its own microbiome. Even your fingertips. You can connect a computer keyboard to its user by the bugs your fingers leave behind on the keys. My point: given the big picture, the empty stomach thing may not matter.

      • Hi Mr Kutty,

        Sorry, my mistake… where I read that ’empty stomach’ is actually in the instructions of the probiotics I take … it says “take on empty stomach.”

        I mistakenly thought I had read it here, which explains why I couldn’t find the post/comment here. Anyway, thanks for sharing the helpful info. J.A.R.

  18. I take a prophylactic antibiotic daily to prevent UTIs. I have kidney issues, so I really need this. My digestion is completely disfunctional and I know that I am killing off friendly bacteria. Rather than diarrhea I get lots of bloating and intestinal gas and constipation and colon discomfort.

    Would taking probiotics and eating foods high in soluable fiber help at this point? I have had an unhealthy diet with lots of processed foods etc. previously. I am willing to make dietary changes, but need to be careful because I am diabetic.

    • Oh my goodness, Laurel! I can’t think of a worse thing to do for your gut than take antibiotics everyday. And your gut controls virtually everything. Your gut may be more important than your brain. Find yourself a functional/integrative medicine doctor TODAY! You need to address the root causes of the problem. You need to change EVERYTHING from the top down, but don’t randomly take probiotics/soluble fiber without a plan. Fixing the gut is a long, complex, step-by-step thing. Taking probiotics is just one small intermediate piece of the pie. Don’t wing it. Get professional help. Find out of they have experience fixing guts. Not all funcional MDs do. Also know that if you’re not 100% committed to completely changing your diet and lifestyle, that things are not going to get better. Sorry for the tough love. You need it.

  19. For what it is worth, I want to add my (mere?) anecdotal experience to the mix here.

    I had recurrent diverticulitis that was reaching the stage where I felt the need–with great reluctance–to consult a surgeon. After my last attack in early Fall of 2013, however, I began taking a probiotic capsule (Theralac brand) daily. I have not had an attack of diverticulitis since. (For those who are interested, there is medical evidence correlating probiotic consumption with reduced incidents of diverticulitis).

    Of course, I am not averse to the idea or the possibility that one may obtain similar positive results strictly through consumption of food, without supplementation.

    Your thoughts on this experience?

    • Hi Kevin – I have absolutely no reason to question your experience. If anything, it shows that paying attention to what goes into your gut – food/probiotics/antibiotics/soluble fiber/prebiotics etc. all heavily impact your health. The title of this post is somewhat misleading or may be even goading. I did it to prove a point – that taking supplements alone isn’t going to do the trick for everyone. We need to look at gut the way we look at our heart or brain. Exclude foods that harm it and include foods that help it (and its residents) thrive. If a lifetime of poor eating and antibiotic use has upset the microbial balance, one probiotic brand will not solve the problem. You may need to ‘weed out’ some bad actors with the help of a professional. Then you will need to introduce as many new species of bacteria as you possibly can. Then you need to feed them all with various types of soluble fibers. If you look at the whole picture, taking a probiotic supplement becomes a small piece of the healthy gut pie. That is the point I am trying to make.

      • Thank you very much for your prompt reply. I hope it was clear that my post was not intended to be challenging or antagonistic. I simply wanted to share my particular experience, in order to reinforce the point that, while there may be certain generalized “best practices”, there are no “rules”.

        More particularly, I wanted to stress that regular probiotic supplementation may be of value in treating certain chronic medical conditions.

  20. Excellent article could not agree more. Many companies are working on refining fecal bacteria to put in capsules right now and the big question is will the FDA allow them to proceed quickly or proceed at all. This is the biggest breakthrough in the history of medicine. It can immediately stop c-diff infections and probably cure most if not all serious intestinal diseases eliminte all IBS and IBD and were talking a matter of days or weeks at the longest according to studies done so far just IBS effects ten to twenty percent of the population . Almost all of these problems have been caused by antibiotics. You would think something this dramatic that could save lives and has already been discovered and is this simple would be on the market within six months but unfortunately that is not how are medical system works many will have to die and live horrible lives until this happens. So unless there is a outcry , senate hearings etc, etc things will be stalled. anything that can change the status quo will not proceed quickly. Well lets hope that conflicts of interest will not stall this long and we will be in for a new age of medicine.

  21. Hello again,
    to everyone I think all of the ideas and suggestions are putting bandaids on a problem and the only thing that is going to heal it is the full spectrum bacteria from fecal bacteria encapsulation which is now proven to heal all of the condidtons. I agree and disagree with the with the candida diagnoses. In reality all of these diagnoses are for the same problem whether you label it candida , irritable bowel, spastic colon etc. etc. small intestinal bowel overgrowth the real problem is dysbiosis which is a total chaos and detruction of the normal bowel flora. All these condidtions have been shown to immediately be healed by human fecal bacteria. For now all we can do is the above suggestions which at best may slightly improve symtoms. But obviously if regular probiotics or resistant starch or anti candida products really took care of these problems we would not be having this discussion. everyone has been living with these problems for years which will end when they approve capsules that are from the above which one day we will see.

  22. Hi
    Thanks for the great article. I’m looking for advice.
    After 17 years of taking Paxil for depression and anxiety I decided my life was in a good, stable place and I wanted to get off the drug. I was very conservative in my weaning approach, taking a full 4 months to slowly wean off the drug. Paxil is notoriously difficult to come off of. While I have been very careful to stay away from caffeine and alcohol and have been taking high quality cod liver oil, I still slid into a major depression. My primary care person put me on Wellbutrin – a fail, then Zoloft- fail again, then back on Paxil. Even the Paxil was a fail. All 3 set my heart racing at an alarming pace. My body has said ” no” to further antidepressant use. I have read about b. Vaccae and want to introduce it. I have been unable to locate a product containing it. Do you know of any? I am even willing to eat dirt that I can obtain from pristine land. What do you advise?

    • Hi Allison – sounds like you are in a really bad place. I’m sorry to hear. I wouldn’t go looking for pristine dirt or Mycobacterium vaccae. If pharmaceutical options are off the table, I suggest you take a holistic approach to this. Get yourself an integrative psychiatrist and a whole foods/paleo focused dietitian. I suggest you look at Dr. Kelly Brogan or someone like her. She has a blog you should read every word of. Lots of videos too. I suspect what you will need to do is completely revamp your diet – eliminate every source of inflammation. All the sugar, processed grains and seed oils should be gone. Eat stuff that was alive a few days ago. Then you will need to work with a professional to see if you have leaky gut issues. Any food sensitivities will need to addressed. Heal the gut methodically. It is at THIS STAGE that probiotics comes in. Lactobacillus helveticus and Bifidobacterium longun from Institut Rosell have been shown to influence mood response in some clinical trials. But while these strains may help some, they will not, without all the other changes listed above, fix the whole problem – probiotics are just one piece of the puzzle. The extent that probiotics help depends on the degree of your gut dysbiosis, how consistently you take the product, and if the root cause involved the gut. If the condition was unrelated to gut health, the probiotics may not help.

      You will need to make sure that you are getting adequate magnesium, fat-soluble vitamins (A, D, E and K2) and B-vitamins and certainly lots of Omega-3. All of these things are better from foods, but you can supplement to get things started. Curcumin supplement helps a lot.

