SIBO/SIYO/Heartburn: Detailed Information and How to Find Relief (2020)

SIBO/SIYO/Heartburn: Detailed Information and How to Find Relief (2020)

FYG Livestream on SIBO, What Is It and How to Find Relief!

Conquering SIBO (small intestine bacterial overgrowth)/SIYO (small intestine yeast overgrowth)

What is SIBO/SIYO?

SIBO is a medical condition where you have microbial overgrowth within the microbiome of the small intestine. SIBO has many causes, including poor diet, food poisoning, abnormal intestinal motility, improper bile production and release, chronic stress, hypothyroidism, and long-term use of acid-reducing medications. Long-term use of acid-reducing medications causes opportunistic bacteria that would usually be reduced or eliminated by a lower stomach pH to survive and flourish when pushed through the stomach during normal digestion processes into the small intestine. A higher stomach pH causes ingested proteins to become partially undigested from a lack of stomach acid to break them down properly. Allergic reactions may develop from the undigested proteins. Undigested proteins also cause excessive flatulence and bloating from increased protein fermentation by microorganisms. The standard American diet which contains elevated amounts of carbohydrates and allows opportunistic microorganisms to overgrow within the small intestine from an abundance of food and produce excess gas from increased fermentation.1 2

Many bacteria also produce protective biofilms (one of the most common examples of a biofilm is the “film” on your teeth that appears when you do not brush your teeth after a while), which makes eradication from antibiotics very difficult. Biofilm protects opportunistic bacteria from antibiotic treatment, bactericides, and probiotics.3 Bacteria within biofilm stick together and become embedded within a slimy extracellular matrix composed of extracellular polymeric substances (EPS). Bacteria within the biofilm produce the EPS components, typically a polymeric assortment of extracellular polysaccharides, proteins, lipids, and deoxyribonucleic acids. Sometimes to reduce opportunistic bacterial colonies, you also have to disrupt the biofilm that protects the bacteria. Biofilm disruption can occur by either breaking down the biofilm itself using systemic enzymes or by chelating the iron out of the biofilm to dissolve it. To chelate the iron, you can use either calcium disodium EDTA,4 lactoferrin,5 or NAC.6

You have to be careful when using antibiofilm agents not to reduce probiotic bacterial biofilm and communities if they are not the cause of your dysbiosis. Adding an antibiofilm protocol in addition to your SIBO protocol might be best if a first-line protocol fails. If you know the particular bacteria that you believe is causing your dysbiosis, produce biofilm to see if it helps relieve your dysbiosis. Finally, I would recommend using a biofilm protocol at the lowest therapeutic dose (the dose that you see symptom relief) and the shortest amount of time possible. Contact me for coaching to help individually tailor your SIBO protocol to fit your needs.

Symptoms of SIBO

Symptoms of SIBO dysbiosis (not everyone with SIBO will have all of these symptoms) include indigestion, reflux, flatulence (odor may smell like rotten eggs if it is hydrogen sulfide, may have no odor if is methane), belching (occurs more so with upper gut dysbiosis than SIBO), abdominal pain, excessive bloating anatomically around the belly button, Roemheld syndrome, weight loss, nutrient deficiencies, fat malabsorption (yellow or greasy stool), improper production and release of bile (pale stool), nutrient deficiencies, histamine intolerance, food allergies/intolerances, lactose intolerance, fructose intolerance, salicylate intolerance, poor fat digestion, D-lactate detoxification issues, rosacea, constipation, and diarrhea. Most people with IBS are suffering from SIBO, and SIBO is their true cause of their digestive problems.7 There is also a strong correlation between rosacea and SIBO. In one study, the majority of patients with rosacea were in remission or cured for at least nine months after taking Rifaximin. Rifaximin at the time was being used to treat their SIBO.8

How to Diagnose SIBO

My Hydrogen/Methane Breath Test Were Negative, Can I Still Have SIBO?

Disruption of the Migrating Motor Complex (MMC) and SIBO

Your digestive system eliminates waste through a process known as the migrating motor complex. The cycle of the peristalsis within the gastrointestinal system occurs every two hours. The MMC cycle includes four phases:

  1. The first phase is a period of intestinal smooth muscle calmness lasting forty-five to sixty minutes, which only rare action potentials and contractions occur.
  2. The second phase lasts roughly thirty minutes in which peristaltic contractions occur and progressively increase in frequency. Peristalsis originates in the stomach and propagates throughout the small intestine.
  3. The third phase lasts five to fifteen minutes and consists of rapid, evenly spaced peristaltic contractions. In contrast to the digestive period, the pylorus remains open during these peristaltic contractions, allowing many indigestible materials to pass into the small intestine.
  4. The fourth and final phase is a short transition between the strong muscular contractions that occur in the third phase and the inactivity that occurs in the first phase.

During the migrating motor complex, increased gastric, biliary, and pancreatic secretion occurs to help further digestion and decrease bacterial buildup in the proximal segments of the digestive tract. It is believed that the enteric hormone motilin controls the MMC. Ingestion of food overrides the MMC. Therefore, fasting has to occur regularly to help complete the process. The typical “growling” sounds you hear when you are hungry might be the MMC doing its job, stomach emptying, and the increase of small intestinal motility.

As much as seventy percent of people afflicted with SIBO experience a disruption of MMC rhythm. Excessive methane/hydrogen gasses produced by overgrowth of bacteria in the gut has been linked to decreased MMC function. When the second and third phase of the MMC is reduced, bacteria remain in the small intestine instead of being pushed back into the large intestine. Bacteria are then able to adhere and propagate in the small intestine, which increases inflammation and intestinal permeability. The inhibition of MMC homeostasis drives the vicious SIBO cycle.

Reduction of stomach acid by using acid-reducing medications or H. pylori infection can contribute to poor MMC function. Your body monitors stomach pH to time proper stomach emptying to ensure the digestion of food before it is released into the duodenum. If your stomach pH is elevated from stomach acid reduction, stomach emptying slows down, interrupting proper MMC function and slowing digestion. Lack of exercise, grazing on food regularly, and chronic constipation can contribute to poor MMC homeostasis. Being over-stressed and anxious can also decrease your MMC function. Grounding can help relieve stress and improve your MMC. Finally, inhibited thyroid function and adrenal fatigue can lower MMC function.

Fasting for at least four hours after meals during SIBO protocols might be beneficial in regulating the MMC. The increase in fasting time gives your body time to complete the MMC process. Also, maintaining proper circadian rhythm is important as well. Your circadian rhythm is a natural, internal process that regulates many bodily processes and repeats roughly every twenty-four hours. Try your best only to eat three meals daily, eat one hour upon waking, and eat your last meal before six or seven in the evening to help maintain proper circadian rhythm. Frequent exercise also helps to regulate your MMC properly. Finally, your MMC operates while you are sleeping, which is why proper sleep hygiene may be more helpful than fasting because of the longer total fasting time that generally occurs during sleep.

Are Opportunistic Bacteria One of The Main Causes of Leaky Gut?

Opportunistic bacterial colonies within the small intestine can wreak havoc on your health and lead your intestinal health into a vicious cycle of destruction. The more opportunistic bacterial colonies within your small intestine, the more food they will consume, and the more gas, byproducts, and toxins they produce. Inflammation occurs within the small intestine lining, leading to increased gut permeability and a reduction in the absorption of iron, folate, and vitamin B12. The opportunistic bacteria also consume more nutrients that are now unabsorbed by the gut, leading to increased colonies of opportunistic bacteria and enhanced gas production. You might start having abdominal bloating, diarrhea, pain, and excessive flatulence from the blooming of opportunistic bacteria in the small intestine.9

TThe opportunistic bacteria then begin to decrease fat absorption within the intestines that lead to stool health issues (yellow or fatty stools). The decrease in fat absorption leads to deficiencies in the fat-soluble vitamins A and D. The intestinal lining further degrades and eventually cannot digest large food particles correctly. These larger food particles start to cause food allergies and sensitivities (gluten first, then usually followed by fructose malabsorption and lactose digestion issues from degredation of the intestinal lining.)10

The opportunistic bacteria begin to enter the bloodstream from the loss of integrity in the intestinal wall. Opportunistic bacteria within the bloodstream activate immune responses that trigger fatigue, inflammation, pain, heart disease, and elevated liver enzymes. For example, your immune system reacts to lipopolysaccharides (endotoxins) within the cell wall of Gram-negative bacteria, which causes further inflammation and issues when they enter the bloodstream, which may lead to sepsis if severe enough. The bacteria also excrete biological agents (ammonia and acids, for example) that, when leaked into the bloodstream, cause neurological and cognitive deficits, including brain fog and poor memory. The vicious cycle continues as the body’s immune system tries to eliminate the opportunistic bacteria, which, when reduced, poison the body with acids and toxins. If your microbiome is left untreated, different opportunistic bacteria, then continue to flourish. The vicious cycle then repeats itself, and you become chronically ill.11

The Differences Between Hydrogen, Hydrogen Sulfide, and Methane Dominant SIBO

The differences between hydrogen, hydrogen sulfide, and methane dominant SIBO.

Does SIYO (Small Intestinal Yeast Overgrowth) Exist?

