Resolution of Upper Gut (H. pylori) Dysbiosis – Updated 2023

by | Mar 13, 2023 | Digestive Health, GERD, LPR/LERD, Reflux, Upper gut | 29 comments

gerd-treatment-protocol-2-elimination-of-opportunstic-h-pylori

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

Small intestinal bacterial overgrowth (SIBO) information and diagnosis have 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 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 upper gut dysbiosis.

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 from microorganism buffering of stomach acid
  • Elevated stomach acid production and low resting stomach pH(Zollinger-Ellison syndrome)
  • Belching
  • Dyspepsia (indigestion)
  • Upper gut (primarily underneath your ribcage, above your belly button) bloating and distension
  • Digestive symptoms occur when eating food sources that contain elevated amounts of protein (steak, for example) or when consuming excessive amounts of sugar
  • 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 sores (H. pylori)8
  • Cold sores (Herpes simplex 1)9
  • Tinnitus10
  • Ear infections11
  • Visual snow
  • Brain fog, mental cognition issues
  • Migraines
  • Multiple Sclerosis (H. pylori)12
  • Rheumatoid arthritis (Klebsiella)
  • Ankylosing spondylitis (Klebsiella)
  • Hellp syndrome (Preeclampsia) (H. pylori)
  • Raynaud’s phenomenon (H. pylori)
  • Chronic fatigue syndrome (Epstein-Barr virus)13
  • Acne14
  • Rosacea15
  • Elevated hydrogen sulfide (if the dysbiosis produces hydrogen sulfide) production
  • Elevated ammonia production
  • Th1 dominance (if you are dealing with Gram-negative, non-histamine producing bacterial dysbiosis)
  • Th2 dominance (histamine intolerance, mast cell activation disorder), primarily if the dysbiosis produces histamine
  • 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 deconjugation of bile, leading to yellow or pale stool and rectal burning
  • 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 dysbiosis)
  • Constipation (generally, diarrhea can occur acutely, most people with bacterial upper gut dysbiosis also deal with methane dominant archaea in the small intestine or have hydrogen sulfide dysbiosis)
  • Diarrhea
  • Adrenal fatigue
  • Vagus nerve dysregulation29
  • Anxiety30
  • Depression31
  • Circadian rhythm disruption and poor sleep32
  • Sleep apnea33

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
  • Hookworms
  • 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

Testing our upper gut for the different supposed dysbiotic microbes that can cause digestive issues can be challenging. 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 dysbiosis because the upper anatomical location of the organs and the microorganisms being eliminated through our stool and being able to be 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 microorganisms 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 untested microorganisms that could be causing digestive issues within our upper gut. H. pylori are the most commonly known upper gut pathogen and can be very difficult to detect dysbiosis accurately. We need more data on the microbiome composition of our upper gut.

Antibiotics may be needed to relieve upper gut bacterial dysbiosis, especially if it becomes systemic and infects our vagus nerve or organs, including our brain. One can use the following in-depth protocol to reduce or relieve upper gut bacterial dysbiosis. If you are dealing with Candida dysbiosis, then follow my Candida protocol to hopefully find relief. If you are dealing with parasitical dysbiosis in your upper gut, then I recommend following my anti-parasite protocols to hopefully improve your digestive health.

Certain supplements are more localized to the upper-gut, while others affect your 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 (ethylenediaminetetraacetic acid)
  • NAC (N-acetyl cysteine)
  • Oil of oregano
  • Oil of thyme
  • Systemic enzymes

Please discuss any protocol or information given in the following with your healthcare professional before taking my advice.

Supplementation Protocol to Relieve Th1 Inducing Upper Gut Bacterial Dysbiosis

Part 1: Anti-bacterial Supplements

Multiple agents may be needed to achieve remission depending on the severity of your upper gut dysbiosis.

Recommendations to Improve Your 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 it in your mouth for fifteen to twenty minutes daily. Spit out the oil after swishing. Then brush your teeth and swish your mouth out. Add a couple of drops of either organic cinnamon bark essential oil or organic orange essential oil to help further relieve dysbiosis.