      There are lots of supplements you can take but you cannot outrun poor diet or lifestyle. It is all about healing the gut, reducing inflammation, fixing lifestyle issues like messed up circadian rhythms, activity, community socializing, exposure to sunlight, reducing stress etc. I hope I’ve given you a place to start and may be a different way to look at the situation.

  23. Sometimes, it’s just right to allow our children to play in the mud. They get bacteria that the bottles can’t fully provide. So long as we watch what they put inside their mouth while playing.

  24. Hi Vin,

    I am worried as I have been taking Isotretinoin as prescribed by my dermatologist. I understand that this is really bad for our health. I am having issues like dry lips, dry scalp, and I suspect my gut floral is affected as well.

    I am taking prescript assist now and eating fermented food like tempeh, kimchi and natto once in a while. Is there anything else i should do to improve my situation? Like adding L-glutamine to repair the gut?

    Also, I heard about the gut-brain-skin axis and am very interested in fixing my issues the healthier way.


    • Hi Ken – these are big issues. I suggest you work with a professional to get your gut issues fixed. This is not a minor thing and not something I’m qualified to give guidance over the internet on. Having said that, the medication you are taking has a pretty serious side effect profile and does not address the root cause of the issue. Fix your diet first. Work with a dietitian – there are hundreds of them if you’re willing to use Skype. Eliminate sugar, processed foods, grains, etc. Probiotics are easy for people to understand, but they are just an intermediate step. Fix diet, fix infections if any, use probiotics, gut friendly foods, use several types of prebiotics and eat foods that contains soluble fiber. You need to work with a professional on how to go about – if you wing this on your own, you will make mistakes, as people invariably do.

  25. I would like to say that when they say soil they mean soil, not dirt, and there is a difference. Some people now believe that eating food off of a dirty floor is a health treatment. That’s just funk off the bottom of people’s shoes and other nasty stuff. When they say soil, they mean the stuff your flowers grow in. I know you know this, but it’s funny how people take things…

    • Hi DJ – good point. Extending the ‘5-second rule’ for dropped foods to 10 seconds is not going to do much…unless you drop the food while hiking in the woods or on an organic farm. 🙂 I’m not suggesting we roll our apples in mud before biting into it. I’m suggesting we look at constant hand-washing, Purell-pumping, and unnecessary antibiotic popping in a new light. Our ‘modern’ hygiene is not helping.

  26. Vin,

    good article, just stumbled onto your site. So I’ve read a bit about SBOs and have read good and bad (as usual with anything nutrition/health related). I’m wondering if you’ve done much research on the SBO probiotic supplements as opposed to other non SBO probiotics. One site stated

    “Even though soil probiotics serve as natural inoculation when ingested, this does not make them appropriate strains for probiotic supplements. Now that our gut microbiomes are less familiar with SBOs (due to a decrease in exposure), and most of our gut microbiomes are compromised, they can compete with our resident gut flora rather than complement them”
    “It makes sense to replace probiotics that are supposed to live in the digestive tract since the imbalance causes poor gut health and issues related to compromised immunity. SBOs are different because they were never supposed to be part of the gut microbiome. Supplementing with soil organisms (introducing foreign microbes) when your intestinal tract is not properly colonized with resident bacteria is like inviting a group of squatters over to a vacant home and crossing your fingers that it will all work out. To make matters worse, SBOs are spore forming and they proliferate rapidly – so rapidly, in fact, that many manufacturing facilities who grow the probiotic strains found in the human gut consider SBOs as a contaminant to their facility”

    Since I’m sure your more informed on this than me I’d thought I’d get your take on it. I eat a lot of fermented foods anyway that I make myself like sauerkraut, kombucha, kefir,etc. plus stuff I get from local farms, as well as I eat plenty of prebiotic foods like onions, garlic, avocados, sometimes potatoes so I’m figuring it’s not worth taking a supplement for this, but I think I have let my gut flora get out of whack, might have a candida overgrowth so was looking at some to help with restoring it, such as Mark Sisson’s Primal Flora which looks to contain some of these SBOs.

    • Hi Bryan – I am not an expert on soil based probiotic organisms. Having said that, we all get our probiotic fingerprint in the first few years of life. From our mother’s birth canal, breastfeeding, and our environment – there is a reason why toddlers are wired to mouth everything. Once we’re adults, the only source of probiotics is through fermented foods and the environment.

      I find this quote ridiculous and laughable: “Even though soil probiotics serve as natural inoculation when ingested, this does not make them appropriate strains for probiotic supplements. Now that our gut microbiomes are less familiar with SBOs (due to a decrease in exposure), and most of our gut microbiomes are compromised, they can compete with our resident gut flora rather than complement them”

      Wow! I don’t know where to begin. The second quote is funnier! This basically says ‘Since we now live in civilized, clean, modern homes, those icky bacteria are yucky.’

      Sounds like marketing hype to put down Prescript-Assist. Sure, I have my beef with PA – some of the bugs are not fully characterized. We have no idea how much of each bug is present. We don’t have enough studies to back up the passion with with gut doctors are recommending this stuff. But let’s be honest – it is still the best and most diverse soil based probiotic on the market. Disclosure: our sister brand, InnovixLabs makes probiotics.

      BTW, spore-formers are great! Don’t believe whoever wrote that stuff! Like it or not, you inhale millions of spore-formers and SBOs and a few of them even colonize your gut. A lot of the serotonin and other happy neurochemicals in our body are made by spore-formers. I like Mark Sisson’s product. Just finished taking a bottle. There is another nice one called Just Thrive.

      I’m still laughing about the ‘group of squatters.’ Thanks for that.

      • Yea, I think your probably right. I’m not big on supplements aside from greenpasture’s fermented cod liver oil and butter oil (though not really supplements i think, more like actual foods), and some powdered chlorella/spirulina I take. But might try a round or two of some probiotics to complement my ferments and bone broth to get my gut back on track. So i’ll probably try Mark Sisson’s brand out and see how it goes. Thanks.

          • Thanks Vin, read the article, I’m always open to new veiws/information After reading it though have to disagree with most of the points you made in it in regards to FCLO. I don’t argue the fact that probably most of the fish oils out there, including cod liver oils, you should probably avoid because of how they are processed and their quality. But fermented cod liver oil, and in particular greenpasture’s, is not in the same league as the others listed in that article. I’ve met the owner of the company, David Whetzel, really cool guy, and he is pretty transparent, about as transparent as you can get, with his methods, lab results, etc. His site has a lot of good info and lists studies to back up a lot of what he claims. Your are correct that you can’t ferment fats/oils, but this is not claimed to be the case, at least not by this guy or his company. The liver is fermented though and this is one of a few processes that release the lipids from the tissue by rupturing the cell walls, the others being temperature and chemical.

            Also, the fermentation process is just a natural bacterial/enzymatic process to break down the cell wall. It’s doesn’t putrefy the food any more than making cheese, yogurt, sauerkraut, or many other traditional, “healthy”, fermented foods with very long histories in human cultures. I think the issue with this phobia of fermentation = rotten is just a sympton of our disconnection with our foods and our reliance on industrial agriculture and processed foods. Most people don’t even know what the actual plants look like that they eat, let alone the what it looks like on the inside of a freshly cut open carcass where they get their cuts from. I think this, along with the fact most people no longer make traditional foods like ths, contributes greatly to the misconception of fermented foods and gives rise the the negative description of it being “rotting food”. Though I actually thought you would agree with me on this judging from your comment on the SBO article I quoted but that seems to be what your saying.