In some people, Candida overgrowth can manifest itself in the small intestine and cause similar symptoms as if you are suffering from SIBO. SIYO is a rarer condition, but systemic yeast dysbiosis of the intestines does happen. The same vicious cycle that exists with SIBO occurs in people with SIYO. The yeast in SIYO will rob nutrients from the body, reduce vitamin absorption and fat digestion (by eliminating probiotic bacteria), cause food allergies and sensitivities, worsen histamine intolerance (Th2 dominance), joint pain, cognitive issues, cause systemic yeast dysbiosis or susceptibility (examples include jock itch, vaginal yeast infection, thrush, nail fungus, and Tinea versicolor), and excrete toxic byproducts (mycotoxins and aldehydes).12

Other yeasts besides Candida can cause SIYO; an example of this would be the probiotic yeast Saccharomyces boulardii. Boulardii is an excellent probiotic yeast and is very useful in helping relieve certain medical conditions. Caution should be used when supplementing if someone has a severely compromised immune system.13

The two tests used to diagnose SIYO are an alcohol challenge test and gut microbiome testing (Genova GI Effects or Diagnostic Solutions GI-MAP). During the alcohol challenge test, you will ingest a lot of sugar that feeds the yeast, and then a blood measurement is taken to determine how much alcohol is produced from the fermentation. A stool sample test will test the stool for any excessive yeast colonies and antibodies from a provided sample. If you read about a yeast dysbiosis “spit” test online, it is unreliable and should not be used.14

If you are suffering from SIYO, you should try any of my Candida protocols to eliminate the opportunistic yeast.

Can Someone Suffer from both SIYO and SIBO?

Anyone can suffer from both conditions, and if you treat for either SIBO or SIYO and you still feel ill after treatment with your healthcare professional, you should be tested for the other condition that was left untreated.15

Restore Proper MMC Function Protocols


  • Wait at least four hours in between meals before eating another meal. No snacking!
  • Exercise more and walk as much as possible.
  • Use a squatty potty when you defecate.
  • Supplement with triphala – one capsule, twice daily with food.
  • Magnesium malate – supplement two hundred milligrams per fifty pounds of body weight (if supplementing do not use any other magnesium supplements that are recommended on this blog).
  • Proper defecation posture is very important for motility
  • Ileocecal valve massage
  • Biofeedback therapy
  • SIBO-D:

    If you have elevated stomach pH:

    General Advice to improve your MMC not covered above:

  • Proper sunlight exposure, maintaining a proper circadian rhythm, relieving excessive stress, proper vagus nerve activation, and proper sleep hygiene has been shown to help positively improve MMC function.
  • Aldehydes have been shown to interfere with MMC (increased aldehyde bodly concentration occurs from yeast dysbiosis, mold exposure, or frequent alcohol consumption) function, and molybdenum supplementation can help your body detoxify aldehydes.
  • SIYO hinders coenzyme A production within the gut, which interferes with proper MMC function. It might be a good idea to supplement with coenzyme A if you are suffering from SIYO.
  • Mild SIBO-C (Archaeal) Protocol

    For two to four weeks:

    Choose one strong antimicrobial agent:

  • Thorne Research berberine – take five hundred milligrams, two capsules daily. Use with caution if you have ulcers, gastritis, or hypoglycemia.
  • Allicin-C – follow supplement bottle recommendations.
  • Neem – take two capsules two times daily with meals.
  • Atrantil – follow supplement bottle recommendations.
  • Other protocol advice:

  • Extra virgin coconut oil – consume up to two tablespoons daily, divided between meals. Do not use if you are prone to or are suffering from histamine intolerance or allergic to coconut.
  • Reduce consumption of polyols and go on a gluten-free diet. For symptom relief, consider following a low-FODMAP diet for two weeks.
  • Berberine and allicin have anti-archaeal properties.16 17 18

    Coconut oil is used to reduce yeast overgrowth within the digestive tract and inhibit archaea overgrowth.19

    Severe SIBO-C (Archaeal) Protocol

    For four weeks:

    Choose two potent antimicrobial agents:

  • Thorne Research berberine – take five milligrams, two capsules daily. Use with caution if you have ulcers, gastritis, or hypoglycemia.
  • Allicin-C – follow supplement bottle recommendations.
  • Neem – take two capsules two times daily with meals.
  • Atrantil – follow supplement bottle recommendations.
  • Zane Hellas oil of Ooegano – follow supplement recommendations. Oil of oregano is a broad spectrum, systemic antimicrobial agent, do not use oil of oregano in a first-line protocol.
  • Anti-BioFilm Protocol:

  • PREFERRED: Symbiotics lactoferrin – follow supplement bottle recommendations (can increase up to two grams daily if needed).

  • Calcium disodium EDTA: MRM Cardio Chelate – follow general supplement recommendations.
  • Fulvic acid: Food Grade fulvic acid – follow general supplement recommendations.
  • Guaifenesin: Guai-aid – take one capsule every four to eight hours. Do not exceed four capsules daily. Guaifenesin is a systemic biofilm chelator, I do not recommend it as a first-line anti-biofilm agent in a protocol.
  • NAC: Jarrow Formulas NAC Sustain – one tablet twice daily. NAC is a systemic biofilm chelator; I do not recommend it as a first-line anti-biofilm agent in a protocol. Do not supplement more than twelve hundred milligrams daily. Doses above this recommendation may make the NAC you take become a pro-oxidant.
  • Systemic enzymes: Interphase Plus, PRX Enzyme Formula, Neprinol AMD – follow general supplement recommendations.
  • Other protocol advice:

  • Extra virgin coconut oil – consume up to two tablespoons daily, divided between meals. Do not use if you are prone to or are suffering from histamine intolerance or allergic to coconut.
  • Reduce consumption of polyols and go on a gluten-free diet. For symptom relief, consider following a low-FODMAP diet for two weeks.
  • 5-HTP supplement – start with fifty milligrams nightly and increase by fifty milligrams up to a max of three hundred milligrams nightly depending how well the supplement is improving your motility by increasing serotonin availability within the digestive tract. Do not use it if you are on any medication that modulates serotonin levels (SSRI, for example) or if you suffer from any mental health issues. Discontinue if you have any side effects and do not take longer than a few weeks.
  • Calcium disodium EDTA chelates iron out of the biofilm to break it up and pull it away from archaea.20

    The NAC or lactoferrin will do the same thing as the EDTA by chelating the iron out of the biofilm, breaking it apart.

    Oil of oregano, silver, and neem reduces archaeal overgrowth.21 22 23

    Mild SIBO-D (Hydrogen Bacteria) Protocol

    For two to four weeks:


  • PREFERRED: Nature’s Way enteric coated peppermint oil – thirty to sixty minutes before meals, twice daily.

    Choose one strong antimicrobial agent:

  • Thorne Research berberine – take five hundred milligrams, two capsules daily. Use with caution if you have ulcers, gastritis, or hypoglycemia.
  • Ceylon cinnamon oil – take one drop in one tsp. of extra virgin coconut oil or extra virgin olive oil, twice daily. Use with caution if you have hypoglycemia.
  • Other protocol advice:

  • Extra virgin coconut oil – consume up to two tablespoons daily, divided between meals. Do not use if you are prone to or are suffering from histamine intolerance or allergic to coconut.
  • Reduce consumption of polyols and go on a gluten-free diet. For symptom relief consider following a low-FODMAP diet for two weeks.
  • Coconut oil is used to reduce or inhibit yeast dysbiosis within your digestive tract.

    Severe SIBO-D (Hydrogen Bacteria) Protocol

  • Rifaximin – an antibiotic that is mainly active in the small intestine and is poorly absorbed.

  • Tetracycline/Doxycycline – broad-spectrum antibiotic, follow moderate Candida protocol while on antibiotic to reduce the chance of developing Candida overgrowth.
  • Cephalosporin – second generation or newer.
  • Amoxicillin with Clavulanic Acid
  • Choose one strong antimicrobial agent:

  • Thorne Research berberine – take five hundred milligrams, two capsules daily. Use with caution if you have ulcers, gastritis, or hypoglycemia.
  • Ceylon cinnamon oil – take one drop in one tsp. of extra virgin coconut oil or extra virgin olive oil, twice daily. Use with caution if you have hypoglycemia.
  • Anti-BioFilm Protocol:

  • PREFERRED: Symbiotics lactoferrin – follow supplement bottle recommendations (can increase up to two grams daily if needed).

  • Calcium disodium EDTA: MRM Cardio Chelate – follow general supplement recommendations.
  • Fulvic acid: Food grade fulvic acid – follow general supplement recommendations.
  • Guaifenesin: Guai-aid – take one capsule every four to eight hours. Do not exceed four capsules daily. Guaifenesin is a systemic biofilm chelator; I do not recommend it as a first-line anti-biofilm agent in a protocol.
  • NAC: Jarrow Formulas NAC Sustain – one tablet twice daily. NAC is a systemic biofilm chelator; I do not recommend it as a first-line anti-biofilm agent in a protocol. Do not supplement more than twelve hundred milligrams daily. Doses above this recommendation may make the NAC you take become a pro-oxidant.
  • Systemic enzymes: Interphase Plus, PRX Enzyme Formula, Neprinol AMD – follow general supplement recommendations.
  • Other protocol advice:

  • Extra virgin coconut oil – consume up to two tablespoons daily, divided between meals. Do not use if you are prone to or are suffering from histamine intolerance or allergic to coconut.
  • Reduce consumption of polyols and go on a gluten-free diet. For symptom relief, consider following a low-FODMAP diet for two weeks.
  • Calcium disodium EDTA chelates iron out of the biofilm to break it apart and remove the iron from pathogenic bacteria.

    The NAC or lactoferrin will do the same thing as the EDTA by chelating the iron out of the biofilm.

