Many people are wasting hundreds of dollars on probiotics that are not worth a dime. Knowing exactly what is happening in your body is key to healing your gut. Watching and listening to what your body is telling you is vital. Finding the strains your body is weak in is imperative to the process. A compromised gut is evident through illness, allergies, even auto-immune diseases. Both over-the-counter probiotics and home brewed probiotics are important in this process.

Your intestinal tract is a long tube filled with a lining made up of good and bad bacteria. This bacteria alone weighs three pounds, the same weight as a brick. If you spread it out flat, it would cover a tennis court. When the good bacteria is killed off from antibiotics (against life), birth control pills, GMOs, pesticides, and other damaging elements, it must be rebuilt through probiotics (for life).

Probiotic foods, such as fermented coconut water, sauerkraut, kraut juice, kefir, kombucha, yogurt, kim chi, etc. are easy to make. The biggest challenge is your own fear. In his book Wild Fermentation, Sandor Katz says there is no danger in fermenting fruits and vegetables. Most importantly there has never been a reported death to the FDA from fermented fruit and vegetable products. Fermented fish and meats are different and are susceptible to botulism.

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Ferments rank high in probiotic strains and give the person preparing the food the ability to introduce more strains that are specifically deficient for that person’s intestinal tract. For example, fermented coconut water, a probiotic drink, is beneficial at building up the good bacteria in the gut enabling it to fight off pathogens. Many people with yeast overgrowth say they see powerful die off symptoms specific to killing off yeast strains like candida through fermented coconut water, sauerkraut and kraut juice due to the high lactobacillus content. 

At the same time some say eating fermented foods feed yeasts and should be avoided resulting in a dire point of confusion for many people. This point of controversy can easily be addressed through those with the most severely damaged guts, these people are called canaries-in-the-coal-mine. When they eat a food they should not have their body’s respond immediately. My son is one of these people. Since we have been healing his gut I now realize, I am one of these people, too, it was never visible before due to phantom masking – where your body goes into overdrive to overcome the pathogens masking the symptoms. When  a canary-in-the-coal-mine person eats a food they should not eat they respond with symptoms specific to their body, exposing the weak link in their genetic make-up: stimming, attention issues, anxiety, yeast effects, rashes, dyslexia, brain fog, exhaustion, etc.

While you are building the gut it is necessary to introduce new probiotic strains looking for die off: headache, runny nose, cold-like symptoms, flu-like symptoms, joint pain, body aches, anxiety, depression, confusing thoughts, etc. Usually die off symptoms are specific to each person and generally follow the same pattern of symptoms caused by the illness. For example if your child is autistic and stims with drooling, once you give him the right probiotic with strains he is weak in, his die off may be stimming and drooling. If there is die off that is too great, the dose is too high. 



This is the puzzle, where mom needs to become a detective as healing the gut is sometimes confusing. Those with the most damaged guts can only tolerate one drop of a probiotic liquid on their tongue or one drop in a glass of water sipped throughout the day. That is their starting point. After a month they build to two drops a day and so forth. Others can drink a whole quart or two of the same probiotic liquid and not experience die 0ff until they drink over 2 quarts. If you can tolerate that much of those specific strains you do not need to build those strains. Look further for other weak strains through other probiotic foods or over-the-counter strains.

The goal is to look for die off and progress by building those weak strains. Pushing probiotics so that you are constantly in a die off state, is not the goal as it causes too much inflammation. 

The Herxheimer reaction, also known as Herxing, is key to healing and recovery. This die off reaction is your marker and tells you if you are just wasting time or actually building. You want this. You are looking for this.

When making your own home ferments be sure to add a few drops of the probiotic strains in which you are weak. For example if you find you have pronounced die off with Living Streams Probiotic liquid, which rebuilds against yeast overgrowth, add a few drops to your fermented vegetables. It will make those fermented veggies more potent to your pathogens.

Some people take a fermented food, experience die 0ff, and say “I have histamine issues, I can’t have that.” This is often not the case and the person is experiencing die off, or Herxing. This is what you want, you have found the strains deficient in your body  and you need to focus on them, building them. When you find this weakness, go back and start slow building from there.

