Now, a more modern understanding of microorganisms has lead to an interest in preserving commensal bacteria already present in food. Milk in the cow is generally safe to drink, but cows aren't clean on the outside, and milk is often contaminated during the industrial process. So this leads to a situation where bad bacteria are occasionally mixed in with the good.
Fortunately, testing for specific species of bacteria is cheap and reliable. Milk can be tested for the kinds of bacteria we don't want. Contaminated milk can be pasteurized, and sold as regular milk. Safe milk is chilled and sold as raw milk, preserving its microbiota.
https://en.wikipedia.org/wiki/Commensalism
biological interaction (symbiosis) in which members of one species gain benefits while those of the other species neither benefit nor are harmed.
Contrast that to a large dairy operation. Several hundred cows mean higher pressure to get through them all, and a higher chance that the farmer misses something. Half of all cows are in herds of over 900 animals, which means that many operations are now completely automated, removing the visual inspection that a farmer in a small-scale operation performs. That milk is then sent to a milk processing facility that may process upwards of 100,000 gallons per day. Any bacteria from one cow can and will be mixed with the milk from multiple other farms, and can potentially infect tens of thousands of gallons.
Anecdotaly, we have several friends who cannot digest homogenized milk, but do well with raw milk. We are not sure if this is due to the makeup of the milk fat or due to the (usually harmless) microbiota in the milk.
I'm very interested in this, as it's true for me too! I don't have access to raw milk in my state, but I can find 'creamline' or 'cream top' milk at my farm stand, and that works great for me. Oddly, so does dry/powdered milk, of pretty much any type.
I've tried to research why homogenized milk is different (besides the obvious), but keep running into dead ends. I'd love to read any further info you have.