            So for the 5 points you list his site pretty much has plenty to cover all of those, in particular:

            He periodically gives lab test results on nutrient content on batches they test. I don’t think there process or claims are shrouded like others might and probably are. They have also included tests done on the toxicity of the fclo, from independent researchers.

            So I’m not really trying to attack your article just giving my opinion with the research I’ve done on this (which is a lot).

            • Hi Bryan – if there are any recent 3rd party certificate of analysis available on some website or in the public domain, let me know. I’d like to take a look at it and compare with what I had, specifically, peroxide, acid value, anisidine, TOTOX, mercury, cadmium and the full PCB profile. The first four metrics will worsen as the product (any fish oil, actually) gets closer to the expiration date, but the environmental contaminants will be the same throughout the life of the product. I don’t care much about the EPA/DHA content because this is valued largely as a natural fat-soluble vitamin source.

              This is science, not faith or religion. If the facts on the ground (or in the bottle) have changed, so will my position. Gladly. But I’ve yet to see any new data that nudges me towards a more favorable position.

  27. people who have gut issues like ibs do well on low fodmap diets, your saying prebiotics will help but what about those who have severe adverse effect to them.

    • Hi Ken – this is a fantastic question.

      The reason people do better on low FODMAPS diet is because they have severe gut issues and dysbiosis. It’s not because FODMAPS are bad. The solution is not to remain on low FODMAPS diet – that would be a disaster long-term, as you’ll starve your gut microflora to death. FODMAP foods are basically high soluble fiber that’s present in prebiotics. You NEED a high FODMAPS diet to be healthy. Feeling relief by avoiding FODMAPS is not dealing with the real issue. People who have issues with prebiotics should work with a functional medicine MD to get the gut issues fixed and eventually get on a medium to high FODMAP diet. Avoiding FODMAPS is like taking a OTC pain medicine to get temporary relief. Yes, you’ll feel better. But you haven’t solved the root cause of the problem. And you may actually be creating other bigger problems by remaining on low FODMAPS diet.

      So if you react negatively to prebiotics, take it as a hint that you need to address gut dysbiosis issues.

  28. I found your article searching on probiotics up late struggling through a bad episode of acid reflux that turned into allergies and chest cold with rash from taking zeghrid, vita cost pro 10 20, slippery elm, and licorice all newly introduced to help bad stress induced ibs that’s continued for weeks. Yes low food map and low carb both worked at times. You don’t have any info for those that have gallbladder removal, how that may impact the digestion of good bacteria. No longer can eat onions, garlic, spice, which I use to enjoy. Do you have any advice for those that have impaired immune systems with less than stellar digestive tracts. Sounds like a functional doc is much needed, can’t even take most know antibiotics without having a reaction. Thanks for the article and helpful links.

    • Hi Ruby – I cannot give medical advise but there may be many things going on here – and yes – you definitely will get better if you can find a functional medicine MD near you. They will have to do a lot of tests and then develop a customized protocol based on the test results. It won’t be quick, but it will probably be thorough and helpful in the long term.

  29. Hi Vin,

    As per your recommendation I began taking Prescript-Assist + Multi-Strain Probiotic (by InnovixLabs) after a long period of time taking antibiotics + IBS that I have.
    I am feeling much better already but with around 20 capsules remaining of the InnovixLabs Probiotic they started to get yellowish with some orange dots on it. As I stored as per recommendation I am wondering if it is normal or not. Can I keep taking it?


    • Hi Christian – glad to hear you’re doing better. You may want to look into this program as well:

      Yes, you can keep taking it. The orange dots could be some moisture condensation on the outside of the tablet. This is fine. The bio-tract tablets are quite resistant to moisture and environmental abuses.

    • Hi Lauren – yes, I DO have an opinion on InnovixLabs probiotics. I developed and formulated the product. So, yes, I think they are special. Despite the provocative title of this article, I think some broad-spectrum probiotics should be part of your antibiotics recovery plan. Eating fermented foods and being exposed to nature are as important if not more, to recovering from antibiotics. I also like Prescript-Assist and some Garden of Life items. There is another product called Thrive that I like too. Together, they’ll get you about 75-100 strains. Still far short of what you really need, but it’s a good place to start.

      Remember, probiotics are just one step in getting your gut health back to normal. First you have to eliminate infections and pathogens (with the help of a doctor), then begin to heal the gut. I call this first step ‘Weeding.’ Then you introduce probiotics – ‘seeding’ and finally, you need to eat foods with lot of prebiotic fibers to feed the good bugs. This is, of course, ‘feeding.’

      Weed. Seed. Feed.

  30. Hi I need help.. I took bio k + probiotics for 12 days 3x a day
    I am now constipated and don’t feel good.
    Why did this not wrk to clean me out. I am now having bm’s but only with help of multiple natural aids (olive oil, Lemon, mag, molassses, epdon sslts, phyllium, prune juice) and when I eat I feel heavy an backed up.
    I never did manage to clean myself out from constipation. It’s as though somethings not right inside.. I seem to be passing food I eat since stopping.. (fflax seeds from.bread, spicy food etc)
    I do have lots of gurgling happening but not much action.
    Its clear that my regime of probiotics was not successful. . And it does not seem like standard constipation ( but I really don’t have any previous situations to compare to)
    Hope u cam help me gain dome insight and find a solution . Hopefully economical as well thx!!
    My apologies if this is a duplicate as it did not seem to send thx.

    Potty sqauter

    • Hi Adrienne – you’re having the typical types of gut issues that millions of people have. It is common but not normal. You may need the help of a gut specialist/integrative medicine practitioner to help sort this out. I dont think the Bio K+ had anything to do with the situation. Although some people have funny reactions to some probiotics. The problem was most likely caused by years of inappropriate diet (although I have no idea what you eat) as it is with most people. The Bio K+ may have just highlighted it. You may have SIBO or other issues – again, I dont know. Check with your doctor. People begin thinking about probiotics when the ‘wheels come off’ their gut health. But as I’ve stated in several comments above, probiotics are an INTERMEDIATE PART of the process of gut healing. Fixing your diet, finding out if you have any infections and treating for it, and THEN taking probiotics, followed by PREBIOTIC foods helps. But probiotics did not cause this issue and probiotics alone will not fix it.

      • Hi thank you for your quick reply,
        I have had some time to read the posts and your replies and I have come across some
        Very useful information.
        My diet for the last 10 months has been mostly grain free with salads,veggies and proteins, .. bone broth, working towards a gut healing diet but been pacing myself in making the change.. but as one post talked about a low carb diet can affect digestive system, and that’s when I began to have a difference with my bowel movements.
        It was suggested by my health kinesiology to take this trial of probiotics as I suspected and so does she that I have a candida problem too, due to my symptoms and how I have been getting worst not better.. my approach was to heal my guts then deal with the candida so as to eliminate it from returning due gut perforation!?!
        I was never a big processed food, junk food eater and when I went off of wrk 3.5 years ago for chronic pain/ nerve inpingement I also changed my diet to blood type diet. I am O-.. going to change back to that diet! The affect of my recent diet change 10 months ago by eliminating grains was not a good move for I think.

