SIBO: Hydrogen, Hydrogen Sulfide, or Methane, What Is the Difference?

SIBO: Hydrogen, Hydrogen Sulfide, or Methane, What Is the Difference?

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 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 Dominant Bacteria Associated With Having 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.

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 reduce 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 because it is an antibacterial agent and relieves dysbiosis). Ginger might reduce small intestine and colonic motility similar to Zofran through inhibition of 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 in the prevention of nausea and vomiting. It works by reducing the vagus nerve’s activity, which deactivates the vomiting center in the medulla oblongata. In addition, in people with irritable bowel syndrome, it has been shown to reduce colonic contractions and motility. 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 the use of Imodium because it can cause toxin retention and cause toxic megacolon.

Hydrogen Sulfide Dominant Dysbiosis

Sulfur is an essential mineral for our health. All living cells use sulfur, and it is the seventh most abundant element in the human body. Our skin, hair, nails, muscles, and bones all contain sulfur. Our intestinal mucosal barrier is composed of sulfomucins, and it is essential for the endogenous production of glutathione and insulin. Most of our ingested sulfur the body uses comes from our digestive system and microbiome breaking down protein into amino acids. Cysteine, taurine, homocysteine, and methionine are examples of sulfonated amino acids that we obtain from protein ingestion. We also ingest sulfur-containing foods, including cruciferous vegetables and alliums that supply us with the mineral sulfur.12

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

So what are symptoms of hydrogen sulfide dysbiosis?16 17 18

  • Sulfurous or “rotten egg” smelling flatulence and defecation. May become stronger with ingestion of sulfur-containing foods like cruciferous vegetables and eggs.
  • Chronic fatigue syndrome, elevated hydrogen sulfide is toxic to the mitochondria because it increases oxidative stress.
  • Brain fog and/or short term memory loss.
  • Intolerance to sulfur-containing foods, supplements, and medications, which increase symptoms.
  • Fibromyalgia
  • Halitosis
  • Periodontal disease
  • Low blood pressure
  • Constipation (most people with upper gut hydrogen sulfide dysbiosis also have methane dominant archaea SIBO as a secondary dysbiosis within the small intestine)
  • Diarrhea (if methane dominant archaea is not a secondary dysbiosis)
  • Digestive tract inflammation, irritation, and ulceration.
  • Increased gut permeability (too much hydrogen sulfide reduces butyrate oxidation, increases inflammation, and starves the gut enterocytes, leading to leaky gut)
  • Colon cancer
  • Inflammatory bowel disease (hydrogen sulfide producing bacteria can coexist with Mycobacterium Avium Paratuberculosis the cause of IBD)
  • 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.

    So what microorganisms in our gut can produce hydrogen sulfide (the bacteria that are in bold can be probiotic, not every individual strain can produce hydrogen sulfide):19 20

  • Akkermansia
  • Bacillus
  • Bilophila
  • Citrobacter
  • Desulfovibrio
  • Desulfobacter
  • Desulfobulbus
  • Campylobacter jejuni
  • Clostridium
  • Enterobacter
  • Escherichia coli
  • Helicobacter pylori
  • Klebsiella
  • Odoribacter
  • Salmonella typhimurium
  • Staphylococcus aureus
  • Prevotella
  • Proteus mirabilis
  • Hydrogen Sulfide Dysbiosis Recommendations:

    • If you have hydrogen sulfide dysbiosis, I would suggest following my upper gut dysbiosis protocol if you are having symptoms of it.
    • Follow the Fix Your Gut SIBO protocol if your symptoms are more located within the small intestine (around the belly button).
    • The element molybdenum is also essential for sulfur metabolism in the body; deficiency in molybdenum causes sulfur metabolism issues.
    • Codonopsis root powder – start with one teaspoon daily and make it into a “tea” 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 taken to the therapeutic dose of 2.5 tablespoons total daily. May be taken in divided doses throughout the day and with meals.21
    • Jiaogulan herb – one with each meal, might cause gastrointestinal upset so take with food.22
    • The mineral bismuth may help bring relief from symptoms by absorbing hydrogen sulfide in the gut and eliminating it from defecation.
    • 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 that have hydrogen sulfide dysbiosis.23
    • Finally, consuming a diet low in thiols helps reduce hydrogen sulfide production, reducing symptoms. For some people with severe hydrogen sulfide dysbiosis, you might also reduce the amount of meat and animal protein (like whey) that you ingest because they are rich in sulfurous amino acids.