Supplements to Relieve Stomach and Duodenum Dysbiosis:

  • 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 dysbiosis.
  • Ceylon cinnamon oil – take one to three drops in one teaspoon of extra virgin coconut oil or extra virgin olive oil, twice daily. Use with caution if you have hypoglycemia. Supplement with capsules if your esophagus is inflamed.
  • Allicin-C – take two to eight capsules daily in divided doses with food. Use with caution if suffering from hydrogen sulfide dysbiosis.42
  • Black cumin seed oil – take one teaspoon with breakfast and one with dinner. Supplement with soft gels if your esophagus is inflamed.
  • D-limonene – take one soft gel, twice daily with food.
  • Mastic gum – take two capsules, twice daily with food.43
  • Pylopass – take one to two capsules, daily with food.
  • Lauricidin – swallow one fourth of a teaspoon of mini-pellets with filtered water, two times daily after meals. Can increase to one teaspoon, two times daily after meals if needed.

Supplements Only to be Used For Severe Cases of Dysbiosis:

  • Sodium butyrate – WARNING, Butyrate lysis’s many upper gut dysbiotic microbes on contact. Therefore, it may cause severe gastritis from massive die-off and endotoxin release in some people. It is best to use zinc carnosine with sodium butyrate to help protect the stomach mucosal lining and only take it with food
  • 44
  • Colloidal silver (Mesosilver) – follow supplement bottle recommendations.

Part 2: Supplements to Reduce Biofilm Formation for Someone with Th1 Upper gut Dysbiosis

  • Lactoferrin – take one to four grams daily, in divided doses with food.45
  • Interphase plus – take one to two capsules, on an empty stomach, twice daily.
  • NAC – (should only be used in severe upper gut or systemic dysbiosis), take 600 milligrams, twice daily with food. Avoid if dealing with hydrogen sulfide dysbiosis.46

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

  • Proper Omega 3 intake is important.
  • Thorne curcumin – two capsules with breakfast. Supplement with caution if you suffer from hydrogen sulfide dysbiosis.
  • Boswellia – take one capsule with breakfast and one with dinner.
  • Olive leaf extract – take one to two capsules, twice daily with food.
  • Immunoglobulin Y – follow supplement instructions, mainly studied for its effectiveness against H. pylori.48
  • EGCG – take one to two capsules, daily with food. Elevated long term doses of EGCG might cause liver damage. Do not take more than five hundred milligrams daily for longer than two weeks without the monitoring of a health care professional and monthly liver health blood testing.
  • Zinc carnosine – take two capsules, three times daily with food. If you are using another brand forty to fifty milligrams of zinc from zinc carnosine total, daily in divided doses.
  • Acupuncture and CBD oil may help relieve Th1 dominance. CBD oil is also effective against many upper gut dysbiotic causing bacteria.
  • Proper sunlight exposure should relieve Th1 dominance.
  • Supplement with magnesium or B12 if you are deficient.
  • Ingest fermented vegetables like organic sauerkraut and kimchi, daily as long as you are not suffering from hydrogen sulfide dysbiosis.
  • Reduce hydrogen sulfide (if the dysbiosis produces hydrogen sulfide) production and improve its metabolism.
  • Reduce ammonia production and improve its metabolism.
  • 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 if you have severe stomach dysbiosis, are suffering from hydrogen sulfide dysbiosis, or if you have ulcers/gastritis.
  • I recommend the usage of digestive enzymes or digestive bitters to improve upper gut digestion.

Supplementation Protocol to RelieveTh2 Inducing Upper Gut Bacterial Dysbiosis

Part 1: Anti-bacterial Supplements

Multiple agents may be needed to achieve remission depending on the severity of your upper gut dysbiosis.