        Turns out I have a couple of autoimmune diseases Ankylosing spondylitis and
        Fibromyalgia. I did read your link to the article, but have come across this info previously as well.. currently made the decision to make fermented foods now with my guts reacting this way after taking probiotics..
        You say it’s not as a result of taking the probiotics, but before taking them I have never had this problem ever. Could you perhaps elaborate a bit on how taking probiotics could draw out a condition that may gave already been there?

        I have a strange question for you, kind of embarrassing but can bacteria be passed on through human contacts..kissing, intercourse the degree as to it actually creates health problems for the other person; such as being introduced and causing a flare up. I ask because of what was in your article about “feces banks” “poop banks” another’s bacteria colonizing in u.
        Before my now ex boyfriend got involved I did not have this severe flare up (being in such chronic pain, muscles won’t relax after using). but shortly afterwards approx 3.5 years ago after we made contact so to speak my health declined progressively..
        He had severe gastrointestinal issues… and our saliva and sometimes my vaginal fluids reacted funny to his natural bacteria??? . at one point was kinda fizzy when we kissed and even a stingy feeling below. like it was a chemical reaction of some sort. This has never happened to me before. not my normal!
        I need to ask this, cuz it’s strange and I can’t seem to find any info on this type of reaction and my health is poor now.

        OK thank you for taking my questions.

        I do not take pharmaceuticals, I eat organic, I don’t put chemicals on or in my body.

        • HI Adrienne – glad to see that you are getting more involved in your diet and health. Diet and health are basically the same. If you think you have Candida overgrowth, work with an doctor to get it diagnosed and treated. Don’t guess and self-medicate.

          I am not a fan of blood type diet. Not even close. I’m being nice. There is no one diet that fits everyone’s needs. The O negative person next to you at the grocery store will have a completely different diet/lifestyle requirement. Instead of a blood type diet, bark up another tree – any anti-inflammatory diet will help you. Stick with mostly veggies (leafy and roots), seafood, some meats, eggs, and fruits/nuts as desserts. Be generous with olive oil and Omega-3. Cut out sugar, grains, and Omega-6-rich seed oils. Basically eat stuff that was alive and growing last week.

          Most mainstream docs are not able to properly treat and address the root cause of AS or Fibro. You may need an Integrative MD. BTW, both issues are closely linked to inflammation, diet, and lifestyle.

          About your recent incident – I really don’t know if/how the product you took caused this reaction. My guess is that it is unrelated. I really can’t explain it. People with gut dysbiosis do sometimes have negative reactions to sudden large introduction of probiotics or prebiotics. May be it was that. I’m guessing. Bio K+ has been on the market for years and millions of people take it. It has a great track record of comfortable use. So my guess is that your dysbiosis is probably the cause.

          As for human contact – certainly we all transfer bugs to each other constantly. That is normal and usually healthy. It starts before birth and goes on till we die. Again, it’s normal, healthy and necessary. If you suspect pathogens (bad bacteria) in play, again, that’s a doctor thing and out of my league.

    • Hi Chris – I think it may be time for a from-the-ground-up check up with a Functional Medicine MD and an equally radical change in diet.

  31. Hi. What do you think of “Just Thrive”? It is made up of 4 bacteria, of which some are “spore forming”, whatever that means. It also has bacillus subtilis HU58. Thanks for your trouble.

    • Hi Samia – I like the product a lot. Wish there was more published science on that specific formula. It’s a potent variety of spore forming bacteria. Unlike typical lactic acid bacteria in most probiotic supplements, which die easily, spore-formers go into a cocoon like vegetative state when conditions are not ideal. This cocoon is called a spore. Once they are in the spore state, it is virtually impossible to hurt or kill these bugs. So you get a TON of live bugs with this product. Most other probiotic supplements say there are billions of bugs, but that number is mostly said with fingers crossed.

  32. Hello,

    Any thoughts on – – series of articles that discuss why NOT to take PrescriptAssist.

    See part-3 specifically.


    • Hi N. Kaufman – could Prescript Assist have more clinical science behind it? Yes, certainly. Could we know more about each strain? Again, yes. Does PA dramatically improve everyone’s health? No. An absence of evidence does not mean evidence of absence. Overall, I find the website that you sent me to be somewhat denialist.

  33. I have serious concerns regarding SBO’s, in which you recommend. There seems to be highly controversial info out there, and some of it is very scary, even noting it can seriously harm/kill some people. The problem is SBO’s DO establish themselves, as we know they are spore forming. Some people claim they suffer horribly after taking them, and then can’t seem to get rid of them. Some people have terrible affects as they are difficult to rid of. Personally, I tried SBO’s from HealthForce. I experienced horrible abdominal cramping and constipation from them. Of course, I thought I should increase the dose b/c I thought this might be a necessary evil, only to find increasing did not help, made me worse. So, I stopped taking them all together, and returned to probiotics made by some of my favorite companies (GOL/MegaFood/Nutrigold, etc). What are your thoughts on this? Do you feel they can cause more harm for certain people, and that they may never be able to re-establish themselves after the damage is done? It seems they can be very difficult to get rid of. Thank you

    • Hi Rachel – we (humans as a species) have typically ingested and inoculated our bodies with probiotics through these means: birth (from mom), breastfeeding (from mom), environment (dirt, plants, pets, putting dirty things in our mouths as children etc.) and foods. We even inhale a lot of probiotic from the air. Most of these bacteria are harmless and some are beneficial. If you have a severely compromised microflora, some of the pathogens can take hold and cause issues.

      The fake controversy about SBO (soil based organisms) was started by companies marketing dairy based organisms. Most probiotic supplements are dairy based (yes, we sell one that contains both dairy and environmental bacteria) so, this fake controversy is self-serving. I have been in this industry for decades and I know people profiting from this controversy. If you fall for this ‘controversy,’ the joke is on you. Sorry to be so blunt.

      Having said that, I need to say this as well: most SBO products do not use well characterized strains. The strains are not individually studied. Very few of these products have been shown to do much. There are very few clinical studies on them. It is just a matter of time before some unethical company starts selling backyard garden soil as a ‘probiotic.’ But I have taken Prescript Assist. I have given it to my kids. None of us fell ill nor noticed any miraculous benefits. Some people do really well on it.

      I cannot comment on why you felt the way you did after taking your product. But most people have severely messed up gut flora that any new addition of either probiotic or prebiotic causes big shifts in flora and that can be uncomfortable – people who need probiotics and prebiotic the most are the ones who seem to complain the most when they begin taking these products. Ultimately, it is really, REALLY important that you eat a diet that is very rich in prebiotic fibers (lots and lots of vegetables) and to only take antibiotics when absolutely necessary and to expose yourself to nature, wildlife, farms, dirt and such.

      Get back to basics. Start with fixing your diet to include a LOT of prebiotic fibers. Then add a variety of probiotic supplements in addition to the lifestyle steps above.

  34. Hi,

    What is the typical cycle for Weed. Seed. and Feed?

    I’ve been battling dysbiosis for awhile now (3+ years), and it just keeps coming back. I go in a 3 month period of weeding, then after the 3 month period, I take some probiotics (usually 1-2 months) then I start eating high fiber foods such as sweet potato and fruits.