    Methane Dominant Archaea and SIBO-C

    Your intestinal flora is composed of organisms known as archaea. Archaea are different from bacteria; they are single-celled organisms that lack a nucleus. Archaea, in our digestive system, feeds off hydrogen that bacteria produce during the fermentation of carbohydrates in our gut and carbon dioxide we inhale and produce as a byproduct of digestion. Archaea then produce the odorless gas methane as a byproduct of their metabolism.24 25 26

    The more fermentation and hydrogen gas that occurs in 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 archaea species in 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 in the 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. Colon 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 by 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 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
  • Exercising – 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.
  • Proper defecation posture is very important for motility
  • Ileocecal valve massage
  • Biofeedback therapy
  • Conclusion

    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 is found 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.
    1. Dr John, I am coming here in the hopes that you could shed some light on my situation. I am very thankful for your information. It is not possible for me to get a test done, but I have the following symptoms that lead me to thinking I have SIBO(I wont be able to tell which one):

      – Extreme gas/bloating in stomach and bowels after eating
      – Very bad nausea
      – I was never constipated up until a week ago.
      – Sudden urges to go to the bathroom(never diarrhea up until recently for one session) and very bad pain in bowel area. My stools were very healthy.
      – My symptoms only used to occur when I ate anything with sugar- even sauces. This suddenly started 4 months ago, so I cut out sugar entirely(fruit I could handle but now along with everything else I eat it just bloats me). I have read that SIBO can cause disaccharide intolerence?
      – Once I had a taste of icing on a cake- threw up 30mins later with another sudden bathroom urge.
      – My gluten intolerence has worsened and gives me extreme nausea followed by the above symptoms.
      – I only feel better once my stomach has gone.
      – Eating only protein(clean meats) and fats along with very little carbs(sweetpotato) is the only thing that doesnt make me feel catastrophically nauseas or bloated.
      – The only things I’m doing now to combat this is intermittent fasting(I only eat from 11am to 7pm (which has helped ease symptoms.
      – I am always active- gym is 3xdays per week.
      -I am taking L-glutamine every morning and used to take probiotics(however I have stopped because I’m afraid it would increase the bacterial growth.

      Your help would be much appreciated.

    2. Hi John,
      Thanks so much for such great info! I am wondering what your advice is for people who have both methane and hydrogen producing SIBO. This is rare, but I have read of it happening to others and my breath test is showing that. How would you approach that? I am at a loss.


    3. Hello John,

      I recently purchased your book and I must say that there is a tremendous amount of useful information in it. I do fight with Ulcerative Colitis for a year and a half. Now I am in manageable condition but few things don’t stop to bother me. The first one is bloating and excessive gas and the other fatigue (brain fog).
      Recently I started using Meteoxane ( Simeticon + phloroglucinol ) which seems to help with gases. By reading your book I did not find any info about Simeticon or Phloroglucinol and their safety for long term use. Do you have any info about that?


      • Simethicone is in Fix Your Gut, it breaks up bubbles into smaller bubbles making them easier to pass and it is relatively benign. Phloroglucinol, I could not find a lot of information on it, it is widely prescribed in France apparently. It does seem to have some anti colon cancer effects.

        • I probably have overseen the part where you mentioned Simethicone. Thanks a lot for the answer.

    4. Hello from Missouri. I’m 37 and the mom of triplets; identical twin boys and a girl. Overall, I am extremely healthy except for SIBO that I have been battling since September of last year (2018).

      In mid-September I was diagnosed with a concussion after hitting the back of my head. I had vision disturbances, severe headaches, eye pain, trouble completing thoughts/sentences, etc. Those symptoms lasted almost 6 weeks. The strange thing that I noticed right around that time was that my gut slowed down and my bowel movement frequency decreased. I then found myself constipated. By mid to late November I was miserable with severe bloating and distention. I looked 5 months pregnant. I was belching and very unsettled after eating. I even got nauseous and pukey sometimes. I also noticed that I was passing more gas, and I noticed it was just “air” and not stinky like normal gas.