Recommendations to Improve Oral Microbiome:

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

Supplements to Relieve Stomach and Duodenum Dysbiosis:

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

Supplements Only to be Used For Severe Cases of Dysbiosis:

Part 2: Supplements to Reduce Biofilm Formation for Someone with Th2 Upper gut Dysbiosis

  • 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 when suffering from severe upper gut or systemic dysbiosis), take six hundred milligrams, twice daily with food. Avoid if suffering from hydrogen sulfide dysbiosis.

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

  • Liposomal colostrum – take one tablespoon mixed in with filtered water, and consumed at breakfast.
  • GutPro capsules – take one to two capsules before bed. Take with filtered or bottled water.
  • Supplement with glutathione to see if it helps your histamine issues as long as you do not suffer from hydrogen sulfide dysbiosis, have any mercury amalgams in your oral cavity, or have tested positive for elevated mercury.
  • Sodium ascorbate – take 3,000 milligrams, two to three times daily.
  • Quercetin (use with caution if you have a COMT V158 mutation or suffer from hypothyroidism) – take 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.
  • Reduce ammonia production and improve its metabolism.
  • 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 if you have severe stomach dysbiosis, are suffering from hydrogen sulfide dysbiosis, or if you have ulcers/gastritis.
  • I recommend using digestive enzymes to improve upper gut digestion.
  • Follow a low histamine diet.

Choose either arabinogalactan or GOS to help rebuild your microbiome:

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

Supplementation Protocol to Relieve Th17 Inducing Upper Gut Bacterial Dysbiosis

Part 1: Anti-bacterial Supplements

Multiple agents may be needed to achieve remission depending on the severity of your upper gut dysbiosis.

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 it in your mouth for fifteen to twenty minutes daily. Spit out the 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 relieve dysbiosis.

Supplements to Relieve Stomach and Duodenum Dysbiosis:

  • 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 dysbiosis.
  • Ceylon cinnamon oil – take one to three drops in one teaspoon of extra virgin coconut oil or extra virgin olive oil, twice daily. Use with caution if you have hypoglycemia. Supplement with capsules if your esophagus is inflamed.
  • Allicin-C – take two to eight capsules daily in divided doses with food. Do not use if you are suffering from hydrogen sulfide dysbiosis.
  • Black cumin seed oil – one teaspoon with breakfast and one with dinner. Supplement with capsules if your esophagus is inflamed.
  • D-limonene – take one soft gel, twice daily with food.
  • Mastic gum – take two capsules, twice daily with food.
  • Pylopass – take one to two capsules, daily with food.

Supplements Only to be Used For Severe Cases of Dysbiosis:

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

Part 2: Supplements to Reduce Biofilm Formation for Someone with Th17 Upper gut Dysbiosis

  • Lactoferrin – take one to four grams daily, in divided doses with food.
  • Interphase plus – take one to two capsules, on an empty stomach, twice daily.
  • NAC – (should only be used in severe upper gut or systemic dysbiosis), take 600 milligrams, twice daily with food. Do not use if suffering from hydrogen sulfide dysbiosis.

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

  • Proper Omega 3 intake.
  • Thorne curcumin – take two capsules with breakfast. Supplement with caution if you suffer from hydrogen sulfide dysbiosis.
  • Boswellia – take one capsule with breakfast and one with dinner.
  • Olive leaf – take one to two capsules, twice daily with food.
  • Immunoglobulin Y – follow supplement instructions, mainly studied for its effectiveness against H. pylori.
  • EGCG – take one to two capsules, daily with food. Elevated long term doses of EGCG might cause liver damage. Do not take more than five hundred milligrams daily for longer than two weeks without the monitoring of a health care professional and monthly liver health blood testing.
  • Zinc carnosine – two capsules, three times daily with food. If you are using another brand 40 to 50 milligrams of zinc from zinc carnosine total, daily in divided doses.
  • Acupuncture and CBD oil may help relieve Th17 dominance. CBD oil is also effective against many upper gut dysbiotic causing bacteria.
  • Proper sunlight exposure should relieve Th17 dominance.
  • Supplement with magnesium or B12 if you are deficient.
  • Ingest fermented vegetables like organic sauerkraut and kimchi, daily. Consume with caution if you suffer from hydrogen sulfide dysbiosis.
  • Reduce hydrogen sulfide (if the dysbiosis produces hydrogen sulfide) production and improve its metabolism.
  • Reduce ammonia production and improve its metabolism.
  • 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 if you have severe stomach dysbiosis, are suffering from hydrogen sulfide dysbiosis, or if you have ulcers/gastritis.
  • I recommend using 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 dysbiosis, ask your doctor about developing a regimen from this list. Some of these antibiotics may work with upper gut bacterial dysbiosis.