It is very important that you do not remain in the stage of die 0ff, a status involving a lot of internal inflammation. The body can not heal properly in an inflamed state.

dr natashaDr. Natasha Campbell-McBride, a medical doctor and neurosurgeon who specializes in autism and auto-immunity lays out in her book GAPS, Gut and Psychology Syndrome, the proper method of rebuilding the system through probiotic foods, probiotics and foods that are most digestible. As the intestinal tract builds, it progresses and more can be introduced, in a certain order according to digestibility and killing off pathogens.

Every person with a damaged gut will experience these histamine issues, this is merely a reflection that the body’s detox pathways are clogged, the pathogens are overgrown and healing through rebuilding needs to take place. Often times opening up the detox pathways is assisted through the MTHF gene specifically with methyl B12. Dr. Ben Lynch has produced some of the most comprehensive studies and findings on the topic as well as putting the proper methyl B12 product to aid the situation. Click here and here for assistance in opening up these channels. Beware of any B12 product with added sugars, products ending in -ose, these feed pathogens making your problem worse in the long-run. I have seen very few B12 products that do not contain pathogen feeding ingredients in the product. To date, all B12 lozenges contain these detrimental sugars which feed pathogens.

Dr. Natasha addresses histamine issues directly several times in the book and on GAPS faqs. Click here to read more about healing the gut while experiencing histamine issues.

Taking the same probiotic daily is often a waste of money, especially if you have not tested your strengths in those strains. Most people in the process of healing build up to 11 capsules a day of each product, then hold that dosage for a month and move to other potentially weak strains. Occasionally going back to the built strains to be sure they remain strong.

If you are taking a probiotic you should be increasing your dosage of that probiotic to build up those strains. Starting small in dosage, while looking for die off, then building up and continually looking for further die off is important.

Taking one capsule daily for years will not rebuild the gut if you are not experiencing die off symptoms.

 Click here to learn more about test studies on home brewed probiotics like sauerkraut.



Click here to read more about the highest ranked beneficial probiotics specifically designed for those with Intestinal Permeability.

*If you learned something from this post share it so others can do the same. To support the efforts of this blog shop the affiliate links above like this one. You pay the same shopping through Amazon while the author receives a small referral fee from Amazon. This offsets the costs of this site.

*Nourishing Plot is written by Becky Plotner, ND, traditional naturopath, GAPS who sees clients in Rossville, Georgia. Since her son was delivered from the effects of autism (Asperger’s syndrome), ADHD, bipolar disorder/manic depression, hypoglycemia and dyslexia through food she continued her education specializing in Leaky Gut and parasitology through Duke University, finishing with distinction. This is not a news article published by a paper trying to make money. This blog is put out by a mom who sees first hand the effects of nourishing food vs food-ish items. No company pays her for writing these blogs, she considers this a form of missionary work. It is her desire to scream it from the rooftops so that others don’t suffer from the damaging effect of today’s “food”.




56 Responses to The Proper Way To Take a Probiotic And The Mistakes That Are Wasting Your Money

  1. Heather says:

    I was making my own water Kefir and milk Kefir at home for about 6 months. I also make sauerkraut and fermented beets and carrots. I have stopped the Kefir at the advice of an alternative medicine practitioner due to the fact that I was suffering sore, itchy throats, coughing, breathlessness and fatigue symptoms (Similar reactions to those things that I am intolerant of). I have IBS, MCS and CFS as well as food intolerances and chronic constipation (Which persists even though I am on an EXCELLENT eating regimen). I have been off the Kefir for about a month and no symptoms, had some for two days last week and symptoms recurred.
    My querie is this: If we stop eating a food that makes us sick due to allergies and intolerances, why must we continue to ingest things that are obviously making us sick just because they have probiotic qualities? It doesn’t make sense to me. I understand about die-off but how long must one go through that before they decide that the probiotic is causing problems in itself?

    • cassie says:

      Following. Same question as Heather.

