Fix Your Gut’s Top Four Recommended Probiotic Strains

Fix Your Gut's Top Four Recommended Probiotic Strains

Probiotics should not be taken every day for digestive illnesses or overall health. If you need to supplement with probiotics on a daily basis to help with your digestive woes, then you have an underlying issue that probiotics are masking. Probiotics can also become opportunistic, and supplementation may worsen digestive issues. For some supplementation of probiotics have caused or worsened SIBO (small intestinal bacterial overgrowth), upper gut dysbiosis, d-Lactate issues, histamine intolerance, and sepsis in people with compromised immunity.1 2

With that being said, I believe that some probiotic supplements can be used safely in certain protocols to improve digestive ailments and restore proper digestion. If you have taken an antibiotic or a natural antibacterial agent for a while, probiotics may be useful in modulating the immune system to accommodate proper bacterial flora recolonization in the digestive tract. Probiotics can also be useful in modulating the immune system to keep opportunistic dysbiosis at bay. It might be important to take a probiotic like S. boulardii while you are taking an antibacterial agent if you are hospitalized to prevent C. difficile dysbiosis.

The body can hopefully recolonize probiotic flora on its own eventually, through proper diverse diet. Probiotics may help speed up this process, if they implant, or at the very least reduce dysbiotic flora and increase positive immune expression. Supplementing GOS instead or with a probiotic may help support proper implantation and growth of natural flora. Always take a probiotic four to six hours before/after an antibacterial agent, preferably before bed with a glass of filtered or bottled water. You do not want to ingest traditional tap water because the chlorine in the tap water might reduce the effectiveness of the probiotic.

It is still unknown what probiotic bacteria are important to one’s gut flora. Even if I recommend these bacteria, they may still cause issues for some people. Any bacteria can become opportunistic at any time or trigger the immune system to respond negatively so always be aware of that.

I go in depth further about the different probiotics in my book Fix Your Gut. I recommend different brands of specific probiotic strains and detail specific probiotic protocols.

Digestive ailments require different probiotic strains to help relieve the conditions. The following four strains are my top recommended probiotic strains.

4.Saccharomyces boulardii

3. Bifidobacteria longum

Bifidobacteria is a genus of probiotic flora found in the intestinal tract of humans.3 Bifidobacteria longum is also known to be one of the first colonizing probiotics in newborns.4 Bifidobacteria longum is important to the metabolism, fermentation, and digestion of different carbohydrates in the intestinal tract.5 Bifidobacteria longum also produces lactic acid that helps regulate the pH of the colon and prevent the growth of opportunistic bacteria.6

Bifidobacteria longum has been shown to help improve lactose intolerance,7 prevent diarrhea,8 alleviate some food allergies,9 and help fight colonization of opportunistic bacteria in the colon. Bifidobacteria longum binds with excessive bile acid if they make it to the colon which would help those suffering from bile acid malabsorption and fat digestive issues.10

Finally, Bifidobacteria longum help scavenge free radicals in the intestines, improving intestinal mitochondrial function, improving gut barrier integrity, and reducing inflammation. Bifidobacteria longum has been shown to lower blood pressure and help prevent colorectal cancer.11

The Bifidobacteria longum probiotic I recommend using is: Custom Probiotics B. longum

2. E. coli nissle

E. coli has an unfair stigma when you think of the bacteria. Most people only know E. coli as one of the major bacterial strains that cause food poisoning and severe infections. Most E. coli are harmless and are probiotic bacteria found in humans. They help produce vitamin K2 in our intestines.12 One particular strain, E. coli nissle, has been shown to be extremely beneficial to human gut flora.

The strain was isolated by the German professor, Alfred Nissle during World War I when he isolated the strain from soldier excrement.13 E. Coli nissle was used treat Adolf Hitler, who suffered greatly from IBS. 14 Most recently it has shown to help people suffering from ulcerative colitis, causing the condition to go into remission.15 16 My speculation of this is that it can eliminate Mycobacterium avium paratuberculosis opportunistic infection in people suffering from IBD.

E. coli nissle has been shown to help relieve chronic constipation, pouchitis, IBS, and C. difficile pseudomembranous colitis.17

The E. coli nissle probiotic I recommend using is Mutaflor. Sadly, Mutaflor is banned in the U.S. currently because of it being mislabeled as a food product by the FDA instead of a probiotic. You can purchase it in Canada.