    Cinnamon oil and berberine are great in reducing hydrogen-producing bacterial overgrowth.24 25

    Supplements to Help Relieve a Bacterial Herx Reaction (You might have to take more than one supplement to reduce herx symptomatology):

    Jarrow milk thistle – follow general supplementation recommendation on bottle.

    Sun Chlorella – follow box instructions. I recommend three thousand milligrams daily. Do not use if you are suffering from Th1 dominance.

    Ester-C – take one thousand to two thousand milligrams of vitamin C with every meal. Reduce dosage if it causes or worsens diarrhea.

    Upgraded Coconut Charcoal – follow general supplementation recommendations on the bottle; do not take more than twelve capsules daily, which is around four thousand milligrams.

    Pinella – follow the supplement bottle recommendations. Use Pinella if you are suffering from brain fog. There is alcohol in the tincture, so use with caution if you are sensitive.

    Take a daily Epsom salt bath if you can tolerate sulfur.

    Remain properly hydrated.

    How to Help Maintain a Healthy Probiotic Microbiome While Using the Protocols Above

    Maintenance Protocol

    L-glutamine – take four thousand milligrams, daily with meals, in divided doses (use with caution if you have a sensitivity to glutamic acid ingestion, GABA deficiency, ammonia detoxification issues, or are suffering from severe leaky gut and brain).26

    Life Extension Bio Curcumin – follow general supplementation recommendation on bottle.27

    N-acetylglucosamine (do not use if allergic to shellfish) – follow general supplementation recommendation on bottle.28

    Seacure white fish protein supplement (do not use it if allergic to fish) – follow general supplementation recommendations on the bottle (check the expiration date on your label, a few people have received expired supplements when ordering from Amazon).

    Magnesium glycinate – take four to six hundred milligrams before bed (discontinue if it causes diarrhea).

    Probiotic recommendations – Choose One (only add if you are not suffering from constipation):

    Natren Healthy Trinity – take one capsule daily (do not use with histamine or D-lactate sensitivity).

    GutPro capsules – take three capsules daily.

    D-lactate free Custom Probiotic – use one baby scoop and mix it with filtered water.

    Prebiotic recommendations (I recommend trying two different prebiotics at a time and see how you can tolerate them, start with doses that are half of the recommendations):

    Acacia fiber – I recommend the use of Heather’s Tummy Fiber.




    Partially hydrolyzed guar gum – I recommend the use of SunFiber.

    L-glutamine is the most abundant amino acid and helps rebuild both the stomach lining and the gut.

    The probiotic/prebiotic protocol will hopefully enhance probiotic bacteria colonies in your gut.

    The curcumin is used to increase immune cells in the gut and heal inflammation.

    N-acetylglucosamine is made by the body to increase mucus production in the stomach and intestines to help make the protective lining.

    2. Dr. Brownstein, David, Drugs That Don’t Work and Natural Therapies that Do!, Medical Alternative Press, 2007
    1. What if you test for SIBO with very high Hydrogen numbers (136+ ppm rise> baseline) and barely high Methane (14 ppm rise> baseline) with NO diarrhea, but have constipation or even normal bowel habits (I go once a day usually if diet is consistent).

      Where would you that place someone in terms of treatment? Have you also seen the below research showing that high Hydrogen numbers could also be indicative of fast small bowel transit,and not SIBO? thoughts?

    2. Thank you for always sharing the best along with our team!

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    3. Nice read! I so learned a lot from this article. Thank you so much for posting!

    4. I see you recommended a product called Neprinol AMD. Arthur Andrews Medical sells a Neprinol AFD, is this a similar thing? Or Syntol AMD?

    5. Glutamine RAISES AMMONIA levels which can already be high in SIBO or SIYO. N-Acetylglucosamine helps increase biofilms.

      Not sure if you’re still recommending either?

    6. F*ckin?awesome things here. I very glad to see your article. Thanks a lot and i am looking forward to contact you. Will you please drop me a mail?

    7. Thanks so much for these protocols! So how long do you have to continue with the supplements from the “Restore Proper MMC Function Protocol”? Are these supplements for indefinitely or just for a time? How can you tell if your MMC is functioning properly? Thanks!

    8. I recently started a web site, the information you provide on this site has helped me tremendously. Thank you for all of your time & work.

    9. Glutamine feeds cancer, I hope you will research this, it appears to be one of the things people should NOT be taking when they have these kinds of cancer associated intestinal problems. Like so many things doctors recommend, doing the exact opposite is what is healthy, not what they are prescribing.

      • There are many different types of cancer and many different types of cancer cells. Some use glutamine as a main source of fuel, you are correct, some on the other hand use glucose. Because of this some do well on a ketogenic diet (high glutamine, very low glucose) some do well on Gerson therapy (high glucose, low glutamine).

    10. What are your thoughts on Candibactin AR and BR for treating hydrogen dominant SIBO? Thank you!

    11. In your book “fix your gut”, You say: Take probiotics only if you know that your mmc is working properly.

      How can I know if my MMC is working properly?

      Are loose Bowel Movements an indicator of functionning mmc?

    12. Tested postive for ASCA IGG and IGA. No other testing shows indications of an IBD. Should I avoid yeast products and Saccharomyces boulardii? Is this all related to leaky gut? If I avoid yeast products will the antibodies return to a normal level? Thanks!

    13. Hi John, Thanks for the informative articles.

      I have had SIBO-C for 3 decades, and only recently diagnosed.
      My 10 year old daughter was also diagnosed. Obviously, I’d like to get her the help NOW that I wish I had back then. I suspect a genetic MMC deficiency – she also has sensory processing issues (extra sensitive to tactile stimulation but barely notices hunger or bathroom needs).

      Have you read the research about interferential current therapy for children with slow transit constipation? I am considering trying this for her at home, though it’s difficult to get precise information on how to do it. I am also considering a fecal transplant for both of us. I do not believe it is a cure-all, but it seems that it might help if we simultaneously address the infection, MMC, and leaky gut.

      Do you have any thoughts on either of these two treatments?

    14. Thank you for your article.
      I am sensitive to most of herbal antibiotics. Probably because I’ve used them far too many times. The worst are oil of Oregano and Berberine. Oil of oregano produces irritation of my stomach and LES and Berberine- pain in my gallbladder area, nausea, anxiety, heart palps. I am also sensitive to grapefruit seed extract, Pau D’Arco, Gymnema Sylvestre, Cat’s claw, Uva Ursi, Neem, Allicin (mainly stomach irritation, heart palps and/or severe oxalate reactions). Allicin I think is enough to cause SIBO for me instead of curing it because it inflames my stomach and small intestine so much. The only herbal I am not sensitive to is Olive leaf extract but on its own, it doesn’t work.
      Curcumin is also a no-no for me. It produces severe tachycardia. Vit C in amounts over 1 g just goes straight to oxalate production for me.
      Can you recommend anything else? Thanks.

      • It would appear to me that you are dealing with very strong herx reactions from the herbal antibiotics. I would recommend looking into detoxing methods. IR sauna, castor oil packs, Epsom salt baths, etc.

    15. This is totally embarrassing, but I have a severe case of Hydrogen Sulfide SIBO. Question, have any of you guys experienced symptoms of H2S being expelled through the lungs causing noticeable reactions from others?? It’s a reality that I face on a daily basis.

      • Hi James, This is what I did to fix my SIBO after years and years of suffering that impacted on every part of my life for over 30 years. I was unable to work, socialise or function as a normal person due to the chronic SIBO. This is what worked for me and I have a new life. I used colloidal silver over 3-5 days to wipe out all the bacteria- this stuff works I have used in many, many times to get rid of bacteria. But the game changer was to then add 2 x grapeseed extract supplements(not grapefruit)after my 3 meals per day. I have had little- no issues since doing this, my breath is normal, my stools are normal, my digestion is normal, no more heartburn, or gas. I feel calmer and can socialise without anxiety. I do not take probiotics at all and I do not eat a restricted diet. I hope this helps as it took me years of trial and error to work out what works for me.

        • You’re right Mel. Silver as you say, wipes “out ALL bacteria”. Both the bad AND the good. It’s critically important to reseed with high amounts of beneficial bacteria after using silver.

    16. Hi John! Sorry for my english – i’m European currently living in US. I have a symptoms of IBS-D, probably SIBO but i cannot get breath tested couse here in NY it’s super expensive. First i used 7 days x 3 daily 500 mg Metronidazole, from the first pill i had relief but after 2 weeks after taking all pills it got back to my problems. So now i’m starting with Thorne Berberine-500 2x daily with food and i ordered interface plus. Should i take one or two pills 20 minutes before meal? It’s ok to take multi-vitamins during this? Do you have any advice about specific food diet? And how long should i take all this pill? Thanks for your time and answers!


      • Also should i be on low FODMAP diet while i’m taking Berberine?

      • For the Interfase Plus you want to take it on an empty stomach. Most people take two and up to six in divided doses throughout the day. Now, on the multi vitamin question it is too broad of a question, do you know your methylation profile? How long to stay on the protocol is also to individual of an answer. For diet you can try my modification of the FODMAP diet and see if it brings you some digestive relief.

    17. Hi John,

      I’ve ready most of your book (pertinent to my situation), and am quite impressed with your wealth of knowledge. I am in a quandary and would like your perspective. My breath test came out negative, while my stool test came back positive with methanobrevobactor and some e.coli. So I will retest the breath test soon. However, my question is this: the food I eat, LOW-FODMAP LOW-CARB, still causes me to have pain throughout my body in the form of muscle/tendon spasm. It is like fibro, but throughout the body. When I do anti-microbials, it helps tremendously, and as soon as I stop it comes back. What the heck do you think is causing such symptoms?