      My PCP diagnosed me with SIBO (no breath test or other testing…just went off symptoms). He prescribed Rifaximin. I took 550mg 3xday for 14 days and the symptoms resolved. I felt pretty much back to normal for 4 months. I was having a daily regular bowel movement and the distention was gone.

      Then about six weeks ago (March) the symptoms came back. Strangely, I had eaten a large evening meal of sauerkraut and gotten so sick with gas, diarrhea and nausea that I missed work the next day. I am not sure if that meal was related to the relapse or not, but it seemed so to me, so I thought I would share. Shortly after that, I noticed my daily bowel movements slowed again dramatically and the distention set back in making me look pregnant again. My doctor said 40% of patients relapse so he prescribed another round of Rifaximin. This time I got no relief of symptoms.

      So, as of today I am two weeks post second round of Rifaximin and feeling as bad as ever. I also feel so hopeless about ever getting over this condition and feeling normal and healthy again. I have reached out to my PCP and he is wanting to consider more antibiotics. I’m waiting for him to call today to schedule an appointment.

    5. Hi John,

      Thank you so much for your work it has been so valuable to me and many others.
      I am still trying to get to the bottom of my ongoing gut issues. I am wondering if SIBO or what sort of pathogen or disease could cause both dark orange and white mucus in my stool. I also having burping reflux and intermittent vomiting, abdominal pain the moves but is primarily on the left side. I got a GI map done that showed diantomeba fragilis, a little bit of h. Pylori, high levels of Klebsiella spp., Enterococcus faecium, Firmicutes, Bacteroidetes and i have low Secretory IgA. My kaiser doctor refuses to look at these results and says they are “clinically insignificant.” She just wants me to do a CAT scan, upper and lower endoscopy. Im only 22 and have eaten Perfect Health diet since I was 18. I had diarrhea every day for 6 months, and then i got this test, did herbal anti parasite, and now just have consitpation with mucus. and the other symptoms I mentioned. I have so many food allergies, and I have been on so many antibiotics, 4 years doxycycline for acne, amoxicillin, z packs, so many times. My sister is an MD and i just finished a week of Diflucan because we suspected yeast, but I still have the mucus and random vomiting acid and pain. Please let me know what you think!! thank you!!!

      • You are welcome. It sounds like biofilm to me for sure. The orange is a little weird, it could be from some supplement, food, or bile?

    6. I have both IBS-C and SIBO-C with significant muscle/tendon pain, polyneuropathy in feet/hands, many CNS symptoms, lung asthma-like, GI constipation – bloating/pain and more that all come and go based on diet and antibiotic treatment. The antibiotic that yields the best remission of all symptoms for 1 – 4 days and then recurs is Bactrim (Trimethoprim and Sulfamethoxazole). I have no success with Rifaximin + Neomycin or natural cocktails.

      I have monitored my Gut Microbiota using the Ubiome 16S testing and have recently submitted a Ubiome Plus to get a more detailed look at fungi and other critters. I recently had the GMAP stoll test which is based in part on the Luminex xTG pathogen Panel. I have C. Diff with genes for Toxins A and B, Klebsiella Pn, Citrobactor freundii and Proteus Mirabillis seen on Ubiome and GMAP. No fungi or parasites seen in GMAP but it only looks for a few..

      Bactrim is folate synthesis inhibitor which is effective on many bacteria, many fungi and even parasites since folate is a common requirement which is unique among antibiotics. My odd result from Bactrim could be that its effective against my dominant or worst offending overgrowth such as Klebsiella (Rifaximin is only 44% effective) or its not bacteria or Archean but fungi/yeast or an undetected parasite.

      I suspect there is slowly increasing small intestine damage causing leakage of foods which cause high IgE and allergy symptoms and things like LPS from gram negative bacteria causing cytokines and immune response and other symptoms. The SIBO seems old but the damage has gotten worse leading to severe systemic symptoms.

      Do you have any thoughts on trying to identify the offending bacteria and selecting a treatment targeted at a specific organism in the case of Rifaximin failure?

