Resolution of Upper Gut (H. pylori) Dysbiosis / Repairing Ulcers

Resolution of Upper Gut (H. pylori) Dysbiosis / Repairing Ulcers

GERD Protocol 2: Reduction of H. pylori

More updated information about H. pylori!

Upper Gut Protocols: Resolution of Upper Gut Dysbiosis / Repairing Ulcers

Upper Gut Dysbiosis

SIBO information and diagnosis has been a strong topic of contention in the natural health blogosphere for years. Many of my current clients, including myself, did not primarily suffer from SIBO and instead had issues that were in our upper gut. What is considered to be our upper gut? The upper gut consists of the oral cavity, tongue, tonsils, esophagus, stomach, and duodenum. The liver, pancreas, and gallbladder might also be affected by dysbiosis of the upper gut.

So what are the many different symptoms of upper gut dysbiosis:

  • GERD
  • LERD
  • Bile reflux
  • Endotoxin reflux
  • Barrett’s esophagus
  • Low stomach acid production and elevated stomach pH
  • Elevated stomach acid production and low resting stomach pH(Zollinger-Ellison syndrome)
  • Belching
  • Upper gut (stomach, duodenum, liver areas) bloating and distension
  • Protein fermentation
  • L-glutamine supplementation issues
  • Hiatal hernia
  • Roemheld syndrome
  • Stomach and duodenal ulcers
  • Gastritis
  • Duodenitis
  • Achalasia1
  • Burning mouth syndrome2
  • Sjogren’s syndrome (H. pylori)3 4
  • Sinus infections5
  • Dental caries6
  • Halitosis7
  • Canker sores8
  • Cold sores9
  • Tinnitus10
  • Ear infections11
  • Visual snow
  • Multiple Sclerosis (H. pylori)12
  • Rheumatoid arthritis (Klebsiella)
  • Ankylosing spondylitis (Klebsiella)
  • Chronic fatigue syndrome (Epstein-Barr virus)13
  • Acne14
  • Rosacea15
  • Elevated hydrogen sulfide (if the overgrowth produces hydrogen sulfide) production
  • Elevated ammonia production
  • Th1 dominance (if you are dealing with Gram-negative, non-histamine producing bacterial overgrowth)
  • Th2 dominance, if the overgrowth produces histamine (asthma, allergies, eczema)
  • Th17 dominance
  • Hypothyroidism16
  • Oral, esophageal, liver, pancreatic, and stomach cancer17 18 19 20
  • Type 1 and Type 2 diabetes21 22
  • Pancreatitis23
  • Gallstones24
  • Bile production issues and improper release
  • Gilbert’s syndrome
  • Cirrhosis25 26
  • Hepatitis27
  • Urinary tract infections(Proteus, E. coli, Klebsiella, Citrobacter, Enterobacter, H. pylori, and Pseudomonas)28
  • Interstitial cystitis(Proteus, Klebsiella, Citrobacter, Enterobacter, and Pseudomonas)
  • Constipation (generally, diarrhea can occur acutely, most people with bacterial upper gut overgrowth also deal with methane dominant archaea in the small intestine or have hydrogen sulfide overgrowth)
  • Diarrhea
  • Adrenal fatigue
  • Vagus nerve dysregulation29
  • Anxiety30
  • Depression31
  • Circadian rhythm disruption and poor sleep32
  • Sleep apnea33

So what organisms can cause dysbiosis within our upper gut(most of these listed might not be able to colonize the stomach if proper low pH and stomach acid production occurs and the duodenum if bile production and conjugation is normal).34 35 36 37 38 39 40

