While fats, proteins, and carbohydrates in foods we ingest are degraded by stomach acid and pancreatic enzymes, the lactase enzyme responsible for digestion of the milk sugar, lactose, lines the small intestine. Lactose digestion is therefore a small intestinal process.
The small intestinal ability to digest lactose, among the most abundant sugars in human breast milk (along with human milk oligosaccharides), is a requirement for an infant to extract both direct nutritional benefits and indirect microbial benefits. It is therefore extremely uncommon for a newborn or infant to show evidence for lactose intolerance (congenital lactase deficiency–only a handful of cases ever described). Children of virtually all races and ethnicities are able to digest lactose from human breast milk.
Many children, particularly those of Northern European ancestry, i.e., populations who experienced a survival advantage in the domestication of ruminants such as goats, sheep, and cows and harvested their breast milk, maintain the ability to digest lactose into later life via a genetic variant acquired many generations earlier. Others, however, especially those of Eastern European, Asian, or African descent, lose expression of the lactase enzyme sometime after weaning from breast feeding, typically during childhood, and show lactose intolerance experienced as abdominal pain, bloating, diarrhea, headache, muscle aches and behavioral changes. These are populations that, for the most part (there are exceptions), historically did not domesticate ruminants and harvest their breast milk, or did so more recently (anthropologically speaking).
Lactose that is therefore undigested in the small intestine can reach the colon where microbes ferment it to gases, carbon dioxide and hydrogen, that are responsible for the gas, bloating, and diarrhea of lactose intolerance. This explains how people who lose lactase expression are often able to tolerate modest intakes due to the GI microbiome’s capacity to also metabolize lactose. This includes important commensal species such as Faecalibacterium prausnitzii, Lactobacillus, Bifidobacteria and Roseburia species in the colon. You can exceed the microbial capacity to digest lactose by consuming the 12 grams of lactose present in 8 ounces of cow’s milk, but typically not the 2 grams in 3 ounces of hard cheese.
But what if symptoms of lactose intolerance occur before 90 minutes after ingestion, i.e., before the lactose has an opportunity to reach the colon 24-feet down from the mouth? This may not represent genetically-programmed loss of lactase, but may reflect small intestinal bacterial overgrowth, SIBO, i.e., the ascent of mostly fecal bacterial species up into the 24-feet of small intestine. In other words, simply dismissing acquired lactose intolerance as just loss of lactase can be wrong with considerable consequences for long-term health issues.
Should an adult who was previously tolerant to dairy products experience a reduction in tolerance, a shift in GI microbiome composition and location should be considered, most commonly SIBO. Acquiring lactose intolerance as an adult after years of tolerance is therefore a telltale sign of having developed microbial overpopulation in the small intestine. The danger comes in dismissing intolerance to dairy products as simply “lactose intolerance” when it really represents SIBO. Recall that burying your head in the sand with SIBO invites long-term and substantial health complications that includes weight gain, increased potential for type 2 diabetes, increased potential for Alzheimer’s dementia and other neurodegenerative diseases, and cancers of the gastrointestinal tract (pancreatic, biliary, colorectal). If you developed lactose intolerance as an adult and your doctor simply advised you to avoid dairy products, he/she has potentially performed a grave disservice to your health.
Also, note that lactose intolerance (i.e., a carbohydrate intolerance) is distinct from cow’s milk allergy (to milk proteins). While both are associated with GI symptoms including abdominal discomfort, bloating, and diarrhea, cow’s milk allergy tends to be accompanied by allergic or immune phenomena such as eczema, asthma, rhinorrhea, conjunctivitis, itching, and hives. They can also be distinguished via formal testing (e.g., lactose breath test for lactose intolerance).
On another side-note, note that my method of using prolonged fermentation to make our various yogurts, such as Lactobacillus reuteri yogurt, maximally converts lactose to lactic acid, thus the tartness and pH as low as 3.5-4.0, up to 10-times more acidic than conventional (minimally fermented) yogurts. The minimal quantity of remaining lactose means that, even if you have genuine lactose intolerance, many can still consume L. reuteri and other yogurts created via prolonged fermentation and not experience adverse effects. And, of course, if you experience symptoms of intolerance within 90 minutes of consumption of L. reuteri yogurt, you have SIBO.