      One more question, have you seen successful cases of SIBO/SIFO/SIYO eradication?

      Many thanks for all that you’re doing.

      • Yes, but for many people it takes awhile. Gut issues are chronic health conditions which can take weeks, months, or years to resolve depending on the person. You need to correct vitamin D if it is low, getting sunlight is important. Low-carb FODMAP would starve the probiotic microbiome, it may reduce digestive symptoms, but for most it causes a longer recovery. Without your immune system working properly, motility recovering, and your microbiome restoring, SIBO cannot be conquered.

    18. What do those with slower bowels/constipation issues do about curcumin? curcumin significantly inhibits gastric emptying as well as both large and small intestinal transit.

    19. Hi John,

      Currently reading your great E-book. Really love learning about all the other digestive ailments that exist!! My issue is severe SIBO. Did a one month course of DYSBIOCIDE + FC CIDAL with 20mg glutamine and 450Bil+ of VSL3 per day. Saw incredible improvement afterwards – for about 2 days I was myself again. I’m only 23 and feel I’ve contracted this SIBO from 2-3 of years of Drinking a gallon of RAW milk everyday. Even had a stint of eating raw beef. Ever since I’ve had serious bloating, indigestion, anxiety, diahrea etc. In the process of testing for IBS-D (from IBSChek) – then hopefully starting XIFAXAN. So according to your book – your reccomend whilst taking XIFAXAN – to also take Lactoferrin + InterFase plus and the other supplements? I feel it’s a lot, just wanted to confirm. Thank you sir!!!

    20. I have been suffering with gastritis for quite some time. And my doctor has recommended otc ppi when needed, also avoid irritants such as spicy food, dairy, alcohol. I cannot take the ppi, it just makes me feel awful. Also find it very difficult to be out and about in social situations that involve eating/drinking as I get very nervous, uncomfortable, bloating, pain, nauseous. Are there any supplements I should be taking to heal gastritis as my doctor seems to be of no help, I have cut back drastically on the drinking. Thanks, any info would be appreciated.

    21. Hi John,
      This article is extremely informative and structured so well. I am beyond impressed with your knowledge and ability to translate to those of us in need of answers. I got results from a comprehensive stool sample that shows I have close to no good bacteria and an over abundance of Proteus Mirabilis (sp?). I know that it’s common for this particular bacteria to be present in the gut, but I’m not certain if an over abundance of it would be considered a “bad” bacteria? Also I’m Deficient in B12 and boarderline deficient in Folate. Food intolerances/sensitivities to many foods that cause gastrointestinal distress (gas/bloating) Would this particular scenario call for your protocol? Thanks for your thoughtsI will be purchasing you’re book and encouraging others to do the same. So glad for people like you on this planet!!!

      • Proteus Mirabilis lives in the stomach / duodenum, and acts similar to H. pylori. Some strains produce histamine, some hydrogen sulfide. It makes since you are low in B12 it interferes with stomach acid and the intrinsic factor.

    22. This protocol looks great. The question I’ve had recently from reading different approaches is whether or not we should be restricting fodmaps during treatment. Chris Kresser says we should be eating them while taking antimicrobials, because we need to feed them to kill them, and reducing their food just makes them go into hibernation. What are your thoughts on this?

    23. Hi John,

      So glad i found your website. Very clear and good explanation of the SIBO/SIYO and leaky gut protocol. My test came back positive for candida krusei (probably due to my diabetes type 1 and compromised immune system). I also have SIBO and a leaky gut. I was wondering whether i could treat all three simultaneously? Or do you need to address the SIBO/SIYO problem first before starting the leaky gut protocol?

      Thank you :)

      • Candida krusei is a strong strain of Candida. I would tackle the SIBO/SIYO first and address leaky gut using supplements later. Drinking clean water and getting vitamin D from the sun if possible will help leaky gut.

    24. Hi John,
      I’m new here, but have read a lot and am trying to organize my thoughts. I’ve had diarrhea now turned loose stools for a year now with lots of built-up gas (right away in the morning sometimes waking me up), bloating and most recently 10 lbs weight gain on my normally 135ish lbs frame. Even after three kids, I’ve always weighed about the same. Everything….colonoscopy, hormone testing, blood work, etc….has come back fine. They’re treating me for SIBO but I haven’t been officially diagnosed. Mailed my second stool sample kit in this week just to have that double-checked. They want me to take Prescript Assist, which I know you advise against. I see you recommend Nature’s Way Enteric Coated Peppermint Oil or Oil of Oregano, but I just recently found out I’m pregnant so that’s complicating things a bit. I’m following the low FODMAP diet (started three days ago.) I want to heal my gut, but I don’t want to make things worse for myself long term. And it’s harder to take it on full force given I’m now pregnant (oops). I see Colloidal Silver is safe for pregnant women. Any further suggestions? I’m doing light exercise and stress reduction as well. I really appreciate your insight. Thank you for helping so many.

      • I cannot sadly recommend any supplement since you are pregnant except for lactoferrin, and even then ask your doctor. Do not take an iron supplement if possible while you are having gut issues it will feed the overgrowth. Lactoferrin and magnesium supplementation may help increase iron if you are anemic.

    25. HI Jason,

      I just bought Fix your Gut and your protocol is very clearly outlined. I have some questions mainly regarding the order.

      1) I’m SIBO-D dominate but also have a little SIBO-C. Should I follow SIBO-D protocol?
      2) I have SIBO and Yeast Overgrowth. Do I follow the protocol for both of these at the same time? Or, stagger? Say, SIBO first then Yeast Overgrowth?
      3) Do I start the gut healing protocol AFTER I finish the SIBO/Yeast Overgrowth protocols?
      4) I have Fructose Malabosorption. I noticed some of the supplements like, Vit C as a part of gut healing protocol. Is there a Vit C that is not derived from fructose or does that matter?

      Appreciate your thoughts on this!


      • 1. I would follow the SIBO-D protocol and use a squatty potty to help with the constipation.
        2. I would follow both.
        3. Correct, after.
        4. Pure ascorbate acid should not have any fructose in the final product.

    26. John,

      Probiotic enemas for SIBO instead of oral. Thoughts?

      • Probably, better for SIBO if they implant. Most probiotics do not implant and just modulate the immune system.

      • Might be better, then again it is unknown if probiotics truly implant or not. There maybe a difference in immune reactions in giving an enema compared to ingesting them orally, even if they do not implant. If they do implant they might survive more in an enema but they would only reach the colon. Most strains of Lacto for example live in the upper gut, so they would be useless in an enema. The enema should be mainly Bifido and L. plantarum, they are found in the colon.

    27. Hello and thank you for this really good article. I was shocked that you mentioned Saccharomyces Boulardii…..

      I have had some kind of food poisoning with the family about 8 months ago, we all fell ill after a Chinese takeaway. While being really sick with severe diarrhoea, the doctor decided to put the whole family on antibiotics. As I was having quite scary rectal bleedings at the same time, I thought my ulcerative colitis restarted due to the illness(I was off medicine and colitis for 6 years) so I decided to take Saccharomyces boulardii years from Jarrow for 2 weeks(which helped my colitis last time). About 1 week later painful gazes and increases diarrhoea, it was really bad! During this, the kids came back with a Gastroenteritis which completely finished me, I ended up in the hospital as I had lost 13 kg in 6 weeks.
      While there they found the cause of my rectal bleeding which was an anal fissure caused by constant diarrhoea I had. They also told me that they suspected SIBO but were not really sure what to do so they prescribed me more antibiotics and q week of Enterogermina which helped.

      1 week later, Sibo came back even stronger and I thought…let’s take more Boulardiis, I started to have even more gazes, tiredness and pain.

      For 8 months, I feel that I have lost my memory(I am a coder so it is a bit of a pain), I am also getting angry for no reason and wake up with a very weird taste in the mouth if I eat carbohydrate the night before.

      I am now wondering if the whole issue has been getting worse due to Boulardii!

      I started L-glutamine today, curcumin in organic form. The peppermint oil tablets.

      Also, I have noticed that if I take B complex or probiotics likes acidophilus + bifido, very smelly gazes are produced non-stop with abdominal pain.

      That’s why I came to check your site out because doctors seem to not know what they are doing in my area and if I take probiotics, things get worse…

      Kind of lost really….

    28. Hi John,

      If one doesn’t have issues with dairy, would whey concentrate be a suitable alternative to Seacure? Both in the beginning stages and afterward

    29. Hi John,

      Should one continue the low FODMAP diet during the month long rebuilding phase? Or is this the time to start adding back in starch and FOS?

    30. Is it possible to have SIBO, Candida and parasites at the same time and how do you tell the difference? I’m seriously struggling with chronic pain,gut problems,brain fog etc and I’m only 31. I’ve been like this for as long as I can remember. I’ve ‘trigger points’ all over my body and I’m convinced they’re toxin build ups. I just don’t know what to treat first or if I even have all of them. Thank you

    31. Hi there John,

      Do you think a deficiency in B12/neuropathy can be a first sign of SIBO?
      I had this and kept it under control with supplements but then I started getting gut problems and other symptoms.

    32. Hi John,

      I’m taking interfase plus on empty stomach as directed and always at 20 minutes after taking I get some terrible stomach pain and bloating. Any idea what that could be?

      I’m on Xifaxan and Neomycin , I take them away from the interfase plus.

