Why Supplementing With Probiotics May Make You Ill – Part 2: MMC Issues

Why Supplementing With Probiotics May Make You Ill – Part 2: MMC Issues

Probiotics are supposed to improve digestive health, yet they sometimes make people ill – especially if they have SIBO. Why do supplements touted for improving digestive health make some people worse?

Is it microbial die-off in people with SIBO? If they continue taking the probiotics, will they get better?

In most cases, they will not because one of the reasons why they have SIBO in the first place – poorly functioning MMC and compromised motility.

Microbial Ingestion and our MMC

We ingest microbes on a constant basis through swallowing, eating food, drinking water, and clearing our sinuses. What is our first line of defense? What keeps us from getting sick when we are swallowing all these microbes all the time? The answer is our mitigating motor complex or MMC for short. 1 2 3

The Stomach

Gastric acid eliminates many of the microbes that we ingest because they cannot survive the low pH of the fluid. Our stomach also produces pepsinogen that is activated in the presence of gastric acid (pepsinogen becomes pepsin) to help us digest proteins. Pepsin also inhibits bacterial growth by proteolysis, which is breaking down bacterial proteins necessary for their survival. 4 5 6

Small Intestine

Some parts of the small intestine are a relatively sterile environment like our stomach compared to the rest of our body. There are some bacteria in the small intestine, but they exist in small numbers because of proper MMC function. Our large intestine is a perfect place for bacterial growth; it is an anaerobic competitive environment with many carbohydrates that can be fermented for energy. Bacteria in the large intestine do not have to deal with strong peristalsis waves that occur in the small intestine, immune system components to reduce their populations, or deal with the harsh components of chemical digestion (stomach acid, bicarbonate, bile, and pepsin that are still found in the duodenum). 7 8 9

The few microbes that survive stomach acid and pepsin in the stomach are further reduced by bile in the duodenum. The jejunum of the small intestine contains more microbes than the duodenum and the stomach because it is a very alkaline environment. Large amounts of mucus are secreted by goblet cells in the jejunum to help trap opportunistic microbes during digestion. If the MMC is functioning properly, goblet cells are also able to produce acidic mucus, which can be used to trap further and eliminate pathogens. Like the jejunum, the ileum also contains more microbes than the duodenum and stomach, but it contains GALT lymphoid tissue known as Peyer’s patches. Peyer’s patches produce leukocytes that help combat opportunistic microbes in the lower intestinal tract. 10 11 12 13

Large Intestine

Even though half of the small intestine contains more microbes than the stomach, there are defense mechanisms in each section to help eliminate opportunistic microbes and push the microbes that survive where they belong into the colon. Strong MMC contractions push what organisms survive into the large intestine through the ileocecal valve where they either become healthy flora or are eliminated by the body through our feces. 14

Failure of the MMC

In most people with SIBO, stomach acid levels are below normal (which is why PPI are indicated as a cause of bacterial / yeast overgrowth.) Lower stomach acid and pepsin levels mean that more bacteria survive after consumption and enter the small intestine unchallenged. 15

Less bile is also produced in people that are suffering from overgrowth that further hinders microbial reduction. Microbial toxins that are ingested, or caused by overgrowth damage the interstitial cells of Cajal that control the MMC slowing gastric and small intestine emptying and ileocecal valve closure. 16 17

Bacterial overgrowth also leads the goblet cells to produce too much mucus and by doing so further pull microbes into the small intestine that lead to their survival in an overwhelmed system. The immune system is so overwhelmed that they cannot eliminate the microbes that are trapped in mucus. The goblet cells eventually exhaust themselves, leading to bacteria producing biofilms, which replace beneficial mucus, causing small intestine ulceration. 18

Bacteria move freely from the large intestine into the small intestine further causing issues because of a faulty functioning ileocecal valve. The ileocecal valve connects the small intestine and the large intestine and prevents waste and bacteria from back flowing into the small intestine during proper digestion. When we suffer bacterial overgrowth the ileocecal valve malfunctions further hindering digestion and MMC function. 19

Probiotics and Poor MMC function

So where do probiotics fit into this equation and why should we avoid them if we are suffering from overgrowth or poor MMC?

If you have issues with your MMC the probiotic bacteria you ingest will end up in your small intestine instead of your large intestine where they belong. The bacteria could then become opportunistic, produce hydrogen gas, and worsen SIBO symptoms, or die off causing herx reactions. Either way, they will contribute more to your digestive woes instead of improving them. 20 21

14 Comments
  1. So if we suspect the problem is with the MMC, how do you restore its function? is the use of prokinetics the only way or is it a once damaged always damaged kind of scenario?