    • Darcy says:

      Heather you did not follow her instructions. You found the probiotic that gives you a herx reaction but instead of backing off and going slow you kept going or quit altogether. You also missed her point that it’s not a food allergy you are experiencing, it’s the death of bad gut bacteria. When that happens the dead stuff starts to rot in the gut and needs to be excreted from the body. It’s not a good feeling and that is why you need to back off and go slow.

      • Joshua Finlay says:

        Poor advice, chances are she was suffering from a histamine reaction. Histamine can icnrease gut permeability so there is no benefit to “sticking it out”

        • joanne richards says:

          but, darcy may be right . i was all gung ho at first because i actually like the kefir. i have backed off a little and i am having die off. since i went all out it is really coming out . i would still try it slowly as i was a skeptic and now i am feeling a lot better.

  2. Tdunc13 says:

    I was giving my mom 1 Align capsule daily, as recommended by her physician for chronic digestive issues (constipation, diarrhea, cramps, bloating), but it wasn’t helping, and now I guess I know why. Thank you !

  3. Alex says:

    would an allergic reaction (hives,flushing, itching) to a probiotic qualify as die-off?
    Also, how do you figure out what strains you’re deficient in? Most probiotics on the market contain multiple strains.

    • Becky Plotner says:

      An allergic reaction and die off are two different things. If you ate a probiotic and you got hives, flushing and itching after taking it then yes, that is die off. No one can tell you what strains to take, only your body can tell you. This can be done by seeking out die off symptoms. This means I’m weak in these strains, I need to build them up slowly.

      • Alex says:

        For me, probiotics relieve some of my itchiness, so I would say – it depends, but I’m not a doctor, so my thoughts are not based on any facts – just keep that in mind.

        • Becky Plotner says:

          When there are certain pathogens in the gut like yeasts, they cause itching. When the pathogens are thriving, probiotics that are the antithesis to the pathogens, will stop the itching by killing the pathogens. When too many pathogens are killed and they can’t get out, they cause the same itching, die off, as they are the same pathogens releasing the same toxic gasses.

  4. Anne-Marie Keightley says:

    I need to have a colonoscopy this year. I am concerned all the good bacteria I have built up will be flushed away and I need to start all over again. I drink both milk and water kefir daily, as well as fermented foods. I have never had any experience of die back. I am thinking I will just continue to do what I was doing before the colonoscopy but wondering if that is enough??

  5. Sandra Laws says:

    I’m confused. I currently have all the symptoms of die off…aching joints, gas, runny nose, body aches, etc. without being on the diet yet, so how will I know if I have die off after eating the saurkraut every day? I want to eliminate these symptoms with the kraut. I’m not sure I can stand anymore gas (it’s embarrassing)…no kidding!

  6. Lorrie Murray says:

    I have severe celiac sprue, autoimmune hepatitis, dermatitisherpetaformis, cirrhosis the of the liver caused by the sprue. My small intestines have no villi please help

  7. Sven says:

    Hello. I am writing to inquire if anyone has experienced a similar reaction / and or can provide advice. I did not properly research Kefir prior to consumption… I mixed about 2 – 3 ounces of Siggi’s Kefir over my granola for 10 consecutive days. My stools soon became loose followed by “Candida-Strings and Mucus”. I stopped drinking Kefir 15 days ago and remain with severe bloating and significant “Candida Strings” in my stool. My chest aches under the ribs. My diet includes lots of peppermint tea in addition to avocados, salmon, broccoli, eggs. At this point I’m tremendously concerned because the candida-strings and candida-globs continue to appear with each bowel movement. Any advice is appreciated (supplements, food, herbs, etc) Thanks!

    • Sven, I would like to see a response to your question as well…

    • April C says:

      Stop the peppermint tea, that can cause your sphincter muscle to remain permanently open causing acid reflux. Don’t eat 3 hours before bed. Eat less at each meal. Your symptoms are sound like acid reflux. I have this, I control it without medication, although I took medication for years.

      • Becky Plotner says:

        April, can you please show us the research that found peppermint tea can cause the sphincter to remain open?