  • Amoxicillin
  • Bismuth
  • H2 antagonist (may worsen stomach dysbiosis 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 H2 antagonist to use, imo)
  • 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

Ulcers

The digestive system parts where a person can get an ulcer are the duodenum, esophagus, stomach, and diverticulum. An opportunistic H. pylori infection primarily causes peptic ulcers. Stomach ulcers can also be caused  other types of microbial dysbiosis, chronic gastritis, alcoholism, turmeric, curcumin consumption, especially on an empty stomach, certrain medications (mainly NSAIDS (not Tylenol) and Fosamax), and cancer.55

The most common symptoms of an ulcer are abdominal pain (stomach ulcer during eating, a 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 stomach or duodenal 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 our stomach and gut lining.

DGL licorice has been shown to heal and protect our 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 our stomach lining.

Chamomile helps to relieve inflammation and stimulate our immune system.

See more from this series:

  1. https://www.ncbi.nlm.nih.gov/pubmed/15325006 ↩
  2. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4123373/ ↩
  3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3643302/ ↩
  4. https://www.ncbi.nlm.nih.gov/pubmed/15797493 ↩
  5. Neville BW, Damm DD, Allen CM, Bouquot JE. Oral & maxillofacial pathology (3rd ed.), Philadelphia: W.B. Saunders. pp. 331–36. ↩
  6. Neville BW, Damm DD, Allen CM, Bouquot JE. Oral & maxillofacial pathology (3rd ed.), Philadelphia: W.B. Saunders. pp. 331–36. ↩
  7. Neville BW, Damm DD, Allen CM, Bouquot JE. Oral & maxillofacial pathology (3rd ed.), Philadelphia: W.B. Saunders. pp. 331–36. ↩
  8. Neville BW, Damm DD, Allen CM, Bouquot JE. Oral & maxillofacial pathology (3rd ed.), Philadelphia: W.B. Saunders. pp. 331–36. ↩
  9. Neville BW, Damm DD, Allen CM, Bouquot JE. Oral & maxillofacial pathology (3rd ed.), Philadelphia: W.B. Saunders. pp. 331–36. ↩
  10. https://www.ncbi.nlm.nih.gov/pubmed/557156 ↩
  11. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4177463/ ↩
  12. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480172/ ↩
  13. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2776035/ ↩
  14. https://perfecthairhealth.com/p-acnes-bacteria-may-cause-hair-loss-heres-what-to-do-about-it/ ↩
  15. https://www.ncbi.nlm.nih.gov/pubmed/12224687 ↩
  16. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2695884/ ↩
  17. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2952980/ ↩
  18. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3968118/ ↩
  19. https://www.ncbi.nlm.nih.gov/pubmed/28676707 ↩
  20. https://academic.oup.com/carcin/article/34/10/2193/2464011 ↩
  21. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4000497/ ↩
  22. https://academic.oup.com/jcem/article-abstract/102/5/1468/2926660?redirectedFrom=fulltext ↩
  23. http://www.annalsgastro.gr/files/journals/1/articlessos/4/submission/editor/4-16-1-ED.pdf ↩
  24. https://www.ncbi.nlm.nih.gov/pubmed/23736795 ↩
  25. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4766259/ ↩
  26. https://www.ncbi.nlm.nih.gov/pubmed/23216382 ↩
  27. http://www.merckmanuals.com/home/liver-and-gallbladder-disorders/hepatitis/acute-viral-hepatitis ↩
  28. https://www.ncbi.nlm.nih.gov/books/NBK8035/ ↩
  29. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4017036/ ↩
