Your digestive system eliminates waste through a process known as the migrating motor complex. The cycle of the peristalsis of the gut occurs every two hours.

The MMC cycle includes four phases: 1

  1. The first phase is a period of intestinal smooth muscle calmness lasting 45 to 60 minutes, which only rare action potentials and contractions occur.
  2. The second phase is a period of roughly thirty minutes in which peristaltic contractions occur and progressively increase in frequency. Peristalsis originates in the stomach and propagates throughout the small intestine.
  3. The third phase lasts 5 to 15 minutes and consists of rapid, evenly spaced peristaltic contractions. In contrast to the digestive period, the pylorus remains open during these peristaltic contractions, allowing many indigestible materials to pass into the small intestine.
  4. The fourth and final phase is a short period of transition between the strong contractions that occur in the third phase and the inactivity that occurs in the first phase.

During the migrating motor complex increased gastric, biliary, and pancreatic secretion occurs to help further digestion and decrease bacterial buildup in the proximal segments of the digestive tract. It is believed that the MMC is controlled by the enteric hormone motilin. Ingestion of food overrides the MMC, therefore, fasting has to occur regularly to help complete the process. The typical “growling” sounds you hear when you are hungry might be the MMC doing its job, cleaning your bowels of waste and excessive bacteria through increased peristalsis. 2 3

As much as 70% of people afflicted with SIBO experience a disruption of MMC rhythm. Excessive methane / hydrogen gasses produced by overgrowth of bacteria in the gut has been linked to decreased MMC function. When the second and third phase of the MMC is reduced, bacteria remain in the small intestine instead of being pushed back into the large intestine. Bacteria are then able to adhere and propagate in the small intestine, which increases inflammation and intestinal permeability. Inhibition of MMC homeostasis drives the vicious SIBO cycle. 4

Reduction of stomach acid by using acid reducing medications or H. pylori infection can contribute to poor MMC function. Lack of exercise, grazing, and constipation can contribute to poor MMC function. Being overstressed and anxious can also decrease MMC function. Finally, low thyroid function and adrenal fatigue can lower MMC function. 5

Fasting for at least four hours after meals during SIBO protocols might be beneficial in re-regulating the MMC. The increase in fasting time gives your body longer time to complete the MMC process. MMC also occurs during sleep, which proper sleep may be more helpful because of the longer total fasting time that normally occurs during sleep. Frequent exercise also helps to regulate the MMC properly. 6 7

  1. So basically what can one do to get the bowels going if it has been 5 days now and nothing happening.
    It just seems to be getting worse.

  2. Really great text! Thank you for these important thoughts on handling SIBO!
    I’ve been struggling with digestion issues for a couple of years now and was diagnosed with SIBO just a few months ago. Overall I’ve lost more than 20 pounds throughout the years/months and now trying to get a long with a serious underweight.
    One of my major problems is, that my symptoms are really bad after eating normal servings of all kinds of food (or even after what an ordinary eater would name a small serving). So I started eating quite tiny quantities every hour. Anyway I definitely agree on your thoughts on the MMC cycle, cos I feel so much better after some hours of not eating (although I’m hungry and at some point out of energy).
    But I really don’t know how to get started with those four hours of fasting between the meals or just eating three/four times a day. Cos from my perspective this meals would need to be so huge!
    So do you have any further advice how to eat quite small quantities but considering the MMC cycle?

    And again: thank you for your explanations on SIBO and MMC. They really helped me understanding some important essentials.

  3. thanks, good write up. Ive had SIBO for five years now, IBS for 10 years prior (it was probably just SIBO but less worse then). I just started erythomycin prokinetic last night. I had to throw a fit at kaiser so my specialist would give it to me. She wont continue it for more than three months, even if it works great. Ive done every test. It has to be the MMCs. For one, i dont ever hear my stomach growl. I get recurrent SIBo that doesnt respond to rifaximin anymore, only this drug with flagyl. But im done with antibiotics and have been starving myself basically. I eat six-seven hours apart, 3 times a day. Its tough but keeps the worst symptoms at bay (rotten egg burps, bloating, diahrea, smelly gas, nausea, etc). Do what you can to get a prokinetic, fight for it. And space your meals out

  4. I was diagnosed with hydrogen dominant SIBO two months ago after suffering for years with varied “mystery” symptoms. I took a round of Rifaxamin and felt so much worse. Then, tried Candibactin for six weeks. I’ve been very depressed and anxious. I am now trying Low Dose Naltrexone which I got from a clinic in Scotland. I have not seen a gastrointerologist but am anxious to do so. I’m wondering if you believe a fecal microbiota transplant will help. I’m two days off sugar. I have been a junkie but am now too sick to go on like that.