      Have you seen any efforts to dig deeper than gas type produced such as mass spectrometry of ones breath post glucose/lactulose ingestion to match to a set of bacteria?

      have you seen anyone attempt to look at ones breath using:

      An H2 detector
      A methane detector
      A hydrogen sulfide detector

      I have a volatile organic compound detector which shows I can fill my bedroom with unknown specific VOC after eating. It does not differentiate a specific VOC but I believe it would not respond to H2 but would to Methane or possibly Hydrogen Sulfide.

    7. Hi John, you mentioned Colon Cancer in the Symptoms list. If SIBO isn’t dealt with quickly (1 year) could Colon Cancer or serious health issues develop?

      • I doubt within a year colon cancer could develop, it might be likely if they condition goes on for many, many years, depending on many factors. The type of dysbiosis, inflammation, epigenetics, lifestyle, etc.

    8. Do you happen to know which strain of Bacillus produces Hydrogen Sulfide? No wonder I didn’t respond so great to trying a probiotic that had a bunch of Bacillus, I seem to have tons of Hydrogen Sulfide. I do terrible on Sulfur stuff and if I take Pepto Bismol it’s black tongue and stool time.

    9. Hi John, I am at my wits end too! Sibo-c here. Tried it ALL. I do everything recommended with pretty good results-lowfodmap, allicin, oregano, neem (off and on-its expensive), digestive enzymes, eat only three meals a day or less. I am now struggling with the C big time. Tried the magnesium citrate, works but causes tummy discomfort. I will use it. Running out though and its expensive. I discovered that red pepper is my friend the other night. As usual, I put the stuff on all my food but accidentally a TON poured out on my food, and being it a very nice steak on a bed of baby greens I couldn’t throw it out so tried to eat it any way brushing off the crushed red pepper as I ate. I had mounds of the red pepper so brushing it off, there was plenty there. Next day i had NO TROUBLES going to the bathroom. It was divine. So I am on the hunt for this japenese herbal med Daikenchuto. Any suggestions? Should I try to put my own powder together from an herb place? Thanks! Jeannie

    10. Hi John,
      I’m hoping you can offer some insight. I was diagnosed with SIBO and am on the third day of my 2 week course of Xifaxan. I read in your article that Hydrogen Sulfide SIBO can exist in the stomach which makes so much sense to me. I have odors which occur immediately after eating certain foods/drinks. They have been described as rotten eggs or sewage. For example, if I eat ice cream or have an alcoholic beverage, an odor instantly emits from my stomach within minutes. I would say like 2 minutes. Then it’s continuous from there. This happens on both a full (after a meal) or empty stomach. It is extremely socially crippling and I’m hoping that the Xifaxan will cure this. What’s odd is I cannot smell it, but people around me ask if I have passed gas. Another odd thing is that when I’m sick with some sort of sinus infection or virus, the odor is completely terrible and room filling – the odor can be smelled from across a room. I wish I was exaggerating, but this is my unfortunate life right now. Lentils, lemon water, certain teas (dandelion root and ginger tea), cheese, and fried foods also have a bad effect. I’ve had an endoscopy with a biopsy done (came back normal), lactose intolerance test (also normal), and the SIBO breath test (positive). I also suffer from constipation and GERD. Hoping for any advice you can offer. Thank you in advance.

      • I forgot to mention that I also always have a white tongue, iron deficiency (regardless of a well iron diet), and a lot of aggressive burping.

        • Hi there! Did you find a cure to your odor problem? This exact thing happens to me and the doctors I have seen haven’t really helped. Thanks

        • Sounds like a protozoa infection.

    11. I have suffered from severe silent reflux for a year (sore throat every day). My holistic doctor suggested I may have SIBO and sure enough the results came back severe as well. She wanted to put me on rifaximin which I ordered from Great Britain to save $$$. Before it came I read about macro phage therapy and I thought I would give it a try. I used Florassit with GI phage technology and I can’t tell you how much better I am in about 20 days now. Sore throats are nearly gone, I have put on 4 pounds in a week (I had lost 10 lbs. over the year) and BM’s are normal.