  • Akkermansia
  • Bacteroides
  • Candida
  • Citrobacter
  • Cytomegalovirus
  • Escherichia coli
  • Entamoeba histolytica
  • Enterobacter
  • Enterococcus
  • Epstein-barr virus
  • Giardia
  • Haemophilus
  • Herpes Simplex I and II
  • Hookworm
  • H. pylori
  • Klebsiella
  • Lactobacillus
  • Methanobrevibacter smithii (archaea)
  • Morganella morganii
  • Norovirus
  • Porphyromonas gingivalis
  • Propionibacterium
  • Proteus mirabilis
  • Prevotella
  • Pseudomonas
  • Rothia
  • Schistosoma
  • Staphylococcus
  • Streptococcus
  • Strongyloides stercoralis
  • Yersinia enterocolitica
  • Varicella zoster
  • Veillonella

It can be difficult to test our upper gut for the different supposed overgrowths that can cause digestive issues. I do recommend stool tests like Genova GI Effects, Doctor’s Data Stool Test 3X, or GI Map, but none of them are perfect in detecting upper gut overgrowth because the location of the organs and bacteria being eliminated and cultured properly in a stool test. Your doctor may recommend an endoscope of the esophagus, stomach, and duodenum and a microbe culture from a biopsy to determine the strains that are causing digestive discomfort. It may be difficult to get an accurate culture; the microbes may be transient and not appear in the biopsied area, or the microbiology lab may not be able to culture or detect all of the above organisms and more that may be unknown that could be causing digestive issues in the upper gut. H. pylori are the most commonly known upper gut pathogen and can be very difficult to detect accurately if an overgrowth is present, we need more data on the microbiome of the upper gut.

Hopefully one can use the following in-depth protocol do reduce or eliminate upper gut bacterial overgrowth. There is always a possibility that antibiotics may be needed to reduce upper gut bacterial overgrowth, especially if it becomes systemic and infects the vagus nerve or the brain for example. If you are dealing with Candida overgrowth, then follow my Candida protocol to reduce its overgrowth in the upper gut. If you are dealing with parasites in the upper gut, then follow my anti-parasite protocols to improve your digestive health.

Certain supplements are more localized to the upper-gut, others affect the intestinal or systemic microbiome.

Supplements that would reduce microbiome diversity (possibly systemically for some agents) and should not be used in a first round protocol unless necessary include:

  • Colloidal silver
  • EDTA
  • NAC
  • Oil of oregano
  • Oil of thyme
  • Systemic enzymes

Supplementation Protocol to Reduce Th1 Inducing Upper Gut Bacterial Overgrowth

Part 1: Anti-bacterial Supplements

Depending on the amount of upper gut dysbiosis, multiple agents may be needed to achieve remission.

Recommendations to Improve Oral Microbiome:

  • Oil pulling with either organic extra virgin coconut oil or Californian extra virgin olive oil. Take a tablespoon of either oil and swish in your mouth for fifteen to twenty minutes daily. Spit out oil after swishing. Then brush your teeth and swish your mouth out. Add a couple of drops of either cinnamon bark oil or orange oil to help further reduce overgrowth.

Supplements to Reduce Overgrowth in the Stomach and Duodenum:

  • Berberine – take two capsules, twice daily.41
  • Bismuth – do not use if you have intestinal bleeding, salicylate sensitivity, or are suffering from ulcers. Maybe, very useful for people with hydrogen sulfide upper gut overgrowth.
  • 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. Supplement with capsules if the esophagus is inflamed.
  • Allicin-C – two to eight capsules daily in divided doses with food.42
  • Black cumin seed oil – one tsp. with breakfast and one with dinner. Supplement with capsules if the esophagus is inflamed.
  • D-limonene – one soft gel, twice daily with food.
  • Mastic gum – two capsules, twice daily with food.43

Supplements Only to be Used For Severe Cases of Dysbiosis:

  • Sodium butyrateWARNING, Butyrate lysis’s most upper gut overgrowth on contact, therefore, it may cause severe gastritis in some people from massive die off and endotoxin release. Might be best to be used with zinc carnosine to help protect the mucosal lining and only taken with food.44
  • Colloidal silver (Mesosilver) – follow supplement bottle recommendations.