    • Do not see the gastroenterologist! Mostly they refuse to acknowledge bad gut bacteria! They tell u it’s IBS and treat the symptoms! Never treating the root cause, which makes IBS incurable! U have to cut out the sugar! You have to! Got to and order the FCR freedom cleanse restore. It has ALL the herbal remedies in three different supplements for three different purposes! Freedom fights the bad guys. Restore helps restore digestive tract damage. Cleanse helps clear out the stuff u have killed with the other two. This plus the right diet, which is not easy! I’m working on it now and seeing some improvements but it is a long road and the die off often feels like the issues from having the overgrowth in the first place, but u will see little signs along the way! Candida diet with a few small adjustments becomes the SIBO diet

  5. John, how do you know if the MMC is messed up? By bowel regularity? Is there a test? Likewise, how do you know when its normalized?

  6. It is not a good idea to make upset the MMC, ruining the metabolic rhythm of yours, fasting 4 hours maybe is a tolerable habit but not 6 hours. It is good to stimulate the MMC with good habits, as for example visiting alien places, holy churches, because that can boost MMC due to fear reactions.

  7. Does anyone know if exercising right after eating increases the function of the MMC? I know exercise in general does, but I’m thinking a short and easy walk after each meal might encourage it further. Any thoughts?

    • It should in theory increase the MMC from increased adrenaline, blood pressure, and heart rate. Some people would say that it would pull blood from the digestive organs which may slow it down. All you can do is try and see!

  8. Many thanks for this great information,

    I have been taking Omeprazol for 3 years, and I dont know if it is the reason for my reduced MMC and if it is the causing to not cure from SIBO.
    I was trying some natural herbal antibiotics like chili pepper and ginger, whcih I found very helpful, but it does not cure it for good.
    1- Do you think reducing my meals size and having 5 meals aday is good for me?
    2- Is there any safer replacements for omeprazol, because I tried to quit of it, but this cause a hearburn for me?
    3- how not to loose weight in this fasting system ?

    With my best regards

    • 1. No that would slow down MMC function. It is best to eat three meals daily and chew the food very, very well to prevent poor digestion and overeating.
      2. It is normal for that to occur, it is called rebound reflux. I recommend working with your doctor to titrate the dose slowly on the PPI. Taking d-limonene and zinc carnosine may help with that. I would also get your B12 levels checked and supplement with magnesium to help with PPI caused deficiencies.
      3. Continue working on reducing overgrowth and hopefully absorption of nutrients will normalize and your weight will stabilize.

    • I recommend FCR FREEDOM CLEANSE RESTORE FROM or PCI wellness , WHICH IS THE SAME COMPANY. That plus diatomaceous earth plus the right diet! I’m only 3 months in to this treatment but am seeing results, small things you will notice bc you are very aware of all the little things your body has already been doing , so thru the pain and burping and etc, u will know it’s the stuff working and not the SIBO eating, since much of the die off seems the same as the issue itself! It gets confusing but u will start to see enuf to see its working

  9. Hello,

    I’m curious what actually interrupts the MMC. My natural doc has me taking supplements mid-morning, and I also sip on coffee or tea as well as water. What about other drinks? Bone broth for instance? I’m pretty sure poor MMC is the reason I developed SIBO, and really want to get rid of it and not get another occurrence. I’m up for “fasting” for 3-5 hours between meals, but I can’t find information on what that means.

    Thanks for the great info!

    • It is uncertain if liquids interrupt the MMC. It is unlikely that if it does it would last very long. Bone broth might interrupt it for a little longer because it contains protein that needs to be digested. I would only trust water and maybe tea or coffee.

  10. if sibo, check for an announcement from Dr Mark Pimentel coming in May.

    If your diet is not absolute complete perfection, then you are throwing your money away on everything else. You cannot ingest a morsel of refined sugar or processed food in the day, and likely dairy too. Eat a low fodmap diet. No point to go too low carb since the bugs will merely go into “survival” mode.

