People with digestive issues suffer from different symptoms. Whether it is upper gut dysbiosis, small intestinal bacterial overgrowth (SIBO), or colonic dysbiosis, there is usually a cause, and most people have similar symptoms. What is the cause of different symptoms for people who are suffering from digestive issues? Research indicates that depending on what type of organism is dominant in your microbiome, it mostly determines your digestive issues. Five main gasses produced within our digestive tract include nitrogen, carbon dioxide, hydrogen, hydrogen sulfide, oxygen, and methane. In a healthy digestive tract, most of the gasses that comprise it are nitrogen, carbon dioxide, and hydrogen to a lesser amount. Small amounts of oxygen and possibly methane and hydrogen sulfide are found as well in a healthy gut. Many people are unaware that your stool consists of a mixture of gases and waste products, undigested fiber, and dead microorganisms. Depending on the state of your intestinal gas composition, the concentrations of gases may range from:1

  • Nitrogen (23% to 80%)
  • Carbon dioxide (5.1% to 29%)
  • Oxygen (.1% to 2.3%)
  • Hydrogen (0.06% to 47%)
  • Methane (0% to 26%)
  • Hydrogen sulfide (unknown)

Minute amounts of different gases enter the digestive tract through swallowing air, but most of that air is either belched out or absorbed by the stomach into the bloodstream. Carbon dioxide is produced in our small intestine from gastric acid hydrogen ions interacting with bicarbonate in the duodenum. Carbon dioxide is also generated in the jejunum by the degradation of dietary triglycerides to fatty acids. Bacteria also produce carbon dioxide in the digestive tract through fermentation, but most of the produced carbon dioxide readily enters the bloodstream and is exhaled from the lungs. Carbon dioxide is also converted into the short-chain fatty acetate by acetic producing bacteria and methane by archaea, further reducing its net volume leading to little if any bloating from the gas, unlike large amounts of hydrogen, hydrogen sulfide, or methane. Nitrogen is most abundant within the digestive tract because it is the most abundant gas in our atmosphere. We swallow (air and ingestion of nitrates) and inhale nitrogen. Some of it is exhaled, and some of the nitrogen enters the bloodstream, where it is later diffused into the intestinal lumen and eliminated through stool and flatulence. Some nitrogen is also converted into nitrous oxide by nitrous oxide producing bacteria that are absorbed into the bloodstream to be utilized by the body. Nitrogen and carbon dioxide are the only gases in the intestinal tract that can be diffused between the lumen and the bloodstream when needed to equalize pressure within the digestive tract. The oxygen that we inhale or ingest is rapidly utilized by our cells, and very minute amounts are also diffused into the intestinal lumen. What is not used by the colonic cells is eliminated through stool and flatulence. Finally, differing quantities of hydrogen and methane can diffuse from the intestinal lumen into the bloodstream later to be exhaled. Our intestinal tract and microbiome try to maintain pressure equilibrium so that bloating rarely occurs, but what if we develop dysbiosis that profoundly differs the gas composition of our intestinal tract?2

Hydrogen Producing Bacterial Dysbiosis Causes SIBO-D

If you are diagnosed with SIBO-D (small intestinal bacterial overgrowth with diarrhea), you are likely suffering from hydrogen-producing bacteria dysbiosis of the small intestine. Bacteria produce hydrogen gas as a byproduct of carbohydrate fermentation in our gut. Hydrogen gas exists naturally in our large intestine as a byproduct of fermentation. Some of it is absorbed into the bloodstream and is exhaled, some of it is converted into methane by archaea, and the rest of the hydrogen gas is absorbed by our stool or expelled. Significant amounts of hydrogen gas, however, are not supposed to exist in the small intestine generally due to the lack of widespread fermentation. Too much hydrogen gas causes significant bloating and abdominal distension and discomfort.3 4 5

Bacterial dysbiosis produces toxins that irritate the gastrointestinal lining, causing diarrhea. Most of these toxins overload the TRPV1 receptors in our gut, significantly increasing osmolarity, drawing more water into the bowel, and increasing gut peristalsis, causing diarrhea. Diarrhea is a defense mechanism by the body to protect itself from bacterial toxins and dysbiosis by eliminating both. Some hydrogen dominant producing bacteria also produce serotonin, which in large amounts can further increase motility. Capsaicin found in peppers also activates the TRPV1 receptors, causing diarrhea in many people after consumption.6 7

Hydrogen-dominant bacterial dysbiosis would cause diarrhea, especially in SIBO. If you are suffering from SIBO and are dealing with diarrhea, read my main SIBO blog entry or my book Fix Your Gut for more information on how to deal with this issue.