Supplements to Reduce Biofilm Formation for Someone with Th1 Upper gut Overgrowth

  • Lactoferrin – one to four grams daily, in divided doses with food.45
  • Interphase plus – one to two capsules, on an empty stomach, twice daily.
  • NAC – (should only be used in severe upper gut or systemic overgrowth), 600 mg, twice daily with food.46

Part 3: Supplements That Reduce Th1 Dominance, Improve Upper Gut Digestion, and Rebuild the Microbiome47

  • Proper Omega 3 intake.
  • Thorne Curcumin – two capsules with breakfast.
  • Boswellia – one capsule with breakfast and one with dinner.
  • Olive leaf – one – two capsules, twice daily with food.
  • Immunoglobulin Y – follow supplement instructions, only studied use for H. pylori.48
  • EGCG – one – two capsules, twice daily with food.
  • Zinc carnosine – two capsules, three times daily with food. If you are using another brand 40 – 50 mg of zinc from zinc carnosine total, daily in divided doses.
  • Acupuncture and CBD oil may help relieve Th1 dominance.
  • Proper sunlight exposure should reduce Th1 dominance.
  • Ingest fermented vegetables like organic sauerkraut and kimchi, daily.
  • Betaine HCL – in some people reducing stomach pH may cause severe inflammation from increased endotoxin production from H. pylori and increased burrowing of the bacteria into the mucosal barrier. Use with caution in systemic stomach overgrowth, or if you have ulcers/gastritis.
  • I recommend the usage of digestive enzymes or digestive bitters to improve upper gut digestion.

Supplementation Protocol to Reduce Th2 Inducing Upper Gut Bacterial Overgrowth

Part 1: Anti-bacterial Supplements

Depending on the amount of upper gut dysbiosis, multiple agents may be needed to achieve remission.

Recommendations to Improve Oral Microbiome:

  • Oil pulling with Californian extra virgin olive oil. Take a tablespoon of either oil and swish in your mouth for fifteen to twenty minutes daily. Spit out oil after swishing. Then brush your teeth and swish your mouth out. Add a couple of drops of clove oil help further reduce overgrowth.

Supplements to Reduce Overgrowth in the Stomach and Duodenum:

  • Berberine – take two capsules, twice daily.49
  • Allicin-C – two to eight capsules daily in divided doses with food.50
  • Bismuth (devrom only) – do not use if you have intestinal bleeding or are suffering from ulcers. Maybe, very useful for people with hydrogen sulfide upper gut overgrowth.
  • Manuka honey51
  • Black cumin seed oil – one tsp. with breakfast and one with dinner. Supplement with capsules if the esophagus is inflamed.
  • Clove oil – take one drop in one tsp. of extra virgin olive oil (if you have issues with salicylates, mix it in ghee) twice daily. Supplement with capsules if esophagus is inflamed.52

Supplements Only to be Used For Severe Cases of Dysbiosis:

Part 2: Supplements That Reduce Biofilm Formation

  • Lactoferrin – one to four grams daily, in divided doses with food.
  • Interphase plus – one to two capsules, on an empty stomach, twice daily.
  • NAC – (Should only be used in severe upper gut or systemic overgrowth), 600 mg, twice daily with food.

Part 3: Supplements That Reduce Th2 Histamine Intolerance, Improve Upper Gut Digestion, and Rebuild the Microbiome53

  • Liposomal Colostrum – one tbsp. mixed in filtered water, consumed at breakfast.
  • GutPro Capsules – one – two capsules before bed. Use filtered or bottled water when ingesting.
  • Supplement with glutathione to see if it helps your histamine issues as long as you do not have any mercury amalgams or have tested positive for elevated mercury recently.
  • Sodium ascorbate – take 3,000 mg, two to three times daily.
  • Quercetin (use with caution if you have a COMT mutation) – one capsule on an empty stomach, twice daily.
  • Ingest freshly grated ginger or consume ginger tea once daily.
  • If needed ask your doctor for a prescription for the mast cell stabilizer, cromoglicic acid.
  • DGL licorice may also help to relieve histamine issues.
  • Supplement with magnesium or B12 if you are deficient.
  • Avoid a diet heavy in medium chain triglycerides (coconut oil, mct oil, or Brain Octane oil). If you are suffering from Th2/Th17, these oils may sensitize your gut to histamine, causing further intolerance issues and poor digestion.
  • Betaine HCL – in some people increasing stomach acid production may cause severe inflammation from increased endotoxin production from H. pylori and increased burrowing of the bacteria into the mucosal barrier. Use with caution in systemic stomach overgrowth, or if you have ulcers/gastritis.
  • I recommend the usage of digestive enzymes to improve upper gut digestion.