    But then sometimes the overgrowth/infection just keeps coming back, and I have to go through the cycle again, is there a reason for that being? What are possible underlying causes? I have been through this cycle at least 3 times. And it can feel hopeless sometimes.

    Some say, it’s inappropriate methylation, or blood sugar issues or hormonal issues. Some say it’s food allergies that are causing the relapse of SIBO, and that I will probably have to avoid certain foods for the rest of my life.

    What is your take on it?

    • HI Frank – are you wingin’ it on your own? This is still a fledgling area, even in functional medicine. So the protocol is not standardized – it may never be due to how differently each of us can be messed up. These are hypothetical questions because I cannot give medical advice:
      How are you weeding? What are you weeding for and using what substance/medication? How are you certain when you are done weeding? Seeding is also extremely complex process – takes more than popping a pill. Sweet potato contains some prebiotic fiber. Fruits not so much.

      Also, whatever got you into dysbiosis, probably has caused some other damage along the way. All of which you will have to remedy.

      Get hooked up with a functional medicine doctor.

  35. Wow,
    That’s a great article and commentary. (I read most of the questions and answers)
    The phrase caught my eye in particular: “Many of the bugs in probiotic supplements are transient – they are gone from your body in a few weeks,” for as living organisms, they ought to thrive and multiply rather then whither.

    In my case, just one capsule of Pro Guard is enough to feel better and, after the second one, my numerous ailments seem to melt away. The problem is that after two weeks or so the party is over whether I keep taking the capsules or not, (lots of raw onions, garlic, avocado, potatoes, apples, beans), and I am sent back into the dog house. It makes me think of “Who killed commensal J.R. ☺

    I am desperately helpless( in spite of all the medical professions, incl. the functional docs)

  36. If you really want to recolonize the digestive track then why not do what nature intended which is sit nude on the ground. Remove an inch of soil and then park
    Your butt. The thousands of bacteria will find their way and do what nature intended. Ever notice how animals roll in dirt and sit in the soil with their tails up. A diverse and healthy microbiome are essential to health and taking a pill is not going to do it.

    • Hi Arno – while sitting nude in the dirt may leave you with fewer friends and neighbors, it may not be as effective for gut colonization as you think. It is plausible for bacteria to colonize up the rear, but it is far more likely that, ancestrally, we ate, licked, inhaled most of our probiotics after ages 3 or 4. In other words, go for dirty paws over dirty butt.

      Our probiotic thumbprints still come from our mothers from birth and breastfeeding. Guarding that diversity of flora with a diet rich in soluble fibers and avoiding antibiotics ought to be our goal.

      Sitting bare butt on dirt does sound fun though… 🙂

  37. I was wondering if there was a way to restore the gut flora after loads of antibiotic use for a few years. Have I permanently altered/destroyed my microbiome and can the damage be undone? What is the best way to establish resident strains as opposed to transient strains?

    Does eating fermented food lead to resident/permanent colonies of bacteria? Using DoctorsData, my stool was tested and indicated little to no growth of the bido and lacto species. My functional doctor told me to increase these particular strains. Now, are these strains supposed to have some permanent numbers residing in the gut or are they only transient? Are SBO’s only permanent residents or are they transient? Lastly, are there any probiotic brands besides the SBO probiotics that you would recommend to increase the bido and lacto strains? Thank you!

    • Hi Lucy – ‘loads of antibiotics over a few years’ will certainly alter your microbiome. Chances are good that you’ve permanently lost some good bugs. There is not much you can do about that. But what you DO have control over is the recolonization. Expose yourself to nature/dirt/animals. Eat a diet that’s high in both fermented foods and soluble fiber (prebiotics) and you can take a variety of probiotic supplements to help introduce new bugs. Will doing this undo the damage from years of antibiotic use? Probably not. Again, not much you can do about that now. Don’t worry about establishing more permanent bugs over transient ones – that’s a total waste of your time and energy. Focus on eating prebiotics, eat a wide variety of fermented foods, let your dog lick your face (even though you know where its nose has been), play in the dirt like kids, banish stuff like listerine, hand sanitizers etc, from your house, don’t be so eager to wash your hands with soap after you’ve been gardening/hiking/at the beach. Get all your carbs from root vegetables.

      Our sister company (InnovixLabs) makes a prebiotic product with over a dozen fermentable fibers (start with small doses!)

      No harm in taking Lactobacillus and Bifidobacteria strains. It may even help. A lot. But don’t take it with the expectation of fixing everything.

      You could go hang out with a hunter-gatherer tribe or remote village in a tropical jungle. Crazy? May be. But I’ve done it.

      And if you’re wondering about fecal transplant (after getting over the ick factor), it’s early days. I still think we’re far away from having safe, reliable, consistent donor samples.

  38. Hi, i have anxiety and depression in the past. been taking 50 billion probiotic a day for half year now and i dont feel any health benefit. Recently i change brand into pro-50 50 billions probiotic. I took it for 14 to 16 days. Ive got the worse anxiety and depression ever. After i stop the probiotics i got better. But the anxiety and depression is still haunting me after 3 weeks. Is not as bad as first week but is still enough to effect my daily routine. My question is how long does the probiotics stay in my system? I read some threads that peoples still getting the die off symptoms for 3 months after they stopping it. Thanks!!

    • Hi Erick – probiotics are not a molecule with a ‘half life’ for efficacy. Each strain is different. Each person is different, based on both genetics and diet. Some species remain in your body and others disappear a few weeks after you stop consuming them. This is normal.

      People are looking to probiotics to cure everything. Like they did with Vitamin D and Omega-3 before that. That’s a set up for disappointment. There are many causes for depression and anxiety – psychological, physical, nutritional, and even lifestyle. Finding an integrative medicine MD who can help you connect all these dots and tackle it from a root cause perspective is the way to go. In the meantime, here is an article to help you get at some of the nutritional causes:

  39. Hi – Thank you for all of the interesting health information. Although I did know that antibiotics wreak havoc on our preferred gut residents, that was about the extent of my knowledge so your article has definitely filled in some holes! I came across your site in the midst of my search for information on the suspected health effects of consuming glyphosate – one of which is that it supposedly kills all of the beneficial gut bacteria. Do you have any helpful information, thoughts and/or opinions on this? I sure hope so since I’m totally adrift on this one!

    • Hi Carla – you may want to try Googling Dr. Stephanie Seneff. She’s written a lot about this. It’s hard to find counter-opinions but you should track those down and read it as well.

  40. Hi, lot’s of good information. Thank you! I feel like my kids had an unfair advantage, as they were born c-section, first born after laboring and failure to descend. The second because she was also a large baby and I was told it was likely to result in another c-section. I had no idea about the flora they missed by not going through the birth canal. My question, is there anything they can do as young adults to recoup any of this missing gut bacteria? One as many skin issues and the other suffers from asthma. I mean short of a poop transplant……I don’t think either would be up for that even if I knew where we could go to get one!

    • Hi Laurie – don’t beat yourself up. My kids were born via C-section too. Our understanding of the role microbiome plays in our health is very new. The best thing your kids can do now is take antibiotics only when essential, expose themselves to nature/dirt/environment/animals, eat a diet that is both high and varied in vegetable, nuts, tubers, legumes, and roots. Consume fermented foods and probiotics. Keep pets that go in and out the door. Reading about poop transplants is about as much as most of us can for now.

