SIBO/SIYO/Heartburn: Detailed Information and How to Find Relief – 2023


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

What is SIBO/SIYO?

SIBO is a medical condition where you have microbial dysbiosis within the microbiome of our 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 are usually 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 undigested proteins. Undigested proteins also cause excessive flatulence and bloating from increased protein fermentation by microorganisms. The standard American diet contains abundant 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.

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. 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 must 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, lactoferrin, or NAC.

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 to your SIBO protocol might be best if a first-line protocol fails. If you know the bacterial species that you believe is causing your dysbiosis and it produces biofilm then use antibiofilm agents 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 possible time. 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 suffer from SIBO, and SIBO is the true cause of their digestive problems. There is also a strong correlation between rosacea and SIBO. In one study, most 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.

How to Diagnose SIBO

My Hydrogen/Methane/H2S Breath Test Results 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 our 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, in which only rare action potentials and contractions occur.
  2. The second phase lasts roughly thirty minutes, where peristaltic contractions occur and progressively increase in frequency. Peristalsis originates in our stomach and propagates throughout our 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, our pylorus remains open during these peristaltic contractions, allowing many indigestible materials to pass into our 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 our 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” sound you hear when you are hungry might be the MMC doing its job, the sound of our stomach emptying, and the increasing 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 the overgrowth of bacteria and archaea within our gut have been linked to decreased MMC function. When the second and third phase of the MMC is reduced, bacteria remain in our small intestine instead of being pushed back into our large intestine. Bacteria can then adhere and propagate within our small intestine, which increases inflammation and intestinal permeability. The inhibition of MMC homeostasis drives the vicious SIBO cycle.

Neutralization or reduction of stomach acid from using acid-reducing medications or by having H. pylori dysbiosis can contribute to poor MMC function. Our body monitors stomach pH to time proper stomach emptying to ensure the proper digestion of food before it is released into your 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 our MMC function. Grounding can help relieve stress and improve your MMC. Ileocecal valve massage and abdominal massage can also help improve MMC function. Finally, inhibited thyroid function and suffering from 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 increased 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 a proper circadian rhythm. Frequent exercise also helps to regulate your MMC properly. Finally, your MMC operates while you are sleeping, so 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 our 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 our small intestine, the more food they will consume and the more gas, byproducts, and toxins they produce. Inflammation occurs within our small intestine lining, leading to increased gut permeability and reduced absorption of iron, folate, and vitamin B12. The opportunistic bacteria also consume more nutrients that are now unabsorbed by our 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 within our small intestine.

The opportunistic bacteria then decrease fat absorption within our intestines, leading to stool health issues (yellow or fatty stools). The decrease in fat absorption leads to deficiencies in the fat-soluble vitamins A and D. Your 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 degradation of our intestinal lining.)

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

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 dysbosis can occur within our 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 our 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).

Other yeasts besides Candida can cause SIYO; an example is 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.

The two tests used to diagnose SIYO are an alcohol challenge test and gut microbiome testing (Genova GI Effects or Diagnostic Solutions GI-MAP). If you are going to take an Organic Urine Acid Test to determine if you are suffering from SIYO use one that measures arabinitol. Some yeasts ferment the sugar arabinose into the sugar alcohol arabinitol. 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.

If you are suffering from SIYO, try any of my Candida protocols to eliminate the opportunistic yeast or contact me for coaching.

Can Someone Suffer from both SIYO and SIBO?

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

Restore Proper MMC Function Protocols

SIBO-C:

SIBO-D:

If you have elevated stomach pH:

  • Follow betaine HCL protocol.
  • Urban Moonshine Digestive Bitters – follow the general supplement instructions; do not use the supplement if you are suffering from histamine intolerance, ulcers, or gastritis.

General Advice to improve your MMC not covered above:

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.
  • Consume one to two cups of lemongrass tea daily.
  • Consume low-FODMAP organic soy including tamari and miso daily as long as you are not allergic to soy or are prone to or are suffering from histamine intolerance.
  • If your Prevotella colony levels are low in your gut tests, increasing their colony levels within your digestive system might help relieve Archaea dysbiosis.

Berberine and allicin have anti-archaeal properties.

Coconut oil is used to relieve yeast dysbiosis within the digestive tract and inhibit archaea dysbiosis.

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 oregano – 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).

AND CHOOSE ONE OF THE FOLLOWING ADDITIONAL ANTI-BIOFILM AGENTS:

  • Calcium disodium EDTA: MRM Cardio Chelate – follow general supplement recommendations. Do not supplement if you have mercury amalgams (silver fillings) or are mercury burdened.
  • 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. Do not supplement if you are suffering from hydrogen sulfide dysbiosis or if you have mercury amalgams (silver fillings) or are mercury burdened.
  • 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.
  • Consume one to two cups of lemongrass tea daily.
  • Consume low-FODMAP organic soy including tamari and miso daily as long as you are not allergic to soy or are prone to or are suffering from histamine intolerance.
  • If your Prevotella colony levels are low in your gut tests, increasing their colony levels within your digestive system might help relieve Archaea dysbiosis.
  • Consider using the anti archaeal agent Alinia if needed.

Calcium disodium EDTA chelates iron out of the biofilm to break it up and pull it away from archaea.

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 and neem reduces archaeal dysbiosis.

Mild SIBO-D (Hydrogen Bacteria) Protocol

For two to four weeks:

Antibacterials

OR CHOOSE ONE OF THE FOLLOWING ANTIBACTERIAL AGENTS FROM THIS LIST

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.

OTHER ANTIBIOTICS THAT CAN BE USED OR ROTATED IF NEEDED:

  • Tetracycline/Doxycycline – broad-spectrum antibiotic, follow moderate Candida protocol while on antibiotic to reduce the chance of developing Candida dysbiosis.
  • Cephalosporin – second generation or newer cephalosporin only.
  • 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).

AND CHOOSE TWO OF THE FOLLOWING ANTI-BIOFILM AGENTS:

  • Calcium disodium EDTA: MRM Cardio Chelate – follow general supplement recommendations. Do not supplement if you have mercury amalgams (silver fillings) or are mercury burdened.
  • 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. Do not supplement if you are suffering from hydrogen sulfide dysbiosis or if you have mercury amalgams (silver fillings) or are mercury burdened.
  • 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 dysbiosis.

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).

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

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

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.

Arabinogalactan

Galactooligosaccharide

Holigos

Partially hydrolyzed guar gum – I recommend the use of SunFiber. Might help people suffering from SIBO-C.

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

The probiotic/prebiotic protocol will hopefully enhance probiotic bacteria colonies within our gut.

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

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

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