Choose either arabinogalactan or GOS to help rebuild your microbiome:

  • Arabinogalactan – one scoop mixed in filtered water, consumed at breakfast with the colostrum.
  • Galactomune – one scoop daily mixed well with filtered water at breakfast.

Supplementation Protocol to Reduce Th17 Inducing Upper Gut Bacterial Overgrowth

Part 1: Anti-bacterial Supplements

Depending on the amount of upper gut dysbiosis, multiple agents may be needed to achieve remission.

Recommendations to Improve Oral Microbiome:

  • Oil pulling with either organic extra virgin coconut oil or Californian extra virgin olive oil. Take a tablespoon of either oil and swish in your mouth for fifteen to twenty minutes daily. Spit out oil after swishing. Then brush your teeth and swish your mouth out. Add a couple of drops of either cinnamon bark oil or orange oil to help further reduce overgrowth.

Supplements to Reduce Overgrowth in the Stomach and Duodenum:

  • Berberine – take two capsules, twice daily.
  • Bismuth – do not use if you have intestinal bleeding, salicylate sensitivity, or are suffering from ulcers. Maybe, very useful for people with hydrogen sulfide upper gut overgrowth.
  • 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. Supplement with capsules if the esophagus is inflamed.
  • Allicin-C – two to eight capsules daily in divided doses with food.
  • Black cumin seed oil – one tsp. with breakfast and one with dinner. Supplement with capsules if the esophagus is inflamed.
  • D-limonene – one soft gel, twice daily with food.
  • Mastic gum – two capsules, twice daily with food.

Supplements Only to be Used For Severe Cases of Dysbiosis:

  • Colloidal silver (Mesosilver) – follow supplement bottle recommendations.

Supplements to Reduce Biofilm Formation for Someone with Th17 Upper gut Overgrowth

  • Lactoferrin – one to four grams daily, in divided doses with food.
  • Interphase plus – one to two capsules, on an empty stomach, twice daily.
  • NAC – (should only be used in severe upper gut or systemic overgrowth), 600 mg, twice daily with food.

Part 3: Supplements That Reduce Th17 Dominance, Improve Upper Gut Digestion, and Rebuild the Microbiome54

  • Proper Omega 3 intake.
  • Thorne Curcumin – two capsules with breakfast.
  • Boswellia – one capsule with breakfast and one with dinner.
  • Olive leaf – one – two capsules, twice daily with food.
  • Immunoglobulin Y – follow supplement instructions, only studied use for H. pylori.
  • EGCG – one – two capsules, twice daily with food.
  • Zinc carnosine – two capsules, three times daily with food. If you are using another brand 40 – 50 mg of zinc from zinc carnosine total, daily in divided doses.
  • Acupuncture and CBD oil may help relieve Th17 dominance.
  • Proper sunlight exposure should reduce Th17 dominance.
  • Ingest fermented vegetables like organic sauerkraut and kimchi, daily.
  • Betaine HCL – in some people reducing stomach pH may cause severe inflammation from increased endotoxin production from H. pylori and increased burrowing of the bacteria into the mucosal barrier. Use with caution in systemic stomach overgrowth, or if you have ulcers/gastritis.
  • I recommend the usage of digestive enzymes or digestive bitters to improve upper gut digestion.

H. pylori Harm Reduction Medication List:

Here is a list of believed safer medications that can be used to tackle H. pylori overgrowth or issues, ask your doctor about developing a regimen from this list. Some of these antibiotics may work with upper gut bacterial overgrowth.