      As for skin issues and asthma, both can be affected by inflammation. Try an anti-inflammatory diet, which is also good for your gut bugs.

  41. Hi! Thanks for interesting information. I just want to add that the best researched probiotic product probably is the German ‘Mutaflor’. It was abstracted from the gut of an extremely healthy German soldier in 1917 by a medical professor who then cultivated it on gelatin, and it has in fact been commercially available in German drug-stores ever since. The reason – as I understand – which Mutaflor may help is not at all because it contains 95 % of the strains you need, in fact it contains only one (called E. Coli stamm Nissle 1917) but because it gives your gut a better milieu for the growth of your beneficial strains. (Disclaimer: I have only a personal and scientific interest in Mutaflor and no commercial interests whatsoever)


    • Hi Terja – thank you. Mutaflor is well researched. It is definitely worth taking but only as a part of a much larger effort in gut repair. We still have a personal responsibility of living a gut-friendly lifestyle. One day, this will be considered almost as critical as exercising.

  42. Hi Vin,

    Just found you today. How enchanting. Googling stuff as I’be decided to make my own non-dairy kefir. Interesting that you co-founded Innovix Pharma. I take almost everything Innovix Labs makes. Love, love, love the brand. I researched several brands including Prescription Assist before deciding on Innovix Labs Probiotics. Question, do you avoid recommending it due to a conflict of interest?

    Recently got diagnosed with Primary Progressive MS last year and with the first approved medication just hitting the market on 3/28/17 (Ocrelizumab), I’ve had to turn to God and nature for healing.

    Folake Taylor, MD, FACP.

    • Hi Folake – glad you like our InnovixLabs products. I recommend both brands (OmegaVia and InnovixLabs) on this blog, but only bring up InnovixLabs when I feel it is necessary. I do my best to give our readers honest information about nutrition. I don’t promise unbiased information – I have strong biases against sugar, grains, and high-Omega-6 seed oils. It goes without saying that you cannot outrun a poor diet or unhealthy lifestyle with supplements. And when appropriate, I will recommend another brand, even a competitor. Some of our new readers find it a bit skeptical. So, no, there are no conflicts of interest.

      Re PPMS – given your professional pedigree, your diagnosis, and your presence here. I’m guessing you’ve already done a lot of research on the subject. I seriously doubt I can add anything to your knowledge. Both faith and nature are powerful healers – embrace them both. If you find that nutritional approaches to therapy makes a difference, I’d love to hear from you about it. Take care.

  43. Hi..

    I already consume 6-12gms(i.e 1-2 scoops) of the broad spectrum Prebiotic by Innovix and would like to know if I should also consume the Bob’s red mill potato starch recommended above?.. If yes kindly mention the quantity?

    The information section of prescript assist in Amazon claims it to be vegan. Correct?

    I would also like to know if the beef gelatin used in Omega 7 by innovix is halal approved like OmegaVia?

    Also the pricing of the triple concentrated fish oil (200 capsules) sold on Amazon by Innovix in comparison to omegavia (pharmaceutical grade-only 60 capsules) is something I would like more clarity on. I understand the EPA:DHA content is a bit less when compared to OmegaVia’s but still i would be getting 200 capsules to only 60 capsules from OmegaVia?

    I appreciate all the information presented here.

    • Hi Khan – two scoops of the Broad Spectrum Prebiotic should be fine. There are some mixed feelings about Bob’s Red Mill Potato Starch, especially from the Gut Institute folks. If you want to increase prebiotic consumption, you can go to 3 scoops or better yet, increase the variety of vegetables you eat.

      I believe Prescript Assist is vegan – please check with them.

      All our gelatin softgels are either Halal and Kosher or made with fish gelatin.

      The InnovixLabs Triple Strength item is 75% Omega-3, while OmegaVia is about 90%. Triple Strength is in the ethyl ester form while OmegaVia is triglyceride form. OmegaVia is an ultra-premium product. ranked the InnovixLabs item as #1 best value among 53 other top fish oil brands. There are some differences, but we realize that OmegaVia may not be affordable for everyone and that is why we also make the InnovixLabs brand item.

  44. Hi – I have been through quite a few bouts of diverticulitis. Sounds like adding the prebiotic fiber is a good plan. When looking up the probiotics you mentioned – Prescript Assist and the Innovix Labs Multi Strain, they seem to contain different strains. Do you think that taking the two is beneficial. – Thank you for your thoughts.

    • Hi Chris – both Prescript Assist and InnovixLabs Mult Strain can be beneficial. If I were you, I’d take them separately – take one for a few days without taking the other. And then switch products. This is to make sure that your system agrees with both products. I would also recommend the InnovixLabs Prebiotic, but take it very slow in the beginning. People with digestive issues are the ones who need prebiotic fiber the most, yet they are also, ironically, the ones whose systems protest the most at being given prebiotic fiber.

  45. Hello!

    TY very much for the info, it’s quite integral and that’s rare.

    I have inflammation in my gut area and it has been getting worse the last months, I have been checking with doctors and still I am clueless on what condition I have. With all the research I have done on the internet the only thing that doesn’t make any sense for me, is that taking Prescript Assist made my symptoms worse, every time I have tried to introduce those strains into my gut flora.

    I had good solid evacuations, now it’s more like diarrhea; I had no gases, now I have some when I eat carbs (sugar specially) even in low quantities; I don’t have pain at all but it’s very uncomfortable because the inflammation just stays there all day long, and the only time that has been worsening is whenever I try to supplement with PA.

    Do you have any past experiences with people that doesn’t tolerate PA? Or do you think that it might be related with the inflammation? Cuz all I see is that it’s a marvelous thing for everyone, but that doesn’t seem to be my case.

    • Hi Hector – if you know that Prescript Assist causes this issue, then the obvious solution is to introduce probiotics using other methods. It’s normal for some people to react negatively to certain products. You should work with an Integrative Medicine MD who specializes in gut health to address this issue.

  46. Hi Vin,
    How much prebiotics should I start with a 21 month old toddler? Seems most of the food based prebiotics need to be raw to feed the probiotics. E.g. semi green bananas. My son is a picky eater and due to his condition (suspected ASD) he sometimes goes into meltdown with new food/routine. I think thinking of getting commercial prebiotics and sprinkle them on his meals. Saw a website suggest adult to consume min 5g to have some effect, and not to exceed 30g or the bad bacteria get fed as well:

    May I know how much prebiotics are you giving your kids when they are 21 months old? I’m thinking of starting him at 2.5g to 3g (half adult dose) as he has no issue with 1g to 1.8g of NutraFlora scFOS via Nature’s Way Primadophilus probiotics. And increase by 1 to 2g every 3 days up to 15g (half adult max dose). Is this too much?

    Also, how old are you twins when you start putting Prescript Assist on their food? On Prescript Assist, I found there are 2 version with the same name. There are some difference in the list of SBOs:
    1. by Safer Medical of Montana
    2. by Enviromedica

    Which version did you use?