What are some bacteria within our gut that can produce hydrogen (the bacteria that are in bold can be probiotic, not every individual strain of a listed bacteria produces hydrogen):

Suggestions to Decrease Gut Motility by Absorbing Toxins or Reducing Motility:

  • Activated charcoal
  • Bismuth
  • Peppermint – Menthol found in enteric-coated peppermint supplements reduces migrating motor complex impulses, slowing down intestinal spasms and motility. Menthol is also a 5-HT3 antagonist. Though it reduces motility, it does not seem to cause as much toxin retention as Zofran because it does minimize dysbiosis as well as an antimicrobial agent. Menthol is both an antimicrobial agent and is anti-inflammatory.8
  • Ginger – I recommend either taking New Chapter Ginger Force twice daily with meals, drinking ginger tea twice daily with meals, or eating freshly grated ginger twice daily with meals. Ginger contains galanolactone and gingerols that appear to be potent 5-HT3 antagonists, which might explain its antiemetic properties. However, ginger, unlike Zofran (which has no known effect on gastric emptying), has been shown to increase stomach emptying and improve gastroparesis. It is currently unknown why (my guess is because it is an antibacterial agent and relieves dysbiosis). Ginger might reduce small intestine and colonic motility similar to Zofran through inhibiting 5-HT3 (supplementation of artichoke extract or using a combined motility supplement like Motilpro might overcome this limitation), and it has no action on 5-HT4 receptors (which deals with colonic motility). However, ginger does not seem to cause as much toxin retention as Zofran because it does relieve dysbiosis as an antimicrobial agent. Ginger is also anti-inflammatory.9 10
  • Zofran – Ondansetron is a serotonin 5-HT3 receptor antagonist medication used to prevent nausea and vomiting. It works by reducing the vagus nerve’s activity, which deactivates the vomiting center in the medulla oblongata. In addition, it has been shown to reduce colonic contractions and motility in people with irritable bowel syndrome. Ondansetron is a well-tolerated drug with few systemic side effects. The most common side effects are constipation, dizziness, and headaches. Ondansetron has recently been discovered to cause long QT syndrome and heart arrhythmias in high doses (greater than thirty milligrams). Zofran works well in people with SIBO-D, but may cause constipation to worsen in people with SIBO-C. Finally, I do not recommend Zofran use in people with severe dysbiosis as it can cause toxin retention without absorbing toxins leading to severe health conditions, including toxic megacolon.11
  • Imodium – I do not recommend taking Imodium to treat diarrhea because it can cause bacterial toxin retention and cause toxic megacolon.

Hydrogen Sulfide Dominant Dysbiosis

Sulfur is an essential mineral for proper health. Sulfur is the seventh most abundant element within the human body. Our skin, hair, nails, bones, joints, and muscles all contain sulfur. Our intestinal mucosal barrier is composed of sulfomucins. Proper dietary sulfur intake and utilization by our body is important for preventing leaky gut. Sulfur is used by the body to produce and conjugate bile acids for proper digestion. Sulfur is vital for the formation, regeneration, and repair of bone. Sulfur is essential for the endogenous production of the crucial antioxidant glutathione, collagen, and insulin. Most of our body’s ingested sulfur comes from our digestive system and microbiome, metabolizing protein into individual sulfurous amino acids to be absorbed within our small intestine. Cysteine, taurine, homocysteine, and methionine are sulfur-containing amino acids obtained from protein ingestion in our diet. We also ingest other sulfur-containing foods, including cruciferous vegetables and alliums, that our microbiome ferments and releases the sulfur for us to absorb.12