  • Amoxicillin
  • Bismuth
  • H2 antagonist (may increase growth in the stomach by reducing stomach acid production, but, decreases histamine and may be needed to help recover from gastritis or ulcers, better than PPI, Pepcid is the best one to use.)
  • Tetracycline
  • Third generation cephalosporin

Other antibiotics that have more issues associated with their use:

  • Flagyl
  • Macrolide antibiotics (Clarithromycin for example) – supplementing with magnesium, ubiquinol, and pqq, may help prevent mitochondrial toxicity issues.
  • Rifabutin

Medications to definitely avoid if possible:

  • Fluoroquinolones – supplementing with magnesium, ubiquinol, and pqq, may help prevent mitochondrial toxicity issues.
  • PPI’s

Ulcer

Peptic ulcers are mostly caused by a H. pylori opportunistic infection. Stomach ulcers can also be caused by NSAID use, infections, chronic gastritis, and cancer. The parts of the digestive system, where a person can get an ulcer, is the duodenum, esophagus, stomach, and the diverticulum.55

The most common symptoms of an ulcer are abdominal pain (stomach ulcer during eating, duodenal ulcer is usually three hours after a meal), bloating or a sense of fullness, rush of saliva during pain, nausea, vomiting, vomiting of blood, and melena (tarry, dark stools). If an ulcer is left untreated, a perforation can occur (hole in the stomach), which becomes a medical emergency and must be surgically treated immediately (because of the chance of massive infection and inflammation from bacteria and gastric juice outside the stomach). The main symptom of a perforation is an extreme stabbing pain in the abdomen and fever. 56

Most ulcers are diagnosed based on clinical symptoms. But endoscopies and barium X-rays can also be used to diagnose an ulcer.57

Healing a Ulcer (Supplementation)

Zinc carnosine and L-glutamine have been shown in countless studies to repair the stomach and gut lining.

DGL licorice has been shown to heal and protect the stomach lining in multiple studies.

Zinc carnosine is prescribed in Japan to treat ulcers, and DGL is prescribed in Germany to treat ulcers.

Healing a Ulcer (Herbal)

Marshmellow, DGL extract, slippery elm, aloe vera, help coat and protect the stomach lining.

Chamomile help heal inflammation and stimulate the immune system.

 

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67 Comments
  1. Your article is very helpful. I have histamine intolerance and as it gets worse, I have a lot of reflux and food intolerances increase. I’ve been pushing back the bacteria with Biocidin and it helps but it doesn’t remove it all. I started taking cinnamon oil and black seed and it’s helping too.

    Two days ago, I added mastic gum. (Both my kids have h.pylori sp I may have it too). It causes a burning in my stomach, about 2″ above the navel and takes about 4-5 hours to go away. I can’t find much online about it, but your article stated something about Betaine HCl causing inflammation and endotoxin release as the bacteria die. I’m wondering if this could be a die-off reaction. I don’t normally have gastritis, but my foods are also limited.
    I feel the mastic is helping as it’s slowing my leg tremors (histamine symptom), but the stomach pain is an unknown. Could this be what is happenning? Any explanation for why mastic gum would cause gastritis? And what can I do about it?

  2. Should you use all part (1-2-3) supplements at the same time? Or do it respectively?

  3. Dear John. AMAZING work. Thank you ever so much!

    A few things to ask:

    1. Is Berberine HCl going to cause burrowing as would Betaine HCl? They don’t have the berberine plant complex you recommend in the UK. Would you recommend a strong GoldenSeal rather than Berberine Hcl?

    2. Do you have any info about H. Pylori being able to use fatty acids as a fuel source? I am a nutritionist and have had some success with a “no simple sugars, complex high fiber starch + no fats” diet. This: https://ufile.io/r3bfi is a description of the HP metabolism and it says that HP may be able to use fats (as well as glucose) as an energy source. Care to share your thoughts?