    • Hi Chris – I get how picky eating can be. But this is a battle that you slowly and strategically have to win. At times, it will requires nerves of steel and the patience of a saint. These traits seem to come easily to other parents, but I have to work on it. Daily. And you will too, to get him to eat unfamiliar foods. Generally, foods need to be introduced about 10 to 12 times before their kiddy brains accept it as ‘normal’ and edible. So don’t give up.

      Even relatively benign stuff like cooked potato, rice, sweet potato all become partially prebiotic if you cook and cool it for a while. Cooling process turns the digestible starch partially into prebiotic fiber. If you take it out of the fridge and re-heat it, the starch becomes digestible by humans. But if you eat it cool or at room temp, (I know, not palatable), the starch stays somewhat indigestible to humans and digestible by probiotic bacteria.

      To answer your first question, that is touch. If you are still breast feeding, there should be small amounts of hundreds of prebiotic in breast milk. But ‘a few grams’ is the best I say. I know that is not a direct answer. All I can say is that it should be a lot more than what most people give their kids. Focus on giving virtually all his starch from root vegetables instead of grains. I assume you’ve eliminated gluten by now. If not, do it.

      Semi-green bananas are a hard sell even to grown ups, so I dont expect kids to go for it. There are easier ways. Try powdering the Jarrow Prebiotic XOS + GOS. Try 1/8th tsp of the Innovix Prebiotic mixed in with stuff. If he doesnt get too gassy, then gradually go up to quarter spoon or half spoon. Eventually more.

      I’ve often suggested that adults should get 5 grams of prebiotic daily. But that is honestly nothing. Adults ought to be aiming for 20 grams. Not eating or reducing prebiotic foods because it could feed bad bacteria is nonsense. The goal is to feed the good bugs and let the good bugs duke it out with the bad ones. At this point, we simply do not know enough how to feed the good and starve only the bad.

      As for how much I gave my kids when they were 21 months old, oh boy, I don’t recall. Probably not enough. I may be trying to erase some of that from my memory – that was not easy with twins. Meltdowns in stereo! Ugh.

      I dont think 15 grams of a good prebiotic is too much, but take your time getting there and make sure you use several forms of prebiotic fibers because different prebiotic feed different bugs in different sections of the gut. That’s why I formulated this: both my kids get a teaspoon of this and 2 to 4 tablets of the Jarrow Prebiotic every day.

      The first time I tried Prescript Assist with my kids’ food was probably about when they were 2 or 3. Yes, there are multiple products under that name because the company selling it had a change in their line up. Not sure if it’s reliable any more. I always used the Enviromedica product.

  47. Hi Vin,
    Good tip on keep trying on introducing food to kids! Innovix Labs prebiotics is top is my list when I start looking for prebiotics. Unfortunately it is not available where I live. Hence I make do with what is available here while figuring out how to get freight forwarder to bring Innovix Labs. I’m a big fan of Innovix Lab’s probiotics and fish oil. Still have 2 bottles of Innovix Labs probiotics, with help from colleague who was in US recently and bring back for me. But I wasn’t looking at prebiotics 2 months ago – I should but I didn’t. Currently make do with Hyperbiotics + Jarrow XOS+GOS + Jarrow Inulin FOS while checking out the freight forwarders when I have the time – complicated logistics.

    Put my son on gluten free last week with minimal sugar (those that comes with Prebiotics/Probiotics). Also switched from dairy to soy. Started on more veges and tubers for the whole family. Due to this recent event, entire family’s diet has changed – for the better!

    Also started feeding him prebiotics with many different probiotics but kept the probiotics total count to less than 30B due to his age. Hopefully some could recolonize his gut. So far I notice he has some improvement with Culturelle’s Lactobacillus GG. Will try Innovix probiotics soon – hopefully some will survive the stomach acid without the capsule. Good thing that you changed the delivery mechanism from tablet to capsule! Decided to skip Prescript Assist for now.

    Spouse not keen on FMT due to the risk involved. So that is on hold for time being.

    • Hi Chris – check with the InnovixLabs customer service team at and they may be able to find a way to ship products to your location. As for dairy vs soy, I almost prefer dairy, assuming there is no sensitivity to it. I certainly would NOT give my child soy milk due to the eventual build up of phyto-estrogen like compounds.

  48. Hi,

    I’m delighted to find you. Wish I had a year ago when I spent an extraordinary about of time scoring the internet for informative on probiotics, which strains did what, which brands proved to actually contain the efficacy they claimed… On my own I came to Innovix as my #1 choice, both because of the diversity and quantity of strains, AND could afford it monthly.

    If someone has already asked this, I apologize for repeating- my question is 2-fold:
    1) Prescipt Assist changed its formula and many supporters are disavowing the new formula for differing reasons (insufficient data/testing, ineffective in comparison to original, etc) what do you think about this? Now that no original formula is available any longer, do you equally support the new formula with less/different strains?

    2) I’ve read from more than one source stating that SBOs are not sufficiently long-term tested in humans, and in some cases, specific strands (including some that Prescript-Assist specifically contains) are actually associated harmful colonization gone wild and thought to be a co-contributor to Chrohn’s. Because of their spore-forming abilities, can become pathogenic and over colonize. (
    As a big advocate for Prescipt Assist, what is your stance on this?
    I currently have a great infection in my bladder, and am re-ordering my Innovix Multi Strain.. And am unsure how else I can bolster this along with the obvious dietary elimination. Are SBOs a safe and necessary assist to help my twarted biome? Really appreciate your help and thoughts.

    • Hi Diane – I am not happy with what’s become/becoming of the old Prescript Assist. I’m not sure what’s in the new formula and how it’s made. So I’m distancing myself from the product until I can find out more.

      As for soil based organisms not being tested in humans, perhaps the specific formula/bugs in Prescript Assist, but we breathe in spores by the millions all day long. Every time you go to the part or your backyard, you breathe in a bunch. There is no escaping SBOs. It’s been around forever. We are not new to SBOs. Harmful or runaway colonization has more to do with the state of dysbiosis in the person taking the supplement than the supplement itself. It’s a long and disciplined process to work back from dysbiosis and several supplements can cause gut distress if taken during the recovery process. I know, it’s a catch 22.

      If you really want to increase your gut diversity, get muddy. And eat a LOT of vegetables – variety and quantity. And take prebiotic supplements – there is a good one by InnovixLabs. Take is slow and easy on prebiotic supplements at first. Work up to a couple of scoops over a long period. With prebiotic fibers, you’ll be miserable and gassy if you jump in the deep end of the pool – start slow.

      • Ok, thanks…
        I have several probiotics I can take intermittently to recover from a round of macrobid. Now I’m on a 3 day course of Flucanozol.
        Eating a ton of garlic for ~2wks (and having a die-off reaction, though not too terrible comparatively) eating spleen/kidney/liver/intestines helping foods.
        Removed all things yeast.
        Its the dead of a crappy winter here, so I’m not in the yard much, but we compost, veg & flower garden, and hike with dog on wooded trails. So, peripherally, I’m clearly exposed to SBOs. Just not sure about ingesting them in quantity.
        But my dysbiosis is a life-long battle I’ve never fully recognized or understood in its full scope and depth.
        I’ll add prebiotics and ramp up. Miserable and gassy are my middle names, so it’s par for the course.
        Please LMK if you think of anything else to add to my upward journey out of dysbiosis.