Most of the sulfur within the human body is used up by our cells and microbiome. Some sulfur metabolism byproducts are detoxified and excreted from our body as well. Sulfur has to be converted within our body into sulfate to be used properly. Minute amounts of sulfur are endogenously converted into hydrogen sulfide. Hydrogen sulfide is necessary because it is an endogenous cellular signaling molecule, it is essential for producing mitochondrial energy, it is a vasodilator, and it can reduce mucosal injury and inflammation in very minute amounts. Very minute quantities of hydrogen sulfide are produced from ingested sulfur-containing food in someone with a healthy microbiome. Hydrogen sulfide dysbiosis mainly occurs in the upper gut (oral cavity, stomach, duodenum, liver, gallbladder, and pancreas) but can also cause small intestinal and colonic dysbiosis. Many bacteria that produce hydrogen sulfide from sulfur colonize the upper gut and other parts of your digestive tract.13 14 15

What are the signs/symptoms of hydrogen sulfide dysbiosis? Remember you might have some of the signs/symptoms, but not all of them.16 17 18

  • Intolerance to sulfur-containing foods, supplements, and medications, which increases symptoms.
  • Halitosis
  • Periodontal disease
  • Chronic fatigue syndrome, elevated hydrogen sulfide is toxic to our mitochondria by increasing oxidative stress within our body.
  • Weakness
  • Brain fog and/or short term memory loss
  • Headache
  • Fibromyalgia
  • Neuropathy
  • Dry skin
  • Rashes
  • Brittle hair and nails
  • Eczema
  • Poor wound healing
  • Improper blood glucose regulation
  • Joint pain
  • Easier bone fractures and breaks
  • Low blood pressure
  • Dizziness
  • Sulfurous or “rotten egg” smelling flatulence and/or defecation. May become stronger with ingestion of sulfur-containing foods including cruciferous vegetables, garlic, onions, meat, and eggs.
  • Sulfurous smelling urine
  • Inflamed or painful bladder and/or urination
  • Bloating, especially after eating sulfurous containing foods.
  • Abdominal pain
  • Colon cancer
  • Inflammatory bowel disease (hydrogen sulfide producing bacteria can coexist with Mycobacterium Avium Paratuberculosis the cause of IBD).
  • Gastrointestinal inflammation
  • Gastrointestinal bleeding
  • Constipation (people with upper gut hydrogen sulfide dysbiosis may also have methane dominant archaea SIBO as a secondary dysbiosis within the small intestine, methanogenesis the production of methane requires organosulfur cofactors).
  • Diarrhea (usually occurs around the start of the hydrogen sulfide producing dysbiosis)
  • Digestive tract inflammation, irritation, and/or ulceration
  • Increased gut permeability (too much hydrogen sulfide produced within our gut reduces butyrate oxidation, increases inflammation, and starves the gut enterocytes, leading to leaky gut).
  • Malnutrition (by an inflamed and/or damaged small intestinal lining from both a lack of sulfate body reserves and increased hydrogen sulfide gas being produced causing poor small intestine cellular health)
  • Muscle wasting
  • Weight loss
  • Nausea
  • Reflux

If our microbiome produces too much hydrogen sulfide and our body’s natural ways of detoxifying it in the gut are overwhelmed, it can cause many health issues. In addition, if you have CBS genetic polymorphisms, you may have problems detoxifying sulfur and hydrogen sulfide properly, causing problems.

What are some bacteria within our gut that can produce hydrogen sulfide (the bacteria that are in bold can be probiotic, not every individual strain of a listed bacteria produces hydrogen sulfide):19 20

Hydrogen Sulfide Dysbiosis Recommendations:

  • If you have hydrogen sulfide dysbiosis, I suggest following my upper gut dysbiosis protocol if you are having symptoms of it. Avoid any sulfurous containing supplements listed here even if they are recommended in the protocol (for example, supplement with berberine hcl instead of berberine sulfate).
  • Follow the Fix Your Gut SIBO protocol if your symptoms are greater within your small intestine (around your belly button). Avoid any sulfurous containing supplements listed here even if they are recommended in the protocol (for example, supplement with berberine hcl instead of berberine sulfate).
  • Molybdenum is an essential mineral for sulfur metabolism within our body; deficiency in molybdenum causes sulfur metabolism issues.
  • Codonopsis root powder – start with one teaspoon daily and make it into a “tea,” by mixing it into a cup of warm water; however, leave the root inside the “tea” to consume it afterward. The root can also be blended into a smoothie. You can increase the amount to the therapeutic dose of two and a half tablespoons daily. It may be taken in divided doses throughout the day and with meals.21
  • Jiaogulan herb – take one with each meal, might cause gastrointestinal upset, so take it with food.22
  • Pure Encapsulations zinc picolinate supplementation may relieve symptoms by absorbing hydrogen sulfide within our gut and eliminating it through defecation. Thirty to sixty milligrams daily in divided doses with food may help.
  • Bismuth supplementation may relieve symptoms by absorbing hydrogen sulfide within our gut and eliminating it through defecation. I recommend supplementing with Devrom (contains xylitol, talc, and starch[possible GMO source]). Ask your doctor about performing a crude test on yourself to determine if you have hydrogen sulfide dysbiosis. To take the test, take one to three capsules of Devrom with each meal and consume various forms of sulfur with each meal. If your stool turns black, you likely have hydrogen sulfide dysbiosis. The bismuth in the Devrom combines with hydrogen sulfide within your digestive tract to form bismuth sulfate, a fine black powder that coats your stool during digestion.
  • Supplementing with oral hydroxocobalamin (a form of vitamin B12) can reduce hydrogen sulfide concentrations in the bloodstream and is good for people suffering from low blood pressure with hydrogen sulfide dysbiosis.23
  • Consider supplementing with butyrate. Hydrogen sulfide dysbiosis leads to reduced butyrate oxidation which reduces colonocyte energy production leading to poor health of your colonic lining.
  • Sparga (might help relieve hydrogen sulfide-caused brain fog) – follow bottle supplement recommendations. Leave the drops for five to ten minutes in water before consuming for the alcohol to evaporate.
  • Ubiquinol supplementation might help improve our liver’s sulfur metabolism and reduce excessive hydrogen sulfide-caused mitochondrial oxidative stress. Take the ubiquinol supplement during the morning, supplementing later in the day might interfere with your sleep from increased mitochondrial energy production.
  • Consuming a diet low in thiols helps reduce hydrogen sulfide production, reducing symptoms. For some people with severe hydrogen sulfide dysbiosis, reduce the amount of meat and animal protein (like whey) you ingest because they are rich in sulfurous amino acids.

Methane Dominant Archaea Dysbiosis Causes SIBO-C

Your intestinal flora is composed of organisms known as archaeaArchaea are different from bacteria; they are single-celled organisms but lack a nucleus. Archaea, within our digestive system, use hydrogen and hydrogen sulfide that bacteria produce during the fermentation of carbohydrates or the reduction of sulfur within our gut, the sulfur we ingest from our food and supplements/medications we take, and from the carbon dioxide produced within our digestive tract when the stomach acid from our stomach meets the alkaline pancreatic juice and bile within the duodenum, neutralizing the stomach acid. Archaea then produce the odorless gas methane as a byproduct of their metabolism.24 25 26

The more fermentation and hydrogen gas that occurs within the intestines, the more methane archaea will produce. Cows flatulate a lot more methane than people because they consume a lot more fermentable foodstuff (grass, for example) than we consume and have more archaea by volume. Methanobrevibacter smithii seems to be the most dominant of the archaeal species within our gut, compromising at least ninety percent of our archaea gut flora.27 28

What happens to the hydrogen within our body:

Decreased migrating motor complex (MMC) function and lactose malabsorption have been correlated with archaeal dysbiosis. Decreased MMC function leads to gastroparesis and constipation. Decreased MMC function also leads to an increase of hydrogen (feeds archaea) and methane concentrations within our gut, which causes excessive bloating. Unlike bacteria, it is unknown if archaea produce TRPV1 activating toxins, which might explain why they do not cause diarrhea. Colonic pH is also significantly lower in people suffering from archaea dysbiosis, which can help protect dysbiosis from other organisms that require higher pH to survive and might compete in a healthy environment and the intestinal immune cells.29 30 31

How does archaea dysbiosis further hinder MMC function to the point of chronic constipation?