1. Lactobacillus plantarum

Lactobacilli is a genus of probiotic flora found in the intestinal tract and saliva of humans.18 Lactobacillus plantarum is used in the production of sauerkraut, kimchi, pickles, and sourdough bread. Plantarum is an excellent probiotic that has shown useful in the elimination of the symptoms associated with IBS.19

Lactobacillus plantarum supplementation has also been shown to help relieve depression. The reason the probiotic reduces depression is that it increases hippocampal brain-derived neurotrophic factor (HBDNF) levels in the brain. HBDNF also has been shown to support the survival of neurons, encourage the growth of new neurons in the brain, and is important for proper long-term memory.20

Lactobacillus plantarum can reform the gastrointestinal mucus barrier, and it inhibits opportunistic bacteria by making bactericidal peptides. These peptides have been shown to inhibit Gram-positive and Gram-negative bacteria. L. plantarum has also been found to reduce histamine production and degrade histamine in the gut for people that are suffering from histamine intolerance.21 It also prevents allergies, especially to soybeans.22 Finally, Lactobacillus plantarum stimulates the immune system by producing the amino acid L-lysine in the intestine.23

I do not recommend that people who are Th1 dominant take L. plantarum because it can increase Th1 cytokine production from an immune reaction to the bacteria. When I took it years ago, it caused me to develop severe joint pain, which discontinued when I stopped taking the probiotic, from an increase in Th1 cytokines.

The Lactobacillus plantarum probiotic I recommend using is: Jarrow Formulas Ideal Bowel Support

  1. John, in your experience, does Mutaflor cause any histamine issues?

  2. Hello. Thank you for your usefull advices. But are you sure about lactobacillus plantarum and th1 dominance? Is it scientifucly proved or just an experience? I’m taking this probiotic while I’m gluten sensitive and I have some symptoms like headache, coughing, and having some pain in my neck. Do you think I should not taking it any more. I tought these are natual side effects of changing gut conditiond!

  3. Would it be beneficial or counter productive to take S Boulardi and Mutaflor together?

    • I would not see an issue of taking both of them, but I would not take them at the exact same time, they may compete. I would take them with different meals.

  4. Hi John, love your website! What probiotic would you recommend for a teenager with klebsellia an entrobacte cloacae, with GI pain every morning and constipation. He had Lyme/Bartonella and took antibiotics for a year. I think the GI problem got worse when I gave him inulin to help with constipation. He is currently taking probiotic called HMF forte. He also gas anxiety/ocd

  5. I just found your website and I have been taking probiotics for close to a month just for good health. I was very surprised to read that I shouldn’t be taking them. Can you refer me too something I could read to explain why. So many people think we should be on them including doctors!

  6. My teenage son has Bartonella and has been on long term oral antibiotic treatments. We have tries so many probiotics but they all seem to hurt his stomach badly. What could cause that? Any suggestion which product might work?

  7. Personally I recommend Vivomixx 112.5 billion live cultures as I feel much better with flatulence after 1 month of consumption.

    However, I will look into the 4 you have recommended here. Seems interesting!


  8. Do you recommend probiotics when dealing with Roemheld Syndrome and possibly gall stones? If so, which strain would be optimal? Thank you.

  9. Haha yeah the FDA “accidently ” mislabeled it on behalf of Big Pharma

  10. Every time I try a probiotic that is only bifidos, I get a severe toothache for days = no, I’m not kidding. Over the past 8 years I’ve carefully tried single strain probiotics. B Lactis and several other trials of single bifidos each produces a toothache for days after taking one day’s worth of these products.

    Bifidos can overgrow (saw a study on Pub Med about that) so maybe that’s it, or maybe the bifidos are serving as food for something awful that is eating them.

    I’m never taking another bifido again.

    • Yes, they can overgrow, just like any microorganism. I wonder though if they trigger an immune response and that is what you react to? Bifido are not usually found in the oral microbiome, but they can colonize.