    All else fails, the elemental diet and a prokinetic.

  11. Hi thanks for sharing all the great info on your site!

    I have been battling (sort-of) SIBO for about 2 years now – confirmed by the hydrogen breath test done at Straub Hospital Honolulu. I too believe I’ve had it for many years but it only became seriously problematic a year or so after a week of double IV administered heavy-duty dose antibiotics for a blood infection which hospitalized me (for 7 days!) followed by an intense bout of nasty nasty food poisoning less than a year later… Talk about THE perfect storm!

    This past march I did 10 days of Xifanan (Rifaximin) but did not change much regarding diet. The SIBO symptoms came back oh just a few months later – mine are;

    TONS of hydrogen gas high in my stomach often impossible to burp up and of course much increased muscle & joint pain, MORE tinnitus and now, I have minor “throbbies” with tingly extremities, burning feet, super light headed when getting up rapidly, and for the past few years my hair has been falling out – MORE these past 7 months. :-( and constantly fighting mild depression.

    I did not know all the ins & outs regarding lipopolysaccharides aka LPS and its relation to my chronic joint and muscle pains, the tough protective biofilms, the possible low thyroid connection, the controversy of a higher fat diet being not so optimal (shucks I was happy & excited about doing a modified paleo – (no sweet potatoes!) .

    I just ordered InterPhase and yesterday started on Wobenzyme proteolytic enzymes (for all that nasty inflammation I am sooooooo tired of!!) and now am purchasing the Lactoferrin too.

    I have good herbal antimicrobials Dysbiocide & FC Cidal* (Biotics Research Laboratories) and very good probiotics but will stop taking all these until after I have been on the Interphase, Lactoferrin and proteolytic enzymes for a few days.

    My plan is to:

    1. Follow Dr. Robillards Fast Track digestion Fermentation Potential (FP) diet (don’t eat things that will ferment IN MY GUT & help bacteria multiply).

    2. Dr. Mercolas Wholefood vitamins plus minerals on my “eating” days along with extra iodine & Iron supplements, lots of digestive enzymes, Betaine HCl with my food and of course methylcobalamin form of B12. Sip on homemade kombucha (brewing now!) and eat fermented foods ie; sauerkraut, Kim chee etc.

    3. Take the systemic enzymes-empty stomach… InterPhase, Wbenzyme and Lactoferrin

    4. Do intermittent 1-2 day bone broth fasting. (I made a huge batch of 24 hour beef bone broth steeped with ginger, turmeric, onion, carrot, celery, garlic and shitake.)

    5. Probiotic supplementation


    1. DO YOU KNOW if its best to take the probiotics at night after the day of the biofilm cracking & bacteria killing OR visa versa? OR…

    2. 1-2 days of killing & fasting followed with 1-2 DAYS of eating & probiotics?

    3. Should I take the nutritional supplements even on broth fasting days? And do you think my brand choices are good?

    I am now officially afraid yet rather pissed off at these tiny bugs gassing away in my gut and even did a rare thing for a strong Dragon Aires… I cried on my husbands shoulder! I HATE feeling weak and compromised. Time to kick some ASS!

    • 1. I do not recommend taking probiotics at all during an elimination protocol unless you are hospitalized to protect from C. diff. Instead:
      2. Possibly, but the days of water fasting might make your gut barrier worse off in the long run since glucose is required to synthesize NAG.
      3. Yes and Yes.

      Good luck!

    • The onion and garlic while good for Candida , probably will make u worse while treating SIBO and leaky gut

    • Hi Shelly,

      I’m curious how things are going for you these days? Have you gotten the SIBO under control. I too live in Honolulu area and was recently diagnoised with SIBO. That’s awesome that Straub did it, I didn’t realize conventional doctors were testing for it. For me, It’s gotten so bad that I can’t eat anything without severe pain and bloating. I’m down to 99 lbs at 5’3″ as I’m trying to wean my 9 month old from breastfeeding😥 I feel I have no choice if I want to survive. I’m starting the liquid Elemental Diet in 2 days to starve the bacteria, praying I can’t stomach it and start to gain weight and nutrients. I’m just a little lost with how to keep it under control once I’m off the diet and would love to hear what worked for you and what didn’t, that is If you wouldn’t mind sharing your experience with me. Thank you so much in advance.

      Love and Aloha,

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