Reddit reviews Life on Man

Three books if you're interested in this subject:

Gulp: Adventures on the Alimentary Canal

Missing Microbes by Blaser

Life On Man, by Rosebury.

Blaser is one of the leading researchers in the field; Rosebury was a noted microbiologist who- at one point- headed up a bacterial warfare research program at Fort Detrick (now USAMRIID).

The short answer to your question: the environment. The longer answer is that it is a function of exposure from mom (including birth- the bacterial flora in the vagina changes in the third trimester- which raises some interesting questions about the effects of C-section), the family (which would make for some interesting studies in adopted children), the environment (lactic acid bacteria, etc.), and is modulated by things like diet, and antibiotic use.

Interesting note by Blaser: Helicobacter pylori, which has been implicated in ulcers, may be protective against asthma and allergies.

Now- this is the gastric environment, versus the intestines- and not many bacteria survive the stomach, so H. pylori is a minor but important subset of bacteria in the digestive tract; by numbers, it pales in comparison to those of your colon, for example. But it is rapidly being depleted in Western populations from antibiotic use- including abx that are not prescribed for such use. So, we're losing these bacteria that we can demonstrate have been colonizing our stomachs for tens of thousands of years, and the big question is whether this could be where we're getting the increase in asthma and allergies from.

Very hot topic just right now, lots of interesting work being done.

And the vaginal microbiota change in the 4-8 weeks prior to delivery. It's pretty interesting.

I would recommend Theodor Rosebury's "Life on Man" from 1969. It's dated