      • Irritation from the systemic enzymes. Lipase and protease can irritate the stomach lining and the bloating could be from die off.

        • Isn’t that because the gut lining itself is basically a biofilm?

          • Biofilm from microorganisms are part of the lining yes, but are not located everywhere on the lining itself. Enzymes can break down the mucosa itself causing irritation.

    33. For the moderate case of SIBO protocol, do you take all the supplements at once or do you start out with the anti-bacterial supplements then move on to the biofilm disruptors and so on?


    34. Hi John,

      Would taking a biofilm disruter such as Serrapeptase as well as NAC be too much? Also, should Serra be taken only once a day or before meals?

    35. My daughter has been on xifaxan 400mg 3x day for 10 days. She is at about 85% reduction of symptoms. At 14 days we are supposed to be completed. ( although I can get more meds if needed). I purchased a glucose breath test and wondered if we really need to wait 2 weeks after xifaxan to use test. Nervous to wait that long as sm. intest. can repop the bacteria in that short span. Would it be ok to use allicin while waiting to use the breath test or would that perhaps give a false reading since it would hide the bacterial activity?

      • *You must wait 14 days after finishing a round of antibiotics (even herbal antibiotics) before retesting. This is critical for the accuracy of test! However, don’t wait more than 16 days to retest; you want to retest before regrowth of bacteria (recurrence) has time to occur.

        pulled from another sibo resource

      • It would give a false reading, you would have to be off of all prebiotics, probiotics, and anti-microbial agents to get a correct test.

    36. Hi John,

      Thank you for providing this.

      Question- thoughts on Atrantil.

      Secondly- why not peppermint for methane-dominant SIBO, please?

    37. Can you tell me how much silver to take at a time and how many doses a day for how many days? Thank you, Heather

    38. Simple question, do I take Supplements to Stop a Bacterial Herx Reaction (All Must be Taken Together) while I am on rifaximin? or after I am finished with rifaximin and interface plus? While taking just rifaximin I am ok, whenever I introduce interface plus I get really weak and tired is that normal?

      • You would take them while you are taking the antibiotic and any antimicrobial agents. Yes, it would seem like you are suffering from herx from the IP.

    39. Hi John, thanks for writing this article with so much useful information! The most known biofilm supplement is InterFase Plus however it’s getting more and more difficult to purchase it because technically you can only purchase it through a practitioner and reputable online stores that used to sell it don’t seem to do it anymore (except Amazon but it can be tricky to make sure the that the supplements their sellers offer are not counterfeit). So the other options in your article are NAC or Lactoferrin. So some quick questions regarding other biofilm disruptors:

      1. What do you think about Biofilm Defense from Kirkman?
      2. Could it be as effective as Interfase Plus for SIBO? Aside from the lack of EDTA and Chitosanase, it seems to carry a good combination of enzymes.
      3. If it is not as effective as Interfase, is there a specific protocol you would suggest to make it as powerful as possible?
      4. Could it be combined with other biofilm supplements like NAC or Lactoferrin in order to make a powerful enough combination for strong SIBO Biofilms?


    40. Hi! First off, your website and the information you provide is one of, if not the best, that I have come across!
      I have read through nearly all your postings as well as the comment section and I think I have a handle on the recommendations. I’m a 30 y/o female with a large hiatal hernia. I was able to moderately manage over several years with interment use of L glutamine, zinc Carosine, enzymes, diet (following a AIP diet initially and lifestyle modifications, visceral manipulation (which all resulted in a negative barium study and negative autoimmune markers from previous positive…as well as finally increasing my vitamin D levels and thyroid!). I was amazed and completely sold ! The last year has been extremely stressful, physically and mentally, resulting in a lot of change in my usual diet and exercise routine. Long story short, I’m dealing now with GI distress unlike I have ever experienced before. I’ve tried to redo my diet starting with AIP, but I’m so irritated by sweet potatoe, coconut and anything starchy really that I knew something else was going on! I currently have the most severe reaction to dairy (whey, casein and lactose in any form), then resistant starches, legumes, oligosaccharides and night shades/citrus cause significant upper GI/chest and throat tightness. I typically have a bowel movement 5xweek, more often they are harder stools but sometimes loose and fatty.
      From what I understand, I need to eliminate SIBO via (possibly) multiple rounds of herbal based.
      Treatment while following a low food map diet (though not to stay on too long and maybe able alternate days ?). Once those symptoms have improved, then restore and rebuild the gut lining while also fixing the root of the issue (for me, low stomach acid, weak LES, slow motility). Then, add in soil based probiotics, prebiotics and fermented foods? To deal with SIBO, I bought fc ciudad, Allicin,interfase plus, berberine, oregano oil (idea is to alternate them if one round isn’t working enough). To help with the hernia and gut rehearing, bought zinc Carosine, glutamine, 5-http, r-alpha lipoid acid, triphala, digestive bitters. Does this sound on the right track? I’m also wondering if one is to start supplements for strengthening the LES while taking the supplements to kill of the harmful bacteria. Also, when is it ok to eat fermented veggies or juice? Really appreciate clarification!

    41. Hi John, I am an American with SIBO living in Tanzania. I’ve also struggled with candida over the years. I started your protocol for people with light/moderate sibo with coconut oil, interfase, and berberine on Monday. I didn’t anticipate a herx reaction because I haven’t had any with any other treatment. This is the first time I’ve used a biofilm disrupter though. I don’t have access to any of the supplements you recommend for herx, and I’ve definitely been having a strong reaction. I’ve been running a fever for the past few days with lots of aches, pains, headaches and occasional bouts of nausea. Yesterday I took a warm bath with apple cider vinegar and baking soda. It made my fever go up a bit, but I felt better for a few hours. My question is at what point would it be wise for me to reduce the dosage, i.e. what point would indicate that this is just too hard on my body at this time? I can tolerate a lot but I don’t want to push my body so hard that there is lasting damage.

      • I would reduce the dosage for now and slowly titrate up the dose and see if that helps reduce the herx reactions you are having and your body can adapt.

    42. Hi John,

      What do you think of food allergy testing (any particular test you recommend?) while treating SIBO? Worth waiting mid-treatment or during treatment to track things like possible excessive hydrogen sulphide from eating high-sulfur foods, unknown food intolerances etc, which doesn’t show on breath tests?

      Can you shed light on the relationship between satiety, food cravings, low stomach acid, SIBO, leaky gut and modulating serotonin in the gut? Any research and protocol you know that helps metabolic control and nerve signaling that enables satiety?

      And what do you think about genetic microbiome testing for sibo sufferers? I’ve seen a few labs that do it, but research on that doesn’t seem so conclusive.


      • I do not believe that food allergy testing or genetic microbiome testing is accurate yet. IgG antibodies for example just mark prior or current exposure depending on tiers, not allergic reactions. ELISA maybe better but more research is needed. Proper antibody testing also requires proper immune function for accurate results. Few doses of bismuth may help expose hydrogen sulfide overgrowth if your stool turns black and you are not eating sulfurous foods during the experiment.

    43. Hi John,
      I was diagnosed with SIBO (hydrogen), with only a slight peak of 21 at 160mins using glucose breath test. Also have a genova test showing I have gut dysbiosis from clostridia. Was given two weeks of cipro/flagyl for SIBO which helped with the upper stomach pain and burning but did nothing for the diarrhea. Also, symptoms returned (including neck pain and neurological involvement) two weeks off of abx. Functional med dr is now treating me with 1 month pulsing vanco and probiotics. My question is about SIBO and probiotics/diet. I need to heal gut from clostridia ava leaky gut, but feel like I might be making SIBO worse with added bacteria from probiotics, fermented foods, glutamine. Can you suggest gut healing diet and/or supplements that won’t make SIBO worse? I’m currently on a strict Paleo diet, but have major malabsorption, 45lbs of weight loss in 6 months with no end in site, and hair loss. Current diet showing ketogenic type wasting. Any help is much appreciated!

    44. Hi John,
      I just finished 2 interface+,2 allicin, 2 berberine, 1 neem protocol of 14 days. And the last 3 days I’ve felt better than I felt in a long time (not perfectly, still raw, and sensitive, but a lot better). But today I stopped the herbals, and felt extreme nausea all day, despite eating very little in quantity, and low fodmap, the same kind of severe nausea I experienced before starting herbals, and during the first week of taking them. Does this indicate that the antimicrobials didn’t help at all, and the bacteria is still there? Should I go ahead with the gut repairing protocol anyways?
      Thank you

      • Most of the time multiple protocols of rotating antimicrobial agents are need to rid oneself of SIBO, it can take months or years depending on the type and issues one is facing. Berberine can cause gastrointestinal upset and can cause the stomach to become “raw,” taking some zinc carnosine may help with that.

    45. Hi John,

      thanks for all this useful info. Last year I’ve been diagnosed with SIBO and treated with Rifaximin 800mg/day for 3 weeks without any results. Now I want to try ECPO(Enteric Coated Peppermint Oil) with NAC because I can’t get Interfase in my country and Lactoferrin is expensive.

      And I want to ask, is there a big difference between NAC and NAC Sustain used as biofilm disruptor? Is it really necessary to be disrupting biofilm all day long or isn’t classic NAC as sufficient as NAC sustain when taken with anti-microbial?

      And last question. What do you think is better – ECPO with NAC or ECPO with another anti-microbial such as Berberin for a month? Thanks.

      • No, NAC sustain just lasts longer. It isn’t BUT I only recommend NAC as a last resort since it is a systemic biofilm disruptor and can effect good “biofilm” in other parts of the body.