  2. How does one know if the MMC is not working properly, to the point where it would cause SIBO?

    • Chronic constipation is one of the biggest causes of SIBO and appendicitis. The best thing an asymptomatic person can do who is chronically constipated is to relieve it, which would prevent those issues. Stay hydrated, supplement with magnesium, eat more plant fiber, squat when you use the toilet, and consume proper amounts of Real Salt.

  3. We all know that antibiotics can kill numerous pathogens that cause disease. But do you have to go this far in order to keep yourself healthy? Science says “no.”

  4. Thank you. What you are saying is finally making sense to me and my problems with SIBO, hypothyroidism, chronic constipation. You say, “which is why PPI are indicated as a cause of bacterial / yeast overgrowth.” What is PPI (sorry…I am still learning)?

    You recommend 5-HTP; how much? You also recommend Triphala; does?. Will these two help the chronic constipation? Sounds like I need to stop taking probiotics; what about prebiotics?

    Thank you.

    • Proton Pump Inhibitor

      I cannot recommend a standard 5-htp dose because of side effects associated with its use and that it can react with certain medications.

      Triphala increases intestinal peristalsis, it helps with constipation. Most prebiotics cause issues with SIBO. I wrote a lot of articles about it under the prebiotic tab.

  5. How does one then stop the vicious cycle of IBS, low HCL, chronic SIBO recurrence, mal-digestion/absorption, chronic inflammation asks a person who has digestive issues as long as I am conscious (am now 53) been round and round with anti-inflammatory diets, supplements Functional Medicine, gut healing protocols, antimicrobials (botanical and pharmaceutical) and the last twist after decades of docs is that I have persistent Lyme and co-infection (diagnosed by iGenix Lab and low CD57 count – no rash/bite…) After 1 yr and 9 mos on an anti Lyme (via Lauriciden, bio-film busters, detox and Byron White protocol) i have now developed a load more food allergies and inflammatory mucosal issues in my mouth. I suspect this is all a leaky gut and a handicapped micro biome. how to fix it?!?!? – This article on the MMC makes me wonder if it is not all originating up stream as i find when i swallow it never goes down. about 4 yrs ago I was put on Procalupride (a pro kinetic british pharmaceutical) and honestly it was expensive and hard to say if it did anything. HOW DO YOU ADDRESS THE COMPRIMISED MMC? Please and thanks and how do i find out about your rates?

    • It sounds like you are suffering from both a compromised MMC and mucosial lining. If you are having gastroparesis, ginger may help. If you are constipated however do not go with ginger, instead try triphala. Maybe try GOS (Galactooligosaccharide) to help increase gut diversity.

  6. Hi John – came to your site while looking up Prescript-Assist. Bought your book and read it fully but not clear on how to apply to my situation.

    Long story short: my 18 month old has had ongoing constipation since I weaned her at 9 months. (Her gut flora in her first days of life did not establish ideally, which I think is now affecting her.) A few months ago we started giving her HMF powder daily which immediately solved the problem. But she’s suddenly got constipation again despite daily HMF powder. I fwas going to buy Prescript-Assist, but after reading your site I’m feeling cautious. I’m also now questioning daily probiotics for her but I don’t know what else to do.

    You didn’t really seem to think of probiotics as beneficial in the case of constipation, but HMF powder made an immediate impact for her (other probiotics had not.) Would you recommend Jarrow Ideal Bowel Support for a constipated toddler?

    I read that you think fermented foods should be prepared at home — what are your thoughts on heavily upping intake of fermented foods? Is this how you recommend building back flora naturally?

    • Hello, did any of these remedies work? My toddler has the same problem? I was going to try triphala first since 5 htp scares me a but to try on a toddler so young. Let me know! Thank you!

      • Some help, everyone is different. I cannot recommend anything to give a toddler to increase intestinal transit time except making sure the child is well hydrated and ask the doctor about magnesium. 5HTP is more than likely not safe to use on a developing brain.

  7. Outside of prescriptions (which my insurance won’t cover), what is another means of restoring the MMC? It’s an important, no mandatory process for success, but not many people I’ve found who bother to talk about curing their SIBO discuss. I’ve tried Ibergast with little results, but then again, I was doing elements of good things piece by piece to treat and recover post SIBO that it’s no wonder mine has come back. I’m going to be back on the microbials, but will also be focusing on the MMC, stress, and gut healing at the same time. (Mine is methane dominant- ouch)

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