“Compared with hydrogen producers, methane producers had significantly lower postprandial serotonin levels. These data—although derived from a very small (N=18) study—suggest that methane-producing IBS patients have reduced postprandial serotonin.”32

Serotonin (5-HT3/5-HT4) is one of the neurotransmitters associated with increasing gut peristalsis. Lower amounts of serotonin in the gut equates to lower MMC function that would explain the cause of chronic constipation in methane dominant SIBO. Lowered activation of 5-HT3 receptors in the ileum greatly slows down the emptying of the small intestine, leading to SIBO.33 34

It is more difficult to resolve archaea dysbiosis because they tend to be more antimicrobial-resistant and form thick biofilms.35 Treatment of the dysbiosis might require multiple natural antimicrobial agents, antibiotics, and anti-biofilm agents. Changing your diet to a low FODMAP diet might relieve archaea dysbiosis by limiting the amount of hydrogen they have to metabolize from the lack of carbohydrates hydrogen bacteria have to ferment. Archaea are very hardy and can survive a long time without hydrogen, so it might be possible that switching to a low FODMAP diet short term would also do very little to archaea dysbiosis symptoms.

Increasing MMC function during archaea dysbiosis might be one of the most important things one can do to find relief.

Suggestions to Increase Gut Motility:

  • 5-HTP supplement – I recommend taking a 5-HTP supplement for a short period (at most one month) to help increase serotonin levels in the gut. I will not use this supplement if you are taking any medications that modulate serotonin levels (for example, a SSRI [selective serotonin reuptake inhibitor] medication or if you suffer from any serious mental health issues.36
  • Domperidone – Domperidone unlike metoclopramide does not cross the blood-brain barrier. All of the central nervous symptom side effects are absent with domperidone making the drug much safer. Domperidone is a medication that is an antiemetic, a gastroprokinetic agent, increases gut peristalsis, and has been shown to increase lower esophageal sphincter tone. Domperidone has not been approved to be used in the United States. The intravenous form of domperidone has been linked to prolonged QT intervals and should be rarely used.37
  • Triphala – Triphala is an ayurvedic herb that increases gastric emptying, gut peristalsis, and increases gut muscle tone.38 39
  • Morphine – I cannot recommend this method, and more research should be done using low dose morphine and motility. I do find this interesting and believe it is worth noting, the reaction in the body should be opposite since opioids slow down motility. Low-dose morphine might, however, increase motility by activating the intrinsic nerves of the myenteric plexus, therefore increasing MMC function. One of the ways dopamine is used by the body is to reduce MMC function, and morphine would increase dopamine levels. It does, however, increase serotonin which might explain why it helps increase motility in tiny doses.40 41 42
  • Daikenchuto – DKT is a Japanese herbal medicine composed of ginger, Panax ginseng, Japanese pepper. It has been found to increase motility and reduce bloating in people with SIBO-C.43 44
  • Intermittent fasting – During proper fasting, the migrating motor complex will function better, increasing motility. I recommend only eating three meals daily and try not to eat snacks between meals. I would also not eat after dusk, to help improve motility, liver function, and circadian rhythm. Your longest fasting period is the greatest activation of the MMC and the parasympathetic nervous system is during sleep until you eat breakfast (break fast).45
  • Exercise – Proper regular exercise helps improve migrating motor complex function, especially if you are sedentary. Walking, sprinting, and rebounding on a mini trampoline help motility greatly.
  • Magnesium supplementation
  • Proper defecation posture is very important for proper motility
  • Ileocecal valve massage
  • Biofeedback therapy


If our gut is working correctly different gases are maintained in healthy ratios from fermentation, inhalation, or by digestive processes. If your digestion is healthy nitrogen production occurs the most, followed by carbon dioxide, hydrogen, oxygen, methane, and hydrogen sulfide. The predominant gases found or produced in the small intestine is nitrogen and carbon dioxide. If increased hydrogen, methane, or hydrogen sulfide gas is produced, you might be suffering from upper gut dysbiosis or SIBO. Follow my commendations above to improve your motility and follow my protocols to relieve dysbiosis to find relief.

  11. Beers, Mark. The Merck Manual, Merck Research Laboratories, 2006.
  37. Beers, Mark. The Merck Manual, Merck Research Laboratories, 2006.