    12. Hi John,
      I’m on the elemental diet for SIBO-C. My ND wants me on the diet for 4 weeks due to high methane count (104 being the highest). Can I take 5-HTP during this diet and would you suggest any other supplements during this 4 week period that might enhance the results?

    13. check your spelling above…”deification” needs to be changed to “defication”–there IS a difference, even if constipation makes us pray on the pot…

    14. Where can one purchase Daikenchuto?

    15. Dear John, Let me first say I am deeply sorry about your son, there isn’t anything more tragic.Second thank you for helping us try and heal ourselves.It is bad enough main stream medicine wont help us but like me I have had to spend much time UNDOING the bigger mess they made of me.I am 49 year old female, with idiopathic gastroparesis, pelvic floor disorder (Mayo Clinic) Hoshimotois,some what under control. No, sibo, h pylori, ect.Spent about 300k in four year on help, a bit, better due to major supplements and all the amino-acids we could think of.My question to you sweet John is, May 8 I see a BIH FUNCTIONAL MED DOCTOR.He has tested my thyroid levels, sex hormones but I really would like to see sertoin,gaba, nor-epinephrin, dopamine and glutemate done as well, whitch if all or of these or other would YOU say is worth test to help my GP.God Bless you, Your son would be so proud how you help us, sick and sad people.Sickness is a lonely place, yor contantly mourning for YOUR SELF. xxoo Ava

    16. Hi there,
      I had a stool test and the results showed that I had:

      – Escherichia Vulneris 10E4
      – Enterobacter aerogenes 10E4
      – Klebsiella pneumoniae 10E3

      As well as several candida overgrowths. I was put on a candida diet, and have been taking oregano oil, but it hasn’t helped yet (it’s been 1 month), and was just wondering if the bacteria listed could be a SIBO related overgrowth and if so, which one would it be? I am more constipated usually and bloated with gas.

      Your advice would be greatly appreciated!


    17. Just want to add an anecdotal observation regarding low dose morphine as a treatment to increase gut motility. My son has UC and after having multiple unrelated surgeries he was on Vicadin for too long. He hated giving it up…not due to the usual withdrawals but because he did not need his UC meds while on it. His intestinal processes were without issue. He is also OCD…suspect the Serotonin balancing effect for him was beneficial and a key player in both his UC and OCD. The gut is an unexplored universe of mystery. Thanks for helping to solve some of it. :)

    18. I have hydrogen pridominant sibo but constipation is my main problem along with severe bloating. Methane non existent. Never get diarrhoea. What gives? Doesn’t make sense

      • Based off of your symptoms you either have a damaged MMC OR the test results were incorrect and you have methane overgrowth.

        • What is an MMC? I have similar symptoms and have candida in my blood test but have not been able to alleviate it thru strict candida protocol and AIP. Just had a SIBO breath test done and am awaiting the results. Im worried it will show nothing and I’ll be back to square one.

        • I have methane dominate very high Baseline and 120 Minutes. I have very chronic d, loose stools bloating pain. What are your thoughts on this? There are few of us in a group that are high methane Baseline, no hydrogen but have chronic diarrhea.

          • I should add that i almost match up exactly with the symptoms you listed for sulfide, except for never constipation or alternating, just always constant diarrhea. Please let me know what your thoughts are here?

    19. Does triphala work like ducolax or senna , cascada etc?
      Or it works to stimulate the mmc subtlely?

    20. Hey, thanks for all your the info! I am taking Triphala and plan on taking 5-htp for a short while at bedtime to increase gut motility. How much 5-htp do you suggest? Also, most other SIBO sources list ginger as a prokinetic. Are there sources for this info? I am interested because ginger used to help with BMs, but now seems to do the opposite. Thanks again!


      • Start small with the 5-htp, 50 mg at bedtime. Ginger increases stomach emptying but may slow down the MMC and slow down motility.

    21. SO since you have ginger listed as decreasing motility, would it be bad for someone with IBS-C? If it increases gastric emptying, does it also decrease small intestinal motility then? I have IBS-C and use ginger because it helps my stomach empty faster (using about 500 mg four times a day via drops). Would it be wise to stop?

      • And one follow up, what about the fact that domperidone is basically guaranteed to cause hyperprolactinemia, and all of its negative consequences?