        ECPO slows down motility so if you have hydrogen bacterial overgrowth it is fine but not for archaea.

        I recommend trying ECPO and oil of oregano.

    46. Does Extra Virgin Coconut oil break down biofilm?

    47. Everyone here should take note that Dr. Mark Pimentel, an expert, if not the expert, in the field of sibo/ibs, will make an important announcement regarding a potential new treatment in May. Please check his Twitter or google him for more information.

      • I believe is a novel drug that will be a localized statin that will target methane dominant archaea. I doubt its effects will only be seen in the intestinal tract and stains are not the best because of the multiple side effects associated with their use. Need to see the data about systemic absorption and even then I would be cautious of recommending it.

    48. Hi John,
      I read that interfase-plus damages tooth enamel, is this true?

      • It is possible that the EDTA supplement over a long period of time may reduce mineral intake in the intestines which can lead to weakened tooth enamel.

      • Hi john

        Really need your help. Four years ago became increasing intolerant to food, carbohydrates and then proteins, after a nasty stomach bug and a huge amount of stress. 20 years before this I had contacted salmonella, which led me to become lactose, sugar and yeast intolerant, v prone to candida.

        Now I am intolerant to almost all food, I have tried everything to kill candida, biofilms, herbal and antifungals. Sadly I cannot tolerate bone broth, glutamate or gelatin to help heal my gut

        I am starting to wonder if my problems are due to dibo, that’s why my gut hasn’t been able to heal. Testing in uk is nonexistent, unless you go privately which I cannot afford. I get diareah ( like cow pats) every day with occasional bloating and can’t tolerate prebotics of fermented food.

        I just wanted to pick your brains to see what you would try to kill my possible sibo off

        Thanks so much, as am very desperate. Jane x

    49. Hello.

      I have slow transit constipation possibly caused by sibo because it started form abx.

      I am on 400mg oregano oil and 1500mg neem for 2 weeks with no results. Is there anything else i should add?


      • Maybe try alicin and triphala. Stop snacking in between meals if you havent already and walk at least sixty minutes daily.

    50. Hi I have been having severe constipation and bloating now for 12 months. I took a Genova stool test and it came back saying I had high Fecal Secretory IgA and Staphylococcus aureus as a potential pathogen. I started to take Renew Life 50 billion count probiotic and the bloating immediately went away. I take my probiotic with Triphala and magnesium pills every night to have a movement every morning (I am severely constipated without it). Do you think I have archaea dominant SIBO? And does this mean my MMC is not working properly? if so what protocol should I follow since the one you listed above for the Average Probiotic Protocol is only for people with functioning MMC. Is taking a Saccharomyces boulardii supplement bad if you suffer from SIBO-c? What is the difference between a severe case of SIBO-c an Moderate SIBO-c? Also I was reading that glutamine can cause constipation so I am worried about stopping my triphala/probiotic/magnesium supplement and becoming severely constipated like I was before.

    51. saccahromyces is a transient organism and is incapable of colonizing the gut or “turning pathogenic” – you should get your facts straight before posting

      • Different strains of Saccharomyces are found as normal gut flora and are not transient. Now if you are talking about S. boulardii then you are mostly correct. One would have to take the prebiotic for a couple of months or consume unwashed lychee fruit for a long time period for it to colonize, if it does. However, there are multiple case reports of fungemia that were listed in my blog article about it, therefore it does turn pathogenic.

    52. Curious how much Oregano Oil you would recommend taking as I am going to take that along with berberine as my anti microbial choice.

      I have the 100% pure oregano oil on the way in a dropper so I would need an estimate for drops :) Thanks!

      I am 24 6’1″ and 178lbs if that helps at all haha :)

    53. I’m really excited to try this protocol to see if it helps clear up my IBS and malabsorption. One question though: does the rebuilding phase/reintroduction of probiotics begin AFTER the 3 months on the FODMAP diet, or once we’ve broken down the biofilm and treated with antimicrobials? Hope I didn’t miss this info in the comments section. Thanks!

      • It depends on symptom reduction and MMC function whether or not when the rebuilding protocol should be followed. In addition, it seems to be better to follow the FODMAP diet for two days and on the third day eat FODMAPS that are not polyols or contain gluten. It is also a good idea to rotate antimicrobial agents and antibiofilm agents.

      • John, please give more detail about peppermint oil not being appropriate for archaea-dominant SIBO. According to this paper, peppermint oil can reduce methane emitted by archaea.
        Appl Environ Microbiol. 2012 Jun;78(12):4271-80. doi: 10.1128/AEM.00309-12. Epub 2012 Apr 6.
        Effects of essential oils on methane production and fermentation by, and abundance and diversity of, rumen microbial populations.
        Patra AK, Yu Z.

        • Correct, which is why it is in atrantil. Menthol is in the supplement to slow down the MMC so that the plant tannins do their job. It is a catch 22. It would slow down motility (bad thing with SIBO-C) and eliminate archaea. I rather use other agents to increase motility and reduce archaea.

    54. Hey John, I’m taking Ginger Root (500mg) 2x Daily + ST-TN Capsules 2x Daily (Propionic acid (100mg), sorbic acid (100mg), and caprylic acid (300mg)

      My natro told me the ST-TN is a biofilm buster, and ginger root (antimicrobial) can be used too just like peppermint oil. Would you agree? Should I continue with this?

      • Depends on what type of SIBO you are dealing with. Too much propionic acid in the intestines can be bad and is seen in people with Clostridium overgrowth. Ginger is contraindicated in those with slower motility, but can be used in people with gastroparesis. Caprylic acid is good to deal with some forms of fungal overgrowth as long as it is weak to the CA.

        • What is the CA? and I have the SIBO test but it’s going to take 3 weeks to get the results. The only main symptom I have is Gas, it does not go away. I burp so many times a day. It always feels like theres gas stuck in my stomach and chest 24/7.

    55. Is Cat’s claw is helpful in treating SIBO methane dominant? In Poland, I do not get allicin low fodmap and berberine.

    56. I just ordered your book and am about to read it. I am wondering, however, how to find a practitioner who performs the hydrogen test, or if there is a way to conduct this test on one’s own? I am fairly confident I have SIBO due to the distention of my gut and chronic flatulence and bloating. Still, after reading through some of your site it seems like it would be useful to have a measurable score from some kind of test to know where I’m at… and then if I re-test after doing a protocol, to know if I’ve had success (though I would hope subsiding symptoms would tell me that). So… 1. Do you agree it’s important to have a test score before jumping into a protocol? 2. Can you do the test on your own? And 3. How does one figure out if the biofilm is involved or not? It seems like they are two different protocols and it’s unclear to me how to decide that. I live in Los Angeles, so I figure there must be a practitioner near me, I just haven’t found one yet through word of mouth.

    57. Thanks for the quick response John .

      I got doubt appendix . I did not understand what you meant. I’ve been operated and don’t have appendix .

      I take Levothyroxine Fasting every day. Do you think it can contribute to SIBO ? Because of Mannitol and maize starch .

      • I did not think lactoferrin in bottle. I’m afraid to buy the wrong .
        Do you think I can use 1000mg – 2000mg a day just in capsules for the treatment of antibiotic ?

        Thanks again and sorry for bad English

      • Lack of an appendix is a more likely cause of SIBO occurring. How much mannitol? Yes, you can use that amount in capsules.

        • And how to act in case of being with SIBO and has no appendix ?
          But I have not tried to take Rifaximin .
          You better think natural treatment in this case?

          Thanks John =)

          • IF you take the Rifaxmin you need to deal with the underlying lack of motility, possible low stomach acid, and biofilm for it to be successful.

            • I am very grateful for your help John .

            • Hi John,

              I have celiac, hashimoto’s (I take gluten free tirosint), and sibo. Diagnosed with celiac at 41 and I am 43. I do not have an appendix. My naturopath helped me improve my D pre-sibo, but I probably should’ve been on HCL and digestive enzymes, low fodmap, etc a long time ago because my food wasn’t totally digested. Anyway, I took the standard antibiotic for 12 days in the late spring and overlapped with 30 days of allimax and berberine sometimes taking the biofilm buster you recommend the entire time having D like my prediagnosis days. That messed with the digestion of my thyroid meds. All was well when I finished and started SCD low fodmap which immediately fixed my stools. Problem: during pms I cheated with fodmaps, SCD illegal, etc. and it came back.

              So now I’m 7 days into allimax, berberine, and oil of oregano and have D that is making me exhausted and frankly scared of the damage I’m doing to myself. I see your herxing protocol. Will that help slow my D down? I don’t have sun chlorella, but I have the other things. Also, do you mean 8gms of glutamine a day or 24 grams 8 at a time? Any other advice would be welcome and appreciated. Thank you!

    58. Hi John
      First I would like to thank all his hard work in helping us .
      I’m from Brazil suffer from SIBO to 2 years and here no doctor know about it .
      I start the treatment with Rifaximin 550 mg for 10 days .

      But I got some doubts about the biofilms:
      When should I start and stop with interphase Plus?
      It is highly recommended interphase Plus? Or should I take along others like Jarrow NAC Sustein and coconut oil ?

      At what stage of treatment should I do to use Glutamine ?
      Any food supplement without carbohydrate to show me ?
      Probiotics are needed ?

      Thank you for helping save our lives .

      • When should I start and stop with interphase Plus?

        Start while you are taking the antibiotic and stop after you stop.

        It is highly recommended interphase Plus? Or should I take along others like Jarrow NAC Sustein and coconut oil ?