        • According to the University of Maryland Medical Center, peppermint can actually relax the sphincter muscle which closes off the stomach from the esophagus. This can cause stomach acid to pour back into the esophagus and make heartburn or GERD worse.Jan 20, 2015

          • Liz akjam says:

            Peppermint tea is my worst enemy…brings back my acid reflux in 5 minutes and irritates my hietal hernia.

      • joanne richards says:

        i also had to take prescription (nexxium) medicine for years . right now i am recovering from an emergency colostomy. my surgeon and visiting nurse said it was remarkable how quickly i have healed. thank God mine can be it reversed. i credit my recovery to kefir. i no longer take stomach meds, and i am feeling better every day. try the kefir it really helps, my die off is coming out the main orifice women have and it itches terribly. but i am glad because it is a sign the yeast is dieing!

  8. Julie says:

    Is there any sort of test available that can detect different strain levels in your system and determine deficiencies?

    • Becky Plotner says:

      The Organic Acids Test (OAT Test) may tell you what you need. Combined with a comprehensive stool analysis you may get a full picture.

  9. […] Taking probiotics properly is vital to recovery for this reason.” […]

  10. Clark says:

    I have one question about the die-off. It’s always the same symptoms as problematic foods, as well. For instance, if i eat almonds I’ll get pain in my knuckles. However, if i drink bone broth with leek i get the same pains. How does one know if it is die-off or just the results of a damaged gut lining? Thank you for the info in this site-

  11. Devon J. says:

    The only time i took a probiotic I got so sick with a cough/cold for a month… it was miserable. I coughed so hard and so much that my right shoulder (muscles) were messed up for a year (still not 100%). I suspected die-off and stopped the probiotic after I almost finished the bottle (not really knowing what to do all around) and now I’m afraid to try any sort of probiotic… but I really think I need one. Should I start with just a couple drops of a probiotic drink? I can’t live, trying to take care of 3 kids under 5, with die off symptoms. Is it it possible to take one without getting symptoms?? I’m confused… seems like I read articles about how great people feel from their probiotics… but I don’t know how they get past the die-off phase or how long it should last.

    • Douglas Humble says:

      I’m wondering about this too. I’ve been taking Kombucha for about a month now. They come in a 16 oz bottle and there are 2 servings so I have been taking 8 oz per day. I haven’t had any problems but I tried another product and caught a cold (which I assuming is die off – but I’m still confused on this die off stuff.) This cough I have had has lingered on for weeks now and is driving me nuts. Certainly it isn’t because of the Kombucha but after reading these posts I’m uncertain.

  12. senthuran says:

    hi i have been experiencing histamine issue since from last year when i found out that i have gut dybosis. my natropath has recommended me the prescript assist and i have been taking it for more than a month now. currently I’m on half a dosage, when i increase it to 3/4 i get headache. is this die-off symptom?, also i get breakout on my fore head and on my face (closer to my nose and my cheeks), my bloating and cramps are improving slightly, but i do get cramps and bloating but it is steady progress(two step forward one step back).

    • Becky Plotner says:

      These symptoms are die off, yes. It’s important to be sure during this time that you are not feeding the pathogens that are the problem.

  13. Orlando Vega says:

    Hello, my 2 yr old son was diagnosed with mild autism, had chronic ear infections when younger( a lot of antibiotics), we want to start a GAPS diet, and also some probiotics. I have read CustomProbiotics D-Lactate free are good, if so, should I start him off with small doses at first???

    • Becky Plotner says:

      Yes, this is a very good probiotic.

      • Andy says:

        Hi, I have a serious histamine intolerance.. that built up to me ending up in the emergency room two days in a row getting anaphylactic shock. I currently am taking a histamine free probiotic to increase the strains which keep histamine levels at bay. How do you recommend I take the dosage?

        • Andy says:

          My body is very sensitive.. what do you recommend for me to fix this gut problem, as it makes me depressed, anxious, and extremely nervous. I’m currently getting adjusted 2-3 times a week and it’s helping as well .. your comments are greatly appreciated

          • Andy says:

            Also confused and extreme brain fog

          • Kit Kat says:

            GAPS diet.

