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


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
  • Achalasia
  • Burning mouth syndrome
  • Sjogren’s syndrome (H. pylori)
  • Sinus infections
  • Dental caries
  • Halitosis
  • Canker sores (H. pylori)
  • Cold sores (Herpes simplex 1)
  • Tinnitus
  • Ear infections
  • Visual snow
  • Brain fog, mental cognition issues
  • Migraines
  • Multiple Sclerosis (H. pylori)
  • Rheumatoid arthritis (Klebsiella)
  • Ankylosing spondylitis (Klebsiella)
  • Hellp syndrome (Preeclampsia) (H. pylori)
  • Raynaud’s phenomenon (H. pylori)
  • Chronic fatigue syndrome (Epstein-Barr virus)
  • Acne
  • Rosacea
  • 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
  • Hypothyroidism
  • Oral, esophageal, liver, pancreatic, and stomach cancer
  • Type 1 and type 2 diabetes
  • Pancreatitis
  • Gallstones
  • Bile production issues and deconjugation of bile, leading to yellow or pale stool and rectal burning
  • Gilbert’s syndrome
  • Cirrhosis
  • Hepatitis
  • Urinary tract infections(Proteus, E. coli, Klebsiella, Citrobacter, Enterobacter, H. pylori, and Pseudomonas)
  • 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 dysregulation
  • Anxiety
  • Depression
  • Circadian rhythm disruption and poor sleep
  • Sleep apnea

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):

  • 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.
  • 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.
  • 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.
  • 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 butyrateWARNING, 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
  • 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.
  • 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.

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

  • 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.
  • 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.
  • Allicin-C – take two to eight capsules daily in divided doses with food. Use with caution if you suffer from hydrogen sulfide dysbiosis.
  • 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 honey
  • 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.

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 Microbiome

  • 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 Microbiome

  • 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.

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.

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

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:

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