SIBO: Methane or Hydrogen Dominant, What Is The Difference?

SIBO: Methane or Hydrogen Dominant, What Is The Difference?

The sufferers of SIBO are usually divided into three different categories. People who are either suffering from chronic diarrhea, chronic constipation or an alternating version of both ailments.

What is the cause of the difference of symptoms in people who are both suffering from SIBO?

Research indicates that depending on what type of organisms are the dominant cause of your overgrowth determines what type of SIBO you have.

Are you dealing with an overgrowth of hydrogen dominant bacteria or methane dominant archaea?

Hydrogen Dominant Bacteria and SIBO-D

If you have diarrhea related SIBO predominantly, you are suffering from an overgrowth of hydrogen producing bacteria in your small intestine. Bacteria produce hydrogen gas as a byproduct of carbohydrate fermentation in the gut. A large amount of hydrogen gas exists naturally in our large intestine as a byproduct of fermentation. Large amounts of hydrogen gas, however, are not supposed to exist in the small intestine due to the lack of widespread fermentation. 1 2 3

Overgrowth of bacteria also produces toxins that irritate the gastrointestinal lining that causes diarrhea. Most of these toxins overload the TRPV1 receptors in our gut, greatly increase osmolarity, and gut peristalsis that causes diarrhea as a defensive mechanism to protect the body from the toxins and bacteria. Capsaicin that is found in peppers also activates the TRPV1 receptors that may explain the reason they cause diarrhea in many people after consumption. 4 5

An overgrowth of hydrogen dominant bacteria would cause diarrhea. 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.

Medications / Supplements That Decrease Gut Serotonin / Motility:

  • Ginger – I recommend either taking New Chapter Ginger Force, twice daily with meals, drinking ginger tea twice daily with meals or eating fresh grated ginger twice daily with meals. Ginger contains galanolactone that appears to be a potent 5-Ht3 antagonist that might explain its anti-emetic properties and ability to accelerate gastric emptying. 6 7
  • Peppermint – Menthol found in enteric coated peppermint supplements reduces MMC contractions, therefore slowing down intestinal spasms and motility. 8
  • Zofran – Ondansetron is a serotonin 5-HT3 receptor drug used in the prevention of nausea and vomiting. It works by reducing the activity of the vagus nerve, which deactivates the vomiting center in the medulla oblongata. In addition, in people with IBS, 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 30 mg.) Zofran works well in people with SIBO-D, but may cause constipation to worsen in people with SIBO-C. 9

Methane Dominant Archaea and SIBO-C

Your intestinal flora is comprised of organisms known as archaea. Archaea are different organisms; they are single-celled organisms that lack a nucleus. Archaea in our digestive system feed off of hydrogen that bacteria produce during the fermentation of carbohydrates in our gut. Archaea then produce methane as a byproduct of their digestion. 10 11 12

The more fermentation and hydrogen gas that occurs in the intestines, the more methane archaea will be able to produce. Cows flatulate a lot more methane than humans because they consume a lot more fermentable foodstuff (grass for example) than humans 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 90% of our archaea gut flora. 13 14

What happens to the hydrogen produced in our body:

Decreased MMC function and lactose malabsorption have been correlated with an overgrowth of archaea in the gut. 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 overgrowth, which can help protect the bacterial overgrowth from immune elimination. 15 16 17

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

“Compared with hydrogen producers, methane producers had significantly (P<0.05) 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.” 18

Serotonin (5-HT3 / 5-HT4) is one of the biggest neurotransmitters in the gut associated with regulating proper 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 slow down emptying of the small intestine, which can lead to SIBO. 19 20

It is more difficult to lower archaea overgrowth because they tend to be more antimicrobial-resistant and form thick biofilms. 21 Treatment of the overgrowth might require multiple natural antimicrobial agents, antibiotics, and anti-biofilm agents. Changing your diet to a low FODMAP type diet might reduce archaea overgrowth 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 help with an archaea overgrowth.

Increasing MMC function during an archaea overgrowth might be one of the most important things one can do to help overcome the overgrowth.

Supplements / Medications That 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 an SSRI) or if you suffer from any serious mental health issues. 22
  • Domperidone – Domperidone has the same mechanism of action that metoclopramide does, as a 5-HT4 receptor agonist, but unlike metoclopramide, it does not cross the blood-brain barrier. All of the CNS 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 LES tone. Domperidone has not been approved to be used in the U.S. The IV form of domperidone has been linked to increased QT intervals and should be rarely used. 23
  • Triphala – Triphala is an ayurvedic herb that increases gastric emptying, gut peristalsis, and increases gut muscle tone. 24 25
  • 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 plexis, 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 minute doses. 26 27 28

  1. http://autoimmune-paleo.com/the-sibo-saga-part-1/
  2. http://ndnr.com/gastrointestinal/small-intestine-bacterial-overgrowth-2/
  3. http://www.townsendletter.com/FebMarch2013/ibs0213.html
  4. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3400813/
  5. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2564830/
  6. http://www.ncbi.nlm.nih.gov/pubmed/23490018
  7. http://www.ncbi.nlm.nih.gov/pubmed/16041645
  8. http://www.ncbi.nlm.nih.gov/pubmed/10641042
  9. Beers, Mark. The Merck Manual, Merck Research Laboratories, 2006.
  10. http://www.hollywoodhomestead.com/hydrogen-vs-methane-sibo/
  11. http://www.townsendletter.com/FebMarch2015/sibo0215.html
  12. http://chriskresser.com/sibo-and-methane-whats-the-connection
  13. http://www.hollywoodhomestead.com/hydrogen-vs-methane-sibo/
  14. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0007063
  15. http://www.hollywoodhomestead.com/hydrogen-vs-methane-sibo/
  16. http://www.townsendletter.com/FebMarch2015/sibo0215.html
  17. http://chriskresser.com/sibo-and-methane-whats-the-connection
  18. http://www.nature.com/ajgsup/journal/v1/n1/full/ajgsup20126a.html
  19. http://www.nature.com/ajgsup/journal/v1/n1/full/ajgsup20126a.html
  20. http://www.gastrojournal.org/article/S0016-5085%2898%2983246-0/abstract?referrer=http%3A%2F%2Fwww.gastrojournal.org%2Farticle%2FS0016-5085%2898%2983246-0%2Fabstract
  21. http://www.ncbi.nlm.nih.gov/pubmed/25071757
  22. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2312355/
  23. Beers, Mark. The Merck Manual, Merck Research Laboratories, 2006.
  24. http://gimasterycourse.com/wp-content/uploads/Small-Intestine-Bacterial-Overgrowth-Clinical-Issues-Diagnostic-Testing-and-Treatment-Options-10-5-15.pdf
  25. http://www.jpgmonline.com/article.asp?issn=0022-3859;year=1997;volume=43;issue=1;spage=12;epage=3;aulast=Tamhane
  26. https://www.ncbi.nlm.nih.gov/pubmed/10573360
  27. http://www.ncbi.nlm.nih.gov/pubmed/8848916
  28. http://www.ncbi.nlm.nih.gov/pubmed/10990104
46 Comments
  1. 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!

    Jess

  2. 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. :)

  3. 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.

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

  5. 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!

    Michael

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

  6. 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.

  7. 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.

  8. 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?

  9. 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.

  10. 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.

  11. 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?

      http://fixyourgut.com/campylobacter-a-cause-of-sibo/

      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.

  12. 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?

  13. 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!

  14. 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.

  15. 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.

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

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

    John

    • 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.

  18. 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…

  19. 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 mthfr.net for histamine intolerance article.
      Paul

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