        I would take Interphase and lactoferrin.

        At what stage of treatment should I do to use Glutamine ?

        After you stop taking the antibiotic.

        Any food supplement without carbohydrate to show me ?

        Such as?

        Probiotics are needed ?

        Possibly afterwards, it all depends if your motility has corrected itself or if you have your appendix.

    59. Why would you be worried about S Boulardii to be a systemic infection. I understand that when people immune compromised they do have issues. But S Boulardii doesn’t reproduce in the body. It should clear up on it’s on within a week.

      • Because fungemia has been reported with the probiotic.

        “Many cases of Saccharomyces boulardii fungemia in those taking S. boulardii supplements have now been described; in some cases, homology between the probiotic and infective organisms was confirmed by using molecular typing (32-45). Interestingly, 2 reports suggest that a probiotic supplement (S. boulardii) taken by one hospital inpatient may spread to neighboring patients, to whom it is not being directly administered, and lead to significant sepsis.”

    60. I have a 13 yr old daughter who has been suffering from methane SIBO for 1 1/2 years. Thanks to a group of incompetent group of pediatric gi docs, she was hospitalized for an eating disorder for 8 months! I finally have proof it is SIBO, and I want to know if your protocol is safe for a 13 yr old who has severe Gerd – 2+ tablespoon size amounts of food and acid can come up in her mouth for 1 to 2 hours after she eats. Her new, almost as incompetent pediatric gi doc gave her a 3 day supply of Xifaxan 200mg3x a day + FODMAP diet. She is worse than before. And due to waiting 4 hours between meals it is so hard for her to fit in what is required in 4 meals. She is now verping up longer (up to 3 hours after eating). Her life is all about food now – how eat it and keep it down. Please help. This child has gone through more than any child should ever have to .

      • Dear Laura,

        There is not much I can suggest because of her age. A prokinetic like ginger tea might help. The use of magnesium citrate might help as well at 200 mg per 50 pounds of body weight. Using a squatty potty and a rebound trampoline might help the MMC as well.

        Supplements like oil of oregano and lauricidin might be sage but as a doctor.


      • Laura, I’m so sorry your daughter is going through this. My daughter 11 also has SIBO and I would highly recommend going to a Naturopathic Doctor. We did 2 rounds of Xifaxan 200mg3x a day for 14 days + low fodmap, then we did 550mg3x a day for 10 days = low fodmap and that didn’t help at all because we weren’t treating the methane. Then we went to an ND and took Allimed 2 a day and Candibactin BR 2 with each meal and finally we started to see some relief (1 month protocol). She was able to go back to school part time after being home for 5 months. The Candibactin dose was too much and caused stomach issues so we did a 10 day round of Flagyl 500mg 2x a day (that her new GI doc wanted her to do). That helped a little but not much. We then went back to herbals (neem and allimed, and saw another reduction in pain. We just retested and her numbers are down and her pain has significantly decreased. We are also doing SCD/low fodmap diet. There are some great sibo groups of facebook and I can’t begin to tell you how much they have helped. Things will get better!! We are on our 6th treatment and I know that we will need another after this but there is hope!! Good luck.

    61. Hi John
      I would like to try your protocol: enteric coated pepermint and Interface plus. Will it be hard for the stomach because I have gastritis and acid reflux? Thank you!

    62. Hi John,

      thanks for this great blog, I allready bought our ebook.

      I have an uncommen question to SIBO:
      My symptoms defenitely lead to SIBO. Since I have celiac desease, fructose malabsorption and not tolerating whey, I am sure it’s all about the small intestine.

      Everyone wants to eliminate the carbohydrates and FODMAPS (which I defenitely cant tolerate) with their diets.
      I for myself dont seem to tolerate protein, while I tolerate most mono-disaccharides (corn, rice, glucose – most glutenfree stuff without fiber).

      I tested to just eat Protein on empty stomach, result: soft stool, very pappy and adherent. While I eat just carbohydrates its more like formed stool etc.

      So, are there known forms of SIBO where the wrong bacterias are like e. coli in the small intestine and protein should be avoided instead of carbs?

      Sorry for my bad english!

      Greetings from Munich (Germany) :)

      • Dear Dave,

        There is a possibility that you have E. coli overgrowth which is causing your protein digestive issues. It could also be a lack of protease being produced by the pancreas, and is a pancreatic issue. You have to tailor a diet to how you feel and what causes less bloating.

    63. Hi Jon, would like to ask how long would it take for the interfase plus to show signs that it is working. Also, what can of diet should I follow during this time? Cheers.

    64. Hello John,

      I’ve been looking through many articles and have came across your site. I’ve been diagnosed with SIBO about a year ago, but sadly Rifaximin or any other antibiotics do not work for me? Well rather, they work at first but the symptoms come back at the end of the treatment. Would peppermint oil and Interfase-Plus still be a good solution to this problem? I read in the comments that you recommend rotating antimircrobial agents. Is it between the ones u mention in your article above? Many thanks in advance.

    65. Hi John: Thanks for this website. I found you on MDA and then bought your book. I just finished your SIBO protocol. My NP would only give me three days of Rifaximin so I did that and then followed your moderate SIBO protocol for a month. I have been on vacation for a few days and planned to start the gut rebuilding plan this week. But in the few days since I stopped all of the supps in the SIBO protocol my gut has gone back to its old ways – lots of gas and multiple stools/day. Wondering if you think I should do the SIBO protocol again before starting the gut rebuilding. Any advice would be appreciated. Thanks!

      • Did you change your diet during this period? It all depends on the overgrowth and what is weak to. Did you take any antibiofilm agents?

    66. Hi John, how does one know the severity of SIBO?

      • Lactulose and glucose breath tests that measure hydrogen and methane. Also, a comprehensive stool profile from Genova can help determine bacterial overgrowth.

    67. Dear John,

      Thanks so much for sharing all this information!.
      After 2 months suffering a really bad LPR, I found in your page all the information about possible causes/tests/treatments brilliantly summarised… now I now what steps I need to follow … I refuse to accept my current condition as chronic until I’ve tried all the available options, unfortunately seems many GPs only approach is to prescribe PPIs and treat it as chronic…

      Anyway, again, I will definitely buy your book and will recommend this page to all my friends with similar issues (and they are legion)…I was just wondering: what is your view on the Candida cell wall suppressor supplements? Are those the same as Anti Bio-film agents?


    68. Hi John,

      I currently have almost all of the supplements you listed for treatment of SIBO. But I have a question regarding N-Acetylcysteine. I’ve previously taken the Jarrow NAC Sustain and it caused bad insomnia and mood swings, even with using only 1 pill a day. I can substitute the NAC for Jarrow Lactoferrin, which I also have, but I was wondering if you had any idea why the NAC Sustain would have negative side effects?

      • The NAC could have caused either a herx reaction which can cause some of those symptoms OR could have modulated serotonin in the gut. This modulation of serotonin may be good for some people like if you have Bipolar disorder and has been studied in helping manage the disorder.

    69. Hi John,
      If i have problems digesting fats and fatty liver with insulin sensivity, what macronutrient ratio would be apropiate to treat sibo ?

    70. Hello John! Firstly, I’d like to start by saying a big thank you for what you do! After 15 long years of suffering with a variety of GI symptoms, it has just been discovered that I do test positive for SIBO (Hydrogen & Methane producer) so it is with great interest that I’ve been reading and studying about it. I’ve read your protocol and have a couple of questions which I would be very grateful for answers to:

      1. Do you suggest waiting to add in L-Glutamine until AFTER all anti-bacterial treatment is completed (after 3 months following the Bulletproof Diet with FODMAP) or can one supplement with it (and drink bone broth) from the get-go? 2. I live in CANADA and can only get my hands on the NAC as an anti-biofilm agent. In your experience, will this alone suffice?
      3. Do you ever recommend rotating the anti-bacterial agents? Is it common that one might need to go longer than 4 weeks in using them for relief?
      4. What are your thoughts regarding keeping a little FODMAP in the diet in order to not encourage the bacteria to hibernate?
      Thanks a million John!

      • 1. You can take the L-glutamine during the protocol but you want to take it with food so that its absorption stays in the gastrointestinal tract. NAC may suffice, depends on the severity of your SIBO.
        2. I do recommend rotation in the 2nd edition of my book.
        3. With the use of multiple antibiofilm agents this is probably not needed in most cases. I do recommend doing this on occasion if people do not see results quickly after starting the protocol.

    71. Thanks for putting all this together John. I bought your ebook and it is extremely useful and I’m starting the SIBO protocol. One question if I may, is it safe for me to take lactoferrin if I have elevated iron levels? I have a holistic doctor that I’m working with but I’m just starting the testing with her so it will be some time before we begin a solid protocol. So I’m diving into the light protocol from your book for now as it seems to already be helping (mmc, hcl, etc.)

    72. Hi John,

      Thanks for such a great blog! I have a few random questions about the GERD/SIBO protocols:

      1. I had a hydrogen breath test done and scored a “9,” so I’m told I don’t have SIBO. I do seem to have issues with some FODMAP foods, but not all. Brussels sprouts and avocados are usually fine with me, but cabbage, onions and many others give me heartburn , bloating, etc. Do all FODMAPS need to be cut out even if one doesn’t seem to have a problem with them?

      2. What do you suggest if one has issues with l-glutamine? I think it causes “neurotoxicity” issues for me, but I definitely need something to help heal my gut lining.