      • For some people yes, for others it seems to help. As long as it appears the ginger is helping and not causing constipation it should be fine.

    22. Hello.
      5 years ago I was infected with giardia. The infection was not treated for the first 2 years. Then I took multiple antibiotic courses and my stool antibody analyses (taken 2 times) showed that giardia is gone.
      However, my gut dysbiosis is still untreated. I have mild constipation (I use magnesium to relieve it), bloating and my stool is usually green or dark green. I also have an occassional belching and heartburn. Those symptoms are not severe and aren’t bother me much in daily life.
      The main problem that I have is insomnia and depression which progresses since I was infected 5 years ago. For the last year it has become more severe, and I have anhedonia, irritability and concentration problems now. I think its due to neurotransmitter imbalances and possible brain shrinkage that was caused by prolonged malabsorption and stress.
      Last time I visited my gastroenterologist I got diagnosis: IBS with constipation. I took multiple courses of probiotics and prebiotics without success. However, it seems that I sleep better when I take probiotics with lactobacilus.
      My stool test shows that I have very low lactobacilus level. Everything else is in optimal range. Candida is not found in the stool.
      I now suspect that I have SIBO-C. Do you think that it can be the cause of my symptoms? The problem is that only breath test for SIBO that is available in my location is hydrogen breath test with lactulose. There is no methane test. Should I take hydrogen-only test if never had diarrhea?
      I was negatively tested for h.pylori during gastroscopy. I’m planning to take stool test also.
      I will appreciate any help. Thanks.

    23. I saw you mention egg sensitivity linked with Hydrogen Sulfide SIBO on someone else’s comment. Do you have any more information about this? Is it related to hydrogen SIBO or methane SIBO?

    24. Hi, I was diagnosed a couple weeks ago with hydrogen SIBO. I’ve only experienced one episode of intense diarrhea a couple years ago, which was solved with a probiotic. I have always found that I need to stay on top of things in order to have a daily bowel movement. I don’t consider myself constipated, but if I don’t watch what I eat, I will get constipated. My hydrogen levels are at 50ppm after 75 minutes and peaked at 103ppm at 135 minutes. I am now on a two week course of Xifaxan and I’m one week in. I feel terrible. Tired, moody, however, I’m hoping its in part because of the die-off. I’m not pooping right now verb often because my diet consists of meats, fish, eggs, small servings of brown rice+coconut oil, and well cooked veggies. How am I supposed to poop?? Do you recommend a motility supplement? I am seeing a dietician tomorrow and have no idea what to eat right now. I was low FODMAP and that helped, but not a cure. Thanks.

    25. Hello! Do you have a specific recommendation for the 5-HTP Supplement? I looked up and Pure encapsulations has a 50mg and a 100mg and thorne has a more affordable 100mg. If you need background or specifics read on. Feel free to ignore if the answer is the same no matter what! I came across your site researching side effects from Prescript Assist. I get painful persistent Bloating and difficult to move gas and constipation from it but seemingly only when I eat eggs. I seem to be fine on eggs and PA except when consumed same day/day after. Something else set me off with extreme gas pain and odor yesterday and it is getting worse so it prompted me to come back to the site for more insight. My ND is having me do stool testing (Not sure but breathe doesn’t seem to be an option) and my symptoms are in line with SIBO and/or FODMAPS. I tested positive to 49 IgG so we have classified me as Leaky Gut. Good levels of everything in blookdwork except testoerone and still bruising easily so I got back on Standard Process FerroFood. I also Take Standard Process Adrenal (bovine), Pure Encapsulations Maca-3, Optimal Health Systems Digestion and am following the AIP diet.

      Thank you very much for any insight

      • Both are brands that I recommend but it all depends on the dosage and I suggest to start with the lowest dose possible first since some people have negative reactions to 5-HTP. Because of your negative reactions to eggs look into possible Hydrogen Sulfide SIBO.

    26. I have a question about the 5HT serotonin decreasement.
      In sibo-D the EC cells are creating too much of this serotonin, and causing diarrea. So motility can be adressed with ginger, pepermint or zofran?
      But I dont understand why we would slow down the motility?
      Is the cause of sibo not the damaged cleaning waves in the first place?
      how could we else get sibo if our motility worked too fast?
      So do we need a prokenetic too for sibo-d like resolor?
      Or do we need zofran to slow down things?