  4. Would you clarify: For Th2 dominance only olive oil and not coconut should be used for oil pulling? Wording is confusing as it mentions “either” can be used but only olive is listed.

  5. Why the caution with NAC? I have been taking it almost every day to increase glutathione levels.
    Also, I had my microbiome tested by UBiome and it came back normal for lactobacillus and Bifido organisms, does that mean I don’t have SIBO?
    It did come up negative for some organisms I’ve never heard of so no way to supplement unless they were soil based organisms

  6. Hi John,
    Thank you for putting up such detailed information, the effort you’ve put in is much appreciated. I’ve just been reading your book which is very informative, but a little confused about the H Pylori reduction protocol. Do you recommend taking 1 supplement from each part (1, 2, 3, and 4) or could you start off only taking one and then add more as needed? I was thinking of taking oil of oregano, berberine, lactoferrin, S. Boulardii, and Mastic gum for two weeks, would that be a sufficient protocol? Also I’ve heard of people needing to take supplements for 1 to 2 months; what is your opinion on that? Cheers

    • You should try to take one from each category and more maybe needed from each category depending on the status of the protocol. It might be supplement wise, but you might need to increase the dosage. Some people have followed different protocols for months before they are able to find the right one.

  7. You suggested taking Mastic gum WITH food but in the linked study it was taken before breakfast suggesting that it might be better to take it on the empty stomach. Do you have more info on this?

    • The only reason I suggest to take it with food is so that it does not irritate the stomach lining, it is a general recommendation in my protocol and book. It is best to take on an empty stomach if possible.

  8. Wow, I am glad I stumbled on your comment that Butyrate can cause gastritis as a die-off symptom. I have had my gastritis controlled for a few months now, but when I started taking Butyrate it returned. I tested negative for H Pylori on both a stool and blood test, but I also hear it is hard to diagnose. Looks like I had H pylori after all. Should I continue with the Butyrate, since it does seem to be doing something? Thanks!

    • Reduce the dose if possible and see if it lessens the gastritis flare.

    • I tested several time negative for H pylori, with breath test and stool test (DNA) every time it came back negative. I always wanted to check Hpylori because something said that I should. It is only when I try GI Map that I saw I had H Pylori. The virulent factor CagA came positive and the normal H Pylori strain was normal. So there is a lot of false positive in my view with these conventional tests. Even with Genova it came out twice negative.

  9. Most/all probiotics indicate to be taken with water. What do you think about this article indicating milk might increase absorption?
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4542224/

    • It would make since for L. casei because it is used to ferment dairy and dairy contains all it needs to survive. Milk to increase probiotic delivery may not work properly in strains that cannot ferment lactose. In addition, many people find that they have issues with digesting dairy, which may cause the body to upregulate the immune system which would reduce probiotic growth and facilitate leaky gut.

  10. What do you say about the side effects of the triple therapy (french or italian)?

    Do the given antibiotics destroy bacteria in the small intestine, too? (in case of someone dealing with h pylori and sibo at the same time; would it be hitting two birds with one stone?)

    • It depends on the antibiotic. Some like Rifixamin are strictly used available in the stomach and small intestine. Most antibiotics are systemic in the fact the effect most of the body except the brain (some cross the BBB.)

  11. Have you read The Missing Microbes by Martin Glaser.? His studies point to the fact that h. Pylori is protective against GERD, even thoughnit seems to be causative for ulcers and stomach cancer.

    • Glaser is correct as long as the H. pylori is at normal flora levels in the stomach. When it becomes opportunistic on the other hand it decreases stomach acid, food is poorly digested, and cause gas build up and stomach pressure which causes GERD.

      • What are normal levels of H. pylori, and how are they measured?

        • It is almost impossible to rid the body of H. pylori completely after one is infected with it. Normal flora levels of H. pylori would be levels that did not cause any digestive issues. There are no ways to test yet for this because all methods of testing are either antibody tests for infection or urea breath tests for an overpopulation of bacteria.

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