      3. You specify Jasmine rice to be ok – what about other types of white rice?


      • 1. Not necessarily. Some people are fine with being able to cut out only the FODMAPS that cause them issues. It all depends what bacteria are causing the overgrowth and what they feed on.
        2. Take low doses with food. There is a lot less chance of it being utilized outside of the gut when taken properly.
        3. Other types of white rice are fine as long as they do not cause any issues.

    73. Hi John
      My doctors prescribes xifaxan 550mg twice a day for 30 days but it doesn’t work. Now she changed to Cefalexin 500g twice a day for 30 days. I asked her for methane test and Comprehensive digestive stool test but she said they don’t do both of them. She suggested me to go to see a naturopath doctor. What is your suggestion? Thanks!

    74. Hi John, this is such a great blog! Thank you for sharing all your wisdom with us! I have a quick question for you. I started taking Berberine 500 for SIBO and my burping increased. Did you happen to see such effect in your practice? Why do you thing I react like that? Thank you very much!!

      • Die off of bacteria can sometimes increase gas. If it occurs for longer than a week, switch to a different antimicrobial.

    75. I just want to double check, initially you would do the peppermint for 2/4 weeks. Then you would go into the rebuilding phase? Sorry if this seems obvious.

      • You are correct Alex. The peppermint oil might not be strong enough and you might need to combine it with other natural antimicrobial and and anti-biofilm agents with the FODMAP diet.

    76. Hi John
      What can we do to stop a weight lost from sibo? I am 5’2″ and only 78 lbs now. I lost 20 lbs in 9 months. Right now I lose 1 lb every week even I try to eat 1400 calories a day. Eating is very hard for me now because of the gas pain, constipation, bloating…Thank you!

      • You will need to work with a doctor to tackle the issues of your SIBO. Increased dietary intake of fatty meat, ghee, extra virgin olive oil, and safe carbs like jasmine rice might help you to gain weight. You need to find out what foods trigger you and avoid them. Look into FODMAPS.

        • Thank you, John!

        • Thank you, John! I am taking xifaxan now (twice a day) for 30 days. I want to take enteric coated pepermint now. Is it ok or I should wait until finish antibiotic so I can take the enteric coated pepermint oil together with the priobiotic?

          • Since you are on the antibiotic now I suggest combining it with two of the listed biofilm chelators to help out its efficacy. I would also follow the low FODMAP diet listed on my blog during this period as well.

        • Hi John

          Do you know any dietitians/ nutritionist in AZ that work with SIBO? Thanks!

          • I do not know of any offhand. Let me know if you find anyone.

            • Thanks, John! I found someone but I have to put it aside because I am unable to eat much due to gas pain and abdominal pain. My doctor put me on xifaxan for 30 days (550 mg, twice a day) and I am on day 20 now with about 10% improvement only so I will come back to see her tomorrow to see what need to be done next. I have constipation and a lot of gas pain in upper stomach and small intestine so I guess I also have methane. Unfortunately my doctor office does
              breath test for hydrogen only. They don’t know about methane or treat it. I am taking interfase plus (got information from your site) and allimed 3 times a day now ( got the information from Dr. Siebecker’ site). Don’t know why I see very little improvement. Do you have any suggestion for me? Thanks!

            • It all depends on the bacteria in your gut. I would get a Metametrix Comprehensive Stool Test done which would provide some answers but not all of them. You might not be attacking it strong enough or the bacterium could be resistant to xifaxan.

    77. Hi John thanks for all the great info! I found this review about a antibiofilm product and I’d like you to take a look at it if you could and share your thoughts. In essence it states that most of the enzymes used to destroy the cell walls of yeasts are ineffective.

      Also do you know of any other products similar to interfase plus without the enzyme Lysozyme? One that is common allergen free? Thanks!

      • The review is mostly correct, yeast cell walls are not made of cellulose. Interfase unlike Candex contains chitosanase which would break down the cell wall of yeasts.

        It all depends on what you are using the Interfase Plus for, bacteria or yeast?

    78. I have just completed two weeks on the interfase plus protocol. I experienced fairly extreme Herx reactions on two tablets per day (lowest recommended dose). One week after stopping I am still experiencing headaches, cramping, palpitations and abnormal fatigue. Whilst everyone is different and I could well take this as a positive die off reaction (and I am trying to), could I suggest caution with EDTA based chelators. My guess is to look at the history and depth of your problems related to your own dysbiosis and gauge whether to hit it hard or slow and steady depending on how long the problem has been established in your system. This is what I have learned.

    79. Hi John,

      Sorry for the double post. This was a mistake..didn’t show up the first take.
      On a different note I would like to know what dosage for Interfase Plus. You say follow the directions, but the say between 2 and 8 per day, which is pretty open. Can you suggest the best approach please. I’m going to take one a day for a couple of days and increase every couple of days up to 4 a day.

      • Your dosage seems fine to me. It is always best in most cases to start small with supplements and increase dosage so your body adjusts.

    80. Hi John,

      Should I stop all probiotics/fermented foods while in stage one? Or can I just continue?
      I have bought Interfase Plus and Peppermint capsules and will also continue with Digestive Enzymes and HCL, plus Fast Tract Diet which I’ve been on for 4 months.

      • Yes, stop all probiotics, prebiotics, and probiotic foods in stage one.

        • Can I ask you why this is? I’m just noticing an improvement with certain probiotics. Might help me understand the anti-biofilm workings.

    81. Is it necessary to stop taking probiotics/fermented foods while on the first stage of the protocol (I will take Peppermint oil and Interfase Plus, with Food Enzymes and HCL)?
      I didn’t see this in the book, so I don’t imagine its crucial, but I’d be very grateful to find out, John.

    82. You can combine the two of them. Follow my dosage recommendations for a week then decrease to two capsules daily. They should be taken at the same time except for the timing of the peppermint oil.

      • what should be the order taking the peppermint oil and the anti biofilm? how many capsules of the peppermint? the coconut oil should be taking alone or with food and at what time?


        • Peppermint oil should always be taken 30 minutes before a meal. Anti biofilm supplements should be taken with meals or empty stomach where indicated. Coconut oil should be taken with a meal and can be taken any time.

    83. i bought lactoferrin and papaya enzymes, can i combine the two or should i rotate them?
      protocol dosage of lactoferrin seems high compared to what the bottle says?
      how long between lactoferrin and the anti bacterials?
      thank you.

    84. It usually isn’t needed if combined with the FODMAP diet in most cases.

    85. exist some alternative to Jarrow NAC Sustain by other brand?

    86. why other protocols recomend rotation of antibacterials and ANTI-BIOFILM and you dont?

    87. Thank you for this post. Do you take the supplements to stop a bacterial Herx reaction DURING or AFTER the initial cleansing phase, but before the gut building phase ? How long do you take the supplements to stop Herx ?

    88. I have been reading through your very informative articles on gerd. i have been studying for a long time (because of issues I had and my husband had). I want to tell you my plan and get your input. My husband was diagnosed with gerd around 13? years ago. He tried different medications and settled on prilosec (omeprazole). At one point he was put on an anti inflammatory pain killer for his shoulder and spent the night throwing up. Years later he went on a low carb diet for weight loss and it was the only time he didn’t need the prilosec. (It cured his heartburn until he went off the diet.) I don’t think he is ready to overhaul his diet right now, although he does eat real food most of the time (he still eats some fast food and loves Chick fil a’s lemonade). He went off the omeprazole and is having some heartburn. Not as much as he would have had before having partially healed from tumeric and real food. I have started him on DGL. I am planning on adding zinc carnosine. After I felt his stomach lining had healed some (maybe after 3 weeks?) I was going to add betaine hcl with pepsin.And then maybe some enzymes. I have also heard good things about using gastrazyme to heal the stomach lining. He is already on vitacost brand probiotics, CodMega fish oil (garden of life), magnesium citrate, alive whole food complex vitamin C. He does have chronic jock itch that does seem to worsen with certain starchy foods. I don’t know if I will have to do anything more-if there are any h pylori or candida issues. Any thoughts would be appreciated.

    89. I have been reading through your very informative articles on gerd. i have been studying for a long time (because of issues I had and my husband had). I want to tell you my plan and get your input. My husband was diagnosed with gerd around 13? years ago. He tried different medications and settled on prilosec (omeprazole). At one point he was put on an anti inflammatory pain killer for his shoulder and spent the night throwing up. Years later he went on a low carb diet for weight loss and it was the only time he didn’t need the prilosec. (It cured his heartburn until he went off the diet.) I don’t think he is ready to overhaul his diet right now, although he does eat real food most of the time (he still eats some fast food and loves Chick fil a’s lemonade). He went off the omeprazole and is having some heartburn. Not as much as he would have had before having partially healed from tumeric and real food. I have started him on DGL. I am planning on adding zinc carnosine. After I felt his stomach lining had healed some (maybe after 3 weeks?) I was going to add betaine hcl with pepsin.And then maybe some enzymes. I have also heard good things about using gastrazyme to heal the stomach lining. He is already on vitacost brand probiotics, CodMega fish oil (garden of life), magnesium citrate, alive whole food complex vitamin C. He does have chronic jock itch that does seem to worsen with certain starchy foods. I don’t know if I will have to do anything more-if there are any h pylori or candida issues. Any thoughts would be appreciated.

      • The Jock Itch is definitely a sign of yeast imbalance in a male so he might benefit from the moderate candida protocol on my blog. I would also suggest combining it with the colon cleansing protocol to help try to reset his digestive system in a month. Hopefully after he has completed both protocols his digestion should return to normal Keep me posted.

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