  11. Hi John – any ideas why one would have an overgrowth of e.coli, bifidobacterium longum and lactobacillus fermentum? My recent tests reveal these. I had a test done 10 years ago (at the beginning of my illness) and it revealed dry high e.coli back then too. The strain of e.coli is not stated. The lab simply suggested not to take lactic acid probiotics and FOS for the E. coli. Also detected no eubacterium. I paid a lot for these tests but have no guidance as to what they mean.

  12. Hi,

    Does L Plantarum cause issues if you have an overgrowth of d-lactate forming bacteria?



  13. I am 71 female very prone to urinary tract infections and in most instances identified Escherichia coli in my urine. I heard that taking probiotics could lessen my infliction but as there are so many types in the market please advise what type is suitable or what ingredients in the probiotics I should look for.

  14. How do persons who are histamine intolerant re-balance their intestinal flora after prolonged antibiotics?

    Many thanks.

  15. Hi John,
    Great articles on here, well researched with excellent information. How do your recommendations apply to Pregnant women? I was thinking of adding a high quality probiotic to my Pregnant wife’s (limited) supplement routine… Was initially going to go with Prescript Assist until I read your other article relating to that… Or would you say it’s unnecessary and/or potentially dangerous and she should just stick with fermented foods? Many Thanks, Brendan.

    • I believe she should stick to eating fermented foods and eating a seasonal local variation of the PHD with low mercury seafood ingestion. Of course, ask her doctor, but this is what I would do.

  16. Mutaflor is available in Canada, but only with a prescription from a Canadian doctor. And then try bringing it back across the border…

    • John:
      Sorry to contact you using Kelly, but I really need your help as to help me deal with a tough problem wiith osteoporosis plus the impossiblity to supplement calcium due to heart and calcium deposits in the wrong tissues. Would you be so kind as to recomend me a strain of non sbo bacteria that would help me increase my vit k2 levels? Is there any brand available?
      Deeply appreciate your attention…

  17. John,

    Do you think that jarrow ideal bowel support is ok for those sensitive to histamine?


    Laura Paris

  18. Hello. I had severe UC for two years and had a complete colectomy. I have a j-pouch now. I take 10 2.5 mg of Lomotil daily to slow my gut down. No colon= chronic diarrhea. My question is, what probiotics would you suggest? I still have pain and diarrhea daily. Thank you so very very much for your time.

  19. Yikes, have you looked at the list of ingredients in Mutaflor? Talc, and phthalate are my personal favorites. Both carcinogens. Sounds sketch, John.

    • Yeah, they aren’t great, but most pharmaceutical produced products have questionable additives.

      Talc has been mostly vindicated. Cancer was mainly caused by cross contamination with asbestos, which has been eliminated since the 70’s. Of course you would not want to breathe in magnesium silicate, but ingesting some of it seems to be fine. Silicon dioxide for example is fine for ingestion, but breathing it can cause issues. The same with DE.

      The enteric coating they use is Methacryclic acid which does not contain phthalates (unless it is listed on the formulation itself which it is not.) Some enteric coatings however do contain phthlates.

      I do not like the addition of polyethylene glycol as macrogol.

      The additional ingredients are suspect at best but at the doses they would be in the supplement I would assume it would be fine for most people. That being said you should be aware of these and:

      Maltodextrin might be GMO.

      Titanium dioxide

  20. Hello John,

    I have been reading through your articles about Probiotics. I gathered some good info. But would like to run it by you to see what your thoughts are. I have a fiancé who age 28 who resides in Tokyo Japan. She recently got diagnosed with UC. She was hospitalized for 2 weeks, she was put on 3 diff. Meds. I recommend for her to take some Probiotics and she has never taking any before she has been taking Garden of Life Dr. Formulated Probiotics Urinary Tract + — 50 billion – 60 Vegetarian Capsules. For about 2 weeks now. She said she has been feeling somewhat better than before. I found your page from researching Probiotic Containing Escherichia Coli Nissle for UC. I was thinking of trying to get this probiotic for her but wasn’t sure if it would be helpful or if I should wait till she finishes the Probiotics? She will be on them for quite awhile. Do you have any recommendations?

    Thank you, for your time John I really appreciate it.