  49. Vin –
    Great article, I gained a lot of new knowledge. I’m looking for your opinion on the following issue: Recently, I took antibiotics for 62 days – don’t ask – and did not know, nor was I told that I should be taking probiotics, until the last 10 days. I developed some gut trouble and went on an 11 week probiotic regime, which greatly helped me, but I seemed to reach a point where I leveled out and still have a little trouble. I will begin taking prebiotics based on your article, and I’m a pretty good eater, but anything else you can suggest to assist in my gut rehab?


    • Hi Scott – after 62 days of antibiotics, you may get back the original quantity and volume of probiotics, eventually, with a good diet. But it is unlikely that you’ll get back to the original diversity of your gut. Let’s say you had 800 species of bugs in your gut. You may be down to 780 now. And those 20 may never come back. In other words, each antibiotic therapy is a miniature level extinction event. I know. Not nice to think of it that way. Dr. Martin Blaser talks a lot about this in his book, Missing Microbes. The issue is we don’t know what role those missing 20 bugs played in your health. It may take decades before we know the answer. The research in this are is INTENSE.

      As for your gut rehab, you’re already ahead of your peers by simply being here and reading this stuff. Eat a variety of vegetables, especially ones rich in prebiotic fiber. I generally tell people to eat 25 different vegetables every week. Supplement with both probiotics and prebiotic fiber. Exercise! Yes, exercise helps increase diversity of gut flora. Get a pet. Spend time outdoors. Swim in lakes, oceans, get muddy, do some gardening, and go easy on hand sanitizers. Hike. Camp. Get muddy. Walk in the sun. Keep your Vitamin D levels high, preferably from sun exposure rather than supplements. Work on sleep and stress management/discipline – they have an impact on your microbiome too. It’s a process. But I’d start with increasing the variety and quantity of vegetables in your diet.

  50. Hello Thank you for the information on probiotics…. I took Cipro in the 1990’s you mention that I permanently destroyed my gut do you mean diet and probiotics won’t work for me no matter what?? Thanks for your advice all the best

    • Hi Joan – according to Dr. Martin Blaser (, each antibiotic course is a miniature extinction event in our guts. In other words, we permanently remove or kill some species of bacteria from our guts. And they aint comin’ back.

      Even knowing this fact, sometimes we need antibiotics because bacterial infections can kill. I needed a course of Cipro 10 years ago. Hated taking it, but not taking it could have been worse. What I (and many others) have issues with is the liberal use of antibiotics for conditions that do not require antibiotics, such as a viral infections. Pediatricians pump kids with ear infections full of antibiotics even though a good chunk of ear infections are viral in their cause…this is often to comfort anxious parents who expect to walk away with a prescription.

      Does this mean prebiotic-fiber-rich diet, dirt, pets, fermented foods, probiotics do not help? No, they certainly help, especially if all of those factors are combined. An extreme form of intervention is fecal transplant, which used to be too gross to even talk about but is common knowledge these days. All of these tactics can help. You may not get 100% of your pre-Cipro microbiome back, but don’t let that stop you from trying to enrich and diversify your microbiome.

      Our sister company makes a good prebiotic fiber: but what this product is missing is polyphenols…which are super prebiotics and super bitter if added to foods. You’re better of getting your polyphenols from fruits, veggies, nuts, spices, etc.

      Hope this helps.

  51. Hi Vin, I have been treated for hpylori two times now(with antibiotics), how to make sure that it doesn’t come back? I eat raw garlic every morning on empty stomach , and take probiotic supplement with each meal. i have heard that almost 50% of the world has it, but only a few get infected, so clearly my body is lacking something which others have.

    • Hi Vikrant – this is a medical question, so this needs to be addressed by your doctor. Having said that, it may be of interest to know that H. pylori was (and is) a typical and normal resident of the human gut. Virtually all of us had it decades ago, but in recent years, poor diet, antibiotic use etc, have created an imbalance that permits H. pylori to, well, misbehave. The point I am making is that you are not being attacked by a pathogen but rather a ‘when the cat’s away, the mice begin to play’ situation in the gut. Hope that adds some perspective.

  52. Hi Vin, due to long term chronic infection and antimicrobial use, my gut has become severely compromised. I cannot handle many foods and I think probiotic and prebiotic supplements, along with fermented and prebiotic foods recommended in this article, would be too strong for me right now. What do you recommend for some gentle gut repair in the beginning (herbs, foods, etc.)? I believe I need to do some “Leaky Gut” repair before repopulating my gut with probiotics and prebiotics. Please let me know if that is the right approach. Thank you!

    • Hi Joe – well, this is a tough question to answer because only you know what your gut/body can tolerate at the moment. Before you start thinking about supplements etc., focus on foods and gut-friendly lifestyle changes – what to leave in and what to leave out.

      Leave in: nutrient-dense foods like eggs, seafood, berries, some red meat, bone broth, gelatin/collagen, lots and lots of leafy greens, tubers, and other prebiotic-rich stuff like onions and leeks. Focus on variety.

      Leave out: sugar, alcohol, and gluten. All three worsen the tight junctions in the gut. Stress, infections, deficiencies of some nutrients like Vitamin D3 and A.

      Keep in mind that:
      1) Stress worsens leaky gut.
      2) Exercise improves diversity of gut flora
      3) Outdoor activities like gardening, hiking, green spaces etc improve the gut
      4) Sleep improves gut health

      Your goal should be to identify and remove the triggers – stress, alcohol, allergens, gluten, sugar, etc. Then move on to introducing ‘good stuff’ like a WIDE VARIETY of veggies including prebiotic-rich ones like leeks and onions. Then move on to probiotics, prebiotics, fermented foods, and products like Pepzin GI, Glutamine, Collagen etc.

      It’s a process. You won’t get there overnight…after all, you didn’t get here overnight. Work with a Integrative Medicine MD or nutritionist who specializes in gut health – you’ll need their help, especially if you’re dealing with an infection or something not diagnosed yet.

      Keep us posted on how you do.

  53. Hi, Vin,
    This article has an eye opening knowledge for city dwellers like me. I have been having alot of stress, restlessness and mood swings since last 2 months. I am from Mumbai. I have sinus blockages occasionally due to environmental/Seasonal changes. So to clear them, our family normally have a combination of cetirizine, Mox capsules and Paracetamol anti-biotic tablet each. We are relieved after taking the 2 to 3 doses. Also, I was diagnosed with Covid-19 last year and there were many antibiotics that I had to save myself.
    After going through this article, I am thinking to replenish my gut with good microbes. I am thinking to order Innovix labs prebiotic fibers and InnovixLabs, Multi-Strain Probiotic, 50 Billion.
    What else can I do to help my gut microbes? Also kindly suggest any lifestyle changes. I am allergic to sulpha drugs.

    Thanks and regards,
    Tushar Borad

    • Hi Tushar – follow the guidelines set in the article.

      1) Only take antibiotics when absolutely necessary – they hand them out like sweets in India. This has consequences.
      2) Eat a wide variety of vegetables. Aim for 25 to 30 types a week. And do not overcook them.
      3) Eat a variety of fermented foods.
      4) Exercise.
      5) Take a probiotic and prebiotic supplement.
      6) Spend time in unpolluted nature.

      Hope this helps.

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