      • I have a question about the 5HT serotonin decreasement.
        In sibo-D the EC cells are creating too much of this serotonin, and causing diarrea. So motility can be adressed with ginger, pepermint or zofran?

        They can help reduce muscle spasms and contractions that occur in SIBO-D, therefore reducing diarrhea episodes. Menthol also has antimicrobial effects which may help.

        But I dont understand why we would slow down the motility?

        In SIBO-D motility is sped up, there can be issues with slowing down motility in people with severe gram negative overgrowth. Endotoxin retention may cause toxic megacolon.

        Is the cause of sibo not the damaged cleaning waves in the first place?

        It is.

        how could we else get sibo if our motility worked too fast?

        So do we need a prokenetic too for sibo-d like resolor?

        No, Zofran would be better.

        • Thx for answering.
          I did indeed have Post Infectious IBS as sibo cause from campylobacter.
          I readed ur link.But it doesnt really explain if we need to increase serotonin or slow down serotonin. Zofran slows it down right?
          So if motility is broken in small intestine, why do we slow it down with zofran? I did read all the articles about anto bodies against vinculin and CDTB toxin. But its not clear for me if we can manage the broken MMC more with zofran or a prokentic? Thx for taking ur time.

    27. You wrote that Ginger speeds up gut emptying and yet also DEcreases gut motility. Those are opposites. Which is it?

      And you also wrote “Domperidone has the same mechanism of action that metoclopramide does, which is blocking the 5-HT4 receptors” and yet also wrote that Domperidone INcreases gut motility. I thought that blocking 5-HT4 receptors should DEcrease gut motility, shouldn’t it?

    28. Hey John!

      I am wondering how far to space the supplements I am taking (so that I’m not contraindicating things/reducing effectiveness). They are:

      – interfase plus
      – candibac herbs
      – olive leaf extract
      -‘super garlic’
      – oregano oil
      – peppermint oil
      – lauricidin pellets
      – NAC
      – saccharomyces boulardii
      – factor 4 probiotics

      My issue is that I’ve been vegetarian for a long time and seem to have poor absorption/ constipation – and some accompanying stress problems. A lot of symptoms are similar to adrenal insufficiency and thyroid problems (somewhat like hashimotos, though I don’t seem to have it). I am also really reactive to any estrogen in my diet- have to avoid soy like it is the plague.

      Your mention of 5HTP seemed really helpful.

      I’ve been having a hard time staggering these throughout the day. My doc has me taking interfase 2x per day in between meals with candibac. Trying to figure out how /when to take oregano/peppermint oil/// when to take all the herbs/// when to take the lauricidin /// when to take the saccharomyces boulardii and probiotics. I’m also supposed to be taking a bunch of vitamins (zinc, magnesium glucarate, some copper I was deficient in, and 950s).

      Please help me think about how to schedule this. It is really getting challenging.

      Thank you!

    29. What to do if 5htp is not working it was effective only for two days and than stopped working….my stomach and guts are not mooving at all and nothing seems to help…

      • I would ask your doctor about trying triphala and using osmotive laxatives like magnesium and vitamin C orally while staying well hydrated to see if that helps. In addition, not snacking in between meals, eating only three meals, and walking daily may help.

    30. Hi Guys, I have sibo-c that results in depression. I assume the depression connection is linked to inability to absorb vitamins and possibly (my theory) the body using up what reserves it has to supply serotonin to the gut resulting in a shortage of what is needed to make serotonin in the brain.

      I’ve been managing very well for a while. I’m completely depression free if I’m strict on the diet and I have no wind but still get bloating as it involves high fibre. This is what I do which came about through trial and error:

      Avoid certain foods – lactose, wheat and high sugar
      Try to an anti inflammatory diet – mainly eating lots of sweet potato, and avoiding fried food
      Lots of multivitamins – 5htp, 3x high dose niacin (3x 600% of rda), a multivitamin, 2x vitamin b complex

      The most important part is very high fibre. If I cut out the fibre I feel depressed again it makes a huge difference. I have between 30 and 50 grams of fibre a day. From sweet potatoes, peas, baked beans, high fibre popcorn.