            Be prepared for a long haul though. It gets worse before it gets better, and you really need to prepare for the intro diet.

            I highly recommend the Heal Your Gut Cookbook.

            I’m currently mid intro diet.

  14. Donna Welborn says:

    I switched from regular probiotics to soil-based (tried one brand for 3-4 months and another brand for 2) but I have been having more gas and bowel pains (not severe at all) in different areas and am wondering if I have an overgrowth of something. I had no symptoms of leaky gut before starting these but am wondering if I am messed up now. How would I determine if I have an overgrowth??

  15. Elaine says:

    Natren is an amazing probiotic company ONLY making probiotics. Everything is cold pack delivered.

  16. colashock says:

    I’ve been experiencing the “Worst Die-Off” all symptoms listed on article; at first I thought I couldn’t figure it out than I read Organic Lifestyle Magazine mentioned Herx finally I clued in. I continued eating Fermented Foods/Raw Green Salad/Probiotics/Lactose Free Yogurt(Lactose Intolerant). Ever since I stopped Caprylic Acid, Cytic acne breaking out (inconsistent with my Thyroid Pills from Priority One & Multi-Vitamins). during Parasite Infection, definitely worked BUT my ultimate go-to that I found healing my Gut>> After reading Probiotics Post there is a certain strain my gut/tummy needs build tolerance. I know I don’t consume any Good Fats in my diet. I eat Avocado, I take Coconut Oil, Hemp Seed Oil, use Olive Oil for cooking (Organic), Chia Seeds with Steel Oats (oatmeal), Bananas,. All the foods I hate I forced myself to eat because it’s beneficial, good for digestive tract.
    My ND said I have problems digesting Meat (chicken, turkey, red meat; and Fish) which I am allowed 1 Organic Meat item per month. No Soy. Despite GF Bread, Pasta, or Crackers, not allowed to consume any (Ingredients). Can only drink Green smoothies/Juice, Lemon in water, Water, Herbal Tea, Cranberry Lemonade to flush out. No coffee, sugar, dairy (Lact-Intol), Alcohol (I quit 2yrs ago), Refined foods. I did cheat being Chinese (been on this diet for over 1 yr), when I cheat Symptons flare up The worst thing is “I get stressed very easily & having problems relaxing”.
    Last summer I did a few sessions of Ozone O3 Infrared Sauna with Colon Hyrdotherapy (kinda grossed out & scared me what came out) O3 Sauna made me feel so much better.
    Any advice on my Probiotics if they are good or not? Living in Canada we are restricted to many Brands/Products as Customs Canada Red Flag many US Brands “Gaia Herbs, etc from entering Canada” Cdn Health Agency doesn’t believe in Herbal Products stating that it harms our Health, and only Western medication/Antibiotics will heal!!

    • Becky Plotner says:

      I have removed the probiotics you listed since they all contain ingredients which feed the pathogens we are trying to kill, not beneficial for repair and rebuilding.
      I liked all the beneficial therapeutic ones in this post, at the bottom. The GAPS protocol is the only thing I’ve ever seen to rebuild the Intestinal Permeability, the root cause of the symptoms.

      • Raghavi says:

        Dear Becky, please suggest how to cure atopic dermatitis and food allergy of my one year old son , will GAPS work for him, he is overeating so how can I go for GAPS with only meats, how to reverse his food allergy , is that fermented foods alone is enough or I have to give probiotic capsules to him , he is allergy to many grains except Rice

        Thanks in advance

  17. Nissa says:

    lousy article and the subject matter is not well researched

  18. […] Really interesting article about probiotics and reintroduction into the diet. Read in full here […]

  19. Nikki says:

    I have started taking ortho molecular 100 billion probiotics. My question is should i start off that high? I tend to have really bad depression, anxiety, with die off symptoms. Do i continue to take them even if i notice die off? or should i back off? I do have leaky gut. Im just confused by the article.

    • Becky Plotner says:

      “The goal is to look for die off and progress by building those weak strains. Pushing probiotics so that you are constantly in a die off state, is not the goal as it causes too much inflammation.”

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