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