      I add a lot of spicy sauce to a lot of food which makes it more anti inflammatory and helps keep things moving.

      I assume it works because all the fibre absorbs a lot of gas and keeps things moving. I don’t have any wind at all when I’m strict on the diet.

      I’m hoping for a more permanent cure because it only takes a couple of fried meals or large helpings of sweets and my depression comes back and it takes about a week for it to come back. I recommend The Inflammation Free Diet Plan for helping sticking to an anti-inflammatory diet.

      I have a question myself. Has anyone tried allicin garlic extract or oregano oil as both are shown to reduce methanogens?

      • *i mean a week to get rid of my depression again if I lapse on the diet

      • Generally, alicin, oregano oil, and neem work the best against archaea.

        Spicy foods activate TRPV-1 allowing more water to enter the intestinal tract, you have to be careful with this though. In some people this can worsen leaky gut.

        Maybe try some GOS to increase Lacto and Bifido.

      • There are some probiotics that increase serotonin in the gut. Try AOR “advanced series probiotic-3” (good strains of strep and clostridium) and Mutaflor (good E. Coli, available from Canada). I don’t know why its all the scary sounding things that make serotonin, but it works for my daughter and husband.

    31. Will l-tryptophan supplements increase serotonin levels in the gut/ intestinal motility?

    32. In your book you recommend ginger to increase motility, but here you only recommend for IBS-D. Can you clarify?


      • Ginger increases gastric motility but appears to slow down small intestine MMC function due to being a 5-ht3 antagonist the same way the medication Zofran works on the intestines. The book is behind my blog in some aspects and will eventually be updated to a 3rd edition.

        • Why does ginger help so many with constipation then?

          • Because everything is not set in stone, what may work for some will not for others and vice versa. I have coached a lot of people where ginger did very little for their constipation.

        • when and where can we get a 2nd or 3rd edition? Not finding on here, amazon, kindle or ibooks. Thanks

          • The 2nd edition is on Kindle. If you have already downloaded the first edition you should be able to either update it or delete the current edition and redownload the new one.

    33. what about some research about detoxifying natural juices and immune-system boosters?
      I have not tried any immune booster yet, but this might represent a good option to start with. Sometimes it gets harder than others, but dont lose hope, keep trying…

    34. at wits end here, with sibo, doing research, never finding a real solution bec. every time I think I’ve found it, it involves taking something that aggravates symptoms, for example, you rec. seratonin increase in the gut, but the caveat is don’t do it if you have mental health issues (I have depression & panic attacks directly related to sibo & histamine & other food intolerances). There’s always a caveat, always a problem that comes with the so-called solution. I can eat almost nothing now, suffer from frequent depression, lethargy, & just plain don’t feel well enough to care abt hardly anything on my worse days. I’ve eliminated fodmaps. histamines, gluten, dairy, nuts, seeds, legumes, processed meats, nightshades, etc., etc. guess what–nothing left! I had hope for ozone treatments, but now they sound like just another problem. I give up!

      • Dorothy Baker How have you been? I ready your post and I suffer from the same symptoms…. Xifaxian antibiotics for my Sibo w/C only caused gyno. infections and I’m now more ill than before the treatment. Still have Sibo and more complications. Severe food intolerances-eating almost nothing, low vitamin levels, MTHFR gene mutation and no one can help, 2nd Naturalpath, GI Dr., Endrocrine doctor, PCP, Or not even GYN can’t understand the complications i’m having. Anyone have any thoughts or options?/

      • Hi
        Your situation sounds similar to mine. GAPS diet gave me huge histamine problems which nearly destroyed me. Have you looked into improving your methylation status to metabolise hisamine better?
        Methionine, P5P, vit c (and possibly methylfolate and methylcobalamin MAY help you). Also, if you have a build up of aldehyde in your system (candida toxin) your ability to metabolise histamine will be blocked. Vit b1, b2 & b3 are important to metabolise aldehyde although care needs to be taken with b3 (niacin) if you’re depressed because it can make it worse in some people.
        Check out for histamine intolerance article.

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