You may not be aware of it, but there is a silent battle being waged for control over your small intestine and many, perhaps the majority, of Americans are losing the battle.

I’ve previously discussed the crucial role of the small intestine—the 24-feet of duodenum, jejunum, ileum beyond the stomach and before the colon—in numerous gastrointestinal (GI) processes such as the immune response, nutrient absorption, and small intestinal bacterial overgrowth (SIBO).

Contrary to longstanding belief, the small intestine should be richly populated with microbes. It is not as densely populated as the colon, but there are nonetheless abundant microbes in a healthy small intestine. Unfortunately, a stool specimen submitted for analysis is largely a rectal specimen and may not tell you much about the microbial composition of the ileum 4-5 feet up from the rectum, even less about the jejunum many more feet up. The only practical way to study the composition of the small intestinal microbiome (at least for now; new technologies such as biopsy capsules may change this) is for a gastroenterologist to obtain an endoscopic aspirate, i.e., a small quantity of the fluid obtained during upper endoscopy, submitted for study.

The normal healthy small intestine should be colonized by mostly beneficial microbes, not fecal microbes. It should be colonized by species of Clostridia, Streptococcus, Ruminococcus, Veilonella, Prevotella, Lactobacillus and others

But analyses of duodenal or upper jejunal contents in modern people are revealing plenty of fecal microbes and fungi, especially in people complaining of abdominal discomfort, food intolerances, weight gain, fatty liver, excessive bloating, and diarrhea. This is not the normal situation.

The battle for the small intestine is being lost to fecal and other microbes because most of us have lost species that formerly colonized the upper GI tract and “fought” back fecal microbes. Many of these species produced bacteriocins, natural antibiotics effective in suppressing or killing fecal microbes like E. coli, Pseudomonas, Proteus, and Klebsiella. The species that, in most of us, formerly colonized the upper GI tract were species of Lactobacillus such as L. reuteri and L. gasseri: both upper GI colonizers and vigorous producers of bacteriocins. L. gasseri produces up to 7 bacteriocins, while L. reuteri produces up to 4. (My microbiologist friends tell me they occasionally clean their fermentation vats with L. reuteri, reflecting its potent antibacterial capabilities.)

If you’re having trouble following these arguments, the sequence goes like this: you take an antibiotic such as amoxicillin or azithromycin; because they are susceptible to common antibiotics, you reduce or eliminate beneficial species living in the upper GI tract such as L. reuteri and L. gasseri because these microbes colonized the upper GI tract where they produced fecal microbe-suppressing bacteriocins, fecal microbes are allowed to ascend and proliferate, i.e., SIBO.

The loss of upper GI-colonizing species that produce bacteriocins is therefore a likely contributor to the epidemic of SIBO that, in my estimation, affects 1 in 2, or 160 million, Americans. This is not just experienced as excessive gas, bloating, indigestion, abdominal discomfort, and diarrhea, but also as depression, anxiety, type 2 diabetes, obesity, fatty liver, autoimmune diseases, psoriasis, rosacea, fibromyalgia, restless leg syndrome, and neurodegenerative diseases due to the phenomenon of endotoxemia, i.e., the entry of bacterial breakdown products into the bloodstream.

I believe that this explains why around 90% of people following my recipe for “SIBO Yogurt” are converting from breath-H2 positive to H2-negative by the AIRE device. (We are planning a formal clinical trial to validate.) SIBO Yogurt combines the upper GI-colonizing and bacteriocin producing power of L. gasseri, L. reuteri, and Bacillus coagulans using prolonged fermentation and addition of prebiotic fibers to yield several hundred billion counts of microbes per 1/2-cup serving. The recipe, along with sources of the specific species/strains can be found in my Super Gut book or in the recipe section (for paid members).