  30. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4017036/ ↩
  31. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4017036/ ↩
  32. https://www.ncbi.nlm.nih.gov/pubmed/21673361 ↩
  33. https://www.ncbi.nlm.nih.gov/pubmed/19417972 ↩
  34. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780057/ ↩
  35. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137784 ↩
  36. https://www.ncbi.nlm.nih.gov/pubmed/25865706 ↩
  37. http://journals.lww.com/jpgn/Abstract/2017/05000/Analysis_of_the_Duodenal_Microbiome_in_Autistic.12.aspx ↩
  38. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480535/ ↩
  39. Bauman, Robert. Microbiology with Diseases by Body System, Benjamin Cummins, September 12, 2012. ↩
  40. Black, Jacquelyn. Microbiology: Principles and Explorations, Wiley, May 1, 2012. ↩
  41. https://selfhacked.com/blog/berberine-19-health-benefits-of-berberine-with-references/ ↩
  42. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5052411/ ↩
  43. https://www.ncbi.nlm.nih.gov/pubmed/19879118 ↩
  44. http://www.ncbi.nlm.nih.gov/pubmed/22194341 ↩
  45. http://www.ncbi.nlm.nih.gov/pubmed/14620619 ↩
  46. https://www.ncbi.nlm.nih.gov/pubmed/25339490 ↩
  47. https://selfhacked.com/blog/supplements-people-th1-dominant/ ↩
  48. https://www.ncbi.nlm.nih.gov/pubmed/15298626 ↩
  49. http://www.anaturalhealingcenter.com/documents/Thorne/articles/helicobacter_pylori.pdf ↩
  50. http://www.anaturalhealingcenter.com/documents/Thorne/articles/helicobacter_pylori.pdf ↩
  51. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3609166/ ↩
  52. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3769004/ ↩
  53. https://selfhacked.com/blog/supplements-people-th2-dominant/https://selfhacked.com/blog/deal-histamine/ ↩
  54. https://selfhacked.com/blog/th17/ ↩
  55. Beers, Mark. The Merck Manual, Merck Research Laboratories, 2006 ↩
  56. Beers, Mark. The Merck Manual, Merck Research Laboratories, 2006 ↩
  57. Beers, Mark. The Merck Manual, Merck Research Laboratories, 2006 ↩
  58. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1856764/ ↩
  59. http://naturalmedicinejournal.net/pdf/nmj_nov09lr_kaczor.pdf ↩
  60. http://www.ncbi.nlm.nih.gov/pubmed/2632514 ↩
  61. http://www.bidmc.org/News/InResearch/2009/May/StomachUlcers.aspx ↩
  62. Balch, Phyllis. Prescription for Herbal Healing, Avery Publishing, 2012. ↩
  63. Balch, Phyllis. Prescription for Herbal Healing, Avery Publishing, 2012. ↩
  64. Balch, Phyllis. Prescription for Herbal Healing, Avery Publishing, 2012. ↩
  65. Balch, Phyllis. Prescription for Herbal Healing, Avery Publishing, 2012. ↩

29 Comments

  1. Alexandro Lindgren
    Alexandro Lindgren on March 27, 2024 at 12:59 pm

    Fantastic site A lot of helpful info here Im sending it to some buddies ans additionally sharing in delicious And naturally thanks on your sweat

    Reply
  2. Carol
    Carol on January 12, 2023 at 5:35 pm

    John,
    I have been dealing with many problems for 1 1/2 years. Saw ENT, GI, DC, now NP. Now my teeth are affected. LPR, GERD, diarrhea, hpylori, dysbiosis. Had Modified Barium Swallow test today. Too much to write here. I have not slept one night in over a year. Do you think you can help me?

    Reply
  3. JJ
    JJ on October 1, 2020 at 11:42 pm

    That sodium butyrate supplement on Amazon. Is it truly sodium butyrate? I saw reviews there mentioning that it’s Sodium and Butyrate, not sodium butyrate.