  21. Hello John,
    Do you recommend these probiotics for Celiac disease? Our 24 year-old son has been gluten free for a couple of years and still isn’t well. He has lost 20 pounds and is extremely thin ( 5’7″ 110 pounds). What type of digestive enzymes would you recommend? Thank you.

    • Dear Kendall,

      As long as he has his appendix and is not suffering from SIBO and has good motility, I recommend ingestion of probiotic foods like sauerkraut, fermented pickles, kimichi, and organic sour cream on occasion. I do not recommend digestive enzymes unless absolutely needed.


      • Thank you so much for your reply. Will do the fermented vegetables. What about the probiotics you mentioned above? Do you recommend taking all three for Celiac disease?

        • He can if he chooses to. But I believe that most people should get their probiotics from the occasional ingestion of fermented food.

          • Why should people only ingest fermented foods occasionally?

          • Because fermented foods have some issues associated with their intake.

            Most fermented foods are contaminated with yeast and mycotoxins which is not good for those who are sensitive.

            In addition most fermented foods are elevated in histamine and histamine produced probiotics which can cause issues in those sensitive to it.

      • Hi, love this thread. Was wondering what the significance of not having or having an appendix is? I had mine out in 1999, I’m 44. Vegetarian but recently having some gut issues that won’t go away. Looking forward to your thoughts.

  22. Hi John. Our daughter recently developed PANDAS after taking a strong antibiotic called sulfamethoxazole. She had struggled with autoimmune disorders when she was a tot but we were able to heal her gut through diet and extensive environmental changes. Long story short, we’ve found that while the sulfameth rid her body of a bad strain of E.coli it also allowed the strep found in our bowels to explode in numbers without the healthy E.coli strain to keep it in check. Anywhoo, just wondering if there are any ways you know of to increase E.coli Nissle in the gut sans Euro-probiotics. Thanks for your response.

  23. Hi great informative article your spot on I’ve been taking MUTAPHOR for last 5 months and it’s fixed my constipation that I’ve had for last fifteen years. Not perfect though as I’m sure I have sibo so it’s not a matter of just popping pills.

    I’ve had chronic cold sores all over my chest and face for the last year and in talking like 5-15 at a time I am doing a lot of herbs and have reduced stress the last 2 months. I eat very very well only veggies and meat! My hope is if I start lactoferrin it will do wonders. My only concern and question I would be thrilled if you could answer is do you think lactoferrin will kill mutaphor??? Love to hear your thoughts

  24. Hi John,

    do you recommend Ascended Health’s soil based probiotics?

    i have chronic constipation issues and looking for something to help, since as you say, we can’t get the E coli one you recommend above.

  25. If I purchase the 1st and 3rd product you mentioned… Do I take them together? Or how does it work? Thanks !!!

  26. You say probiotics should not be supplemented long term unless medically necessary. I am dealing with H.pylori and am on a natural protocol to get rid of it. In this instance, would probiotics be ok during and after to rebuild a healthy gut flora along with prebiotics? Also hiw long after I finish the protocol would you advise to rebuild my gut flora? Thanks a lot.

  27. For how long would you recommend the use of lactobacilus plantarum? 1 month? More?

    • Probiotics should never be supplemented long term unless medically necessary. If you are having to take a probiotic for longer than 2 – 3 weeks than your digestion is not optimal and it is a crutch.

  28. I take the brand MegaFood, called Megaflora & I take one everyday, is that ok?

    • Why do you feel like you need to take a probiotic everyday? If your digestion relies on a probiotic everyday then it is not optimal. Focus more on the use of prebiotics and whole FODMAP foods on occasion in the diet to help facilitate proper gut flora.

  29. I just found 3 other single strain probiotics through some other sites and I wonder if you’ll write about them somehow.

    They are
    Lactobacillus Reuteri (NCIMB 30242) :
    Lactobacillus GG :
    and Bifidobacterium infantis 35624 :

  30. Can these probiotics be used to ferment food such as water kefir or any other fermented food as a starter ? Like pouring the contents of one or a few pills into the food to be fermented ?

  31. I don’t have any issues with the probiotic, it seems like a good one.

  32. how would you rate the biokult acidohpilius/plantarum probiotic for someone trying to rebuild their gut health? are there any drawbacks to including the acidophilus along with the plantarum? heres what im talking about

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