    Reply
  4. Neha
    Neha on August 24, 2020 at 7:23 am

    Does it matter if it’s sodium ascorbate or ester-c or quali-c? Any vit c should be equally effective?

    Reply
  5. David
    David on November 20, 2019 at 3:01 pm

    I think American habit of drinking huge cup of Coke (or whatever) with almost every meal is what leads to upper gut dysbiosis in many (if not most) cases.

    Reply
  6. Corinne
    Corinne on April 27, 2019 at 10:05 pm

    Thank you for this amazing information! Can NAC be used with any herbal antimicrobial? Thanking you in advance.
    Kind regards
    Corinne

    Reply
  7. Olivia
    Olivia on October 22, 2018 at 1:38 pm

    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?

    Reply
  8. boran can
    boran can on August 6, 2018 at 8:52 am

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

    Reply
    • John Brisson
      John Brisson on October 3, 2018 at 11:15 pm

      You can do them at the same time.

      Reply
  9. Sebastian
    Sebastian on January 31, 2018 at 8:56 am

    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?

    Reply
  10. Domagoj Podnar
    Domagoj Podnar on December 8, 2017 at 10:16 am

    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.

    Reply
  11. steve
    steve on November 17, 2017 at 11:03 pm

    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

    Reply
  12. Jenny
    Jenny on April 3, 2017 at 1:42 am

    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

    Reply
    • John Brisson
      John Brisson on April 20, 2017 at 12:20 am

      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.

      Reply
  13. Domagoj
    Domagoj on February 15, 2017 at 11:48 am

    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?

    Reply
    • John Brisson
      John Brisson on March 8, 2017 at 12:57 am

      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.

      Reply
  14. Rebecca
    Rebecca on November 2, 2016 at 6:16 pm

    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!

    Reply
    • John Brisson
      John Brisson on November 10, 2016 at 10:06 am

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

      Reply
    • anne maisonneuve
      anne maisonneuve on December 11, 2017 at 6:37 am

      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.

      Reply
      • anne maisonneuve
        anne maisonneuve on December 11, 2017 at 6:38 am

        I meant false negative not positive.

        Reply
        • Deb
          Deb on October 27, 2019 at 1:12 pm

          I found this information to be very helpful but I do have a question about my particular case. My breath test was hydrogen dominate but my symptoms are more like IBS-C. I’ve been taking the regimen from Bio-Botanical Research with low fodmap which I’ve seen great improvement in a lot of aspects of my health when I started it but I was still suffering from bad constipation. A few weeks in, I had a bout of foul gas for the first time since my protocol and was so confused. I worried the regimen wasn’t even working. My nutritionist suggested that I take pyloricil since it has bismuth and zinc carnosine and mastic gum since we suspected hydrogen sulfide. After a few weeks, I can say that I haven’t had really much of a difference only that the odor of the gas is slightly different but still pretty foul. For constipation, I’ve tried Iberogast, Ginger extract 1000mg, magnesium bi-glycinate (seems to have stopped working since I upped my antimicrobial dosages). With everything else considered, I really feel that if I can get my MMC to work right I’d be feeling even better. Any thoughts on what to try next to get it going? I’m wondering if what I’ve been trying (ginger, bismuth, zinc) has actually been hindering my improvement.

          Reply
    • John Brisson
      John Brisson on October 18, 2016 at 11:11 pm

      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.

      Reply
  16. Dennis
    Dennis on April 24, 2016 at 5:08 pm

    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?)

    Reply
    • John Brisson
      John Brisson on April 27, 2016 at 7:00 pm

      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.)

      Reply
  17. Ellen Ussery
    Ellen Ussery on October 4, 2014 at 5:14 am

    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.

    Reply
    • John Brisson
      John Brisson on October 4, 2014 at 8:11 am

      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.

      Reply
      • Peter Brandt
        Peter Brandt on October 5, 2014 at 10:20 pm

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

        Reply
        • John Brisson
          John Brisson on October 6, 2014 at 9:37 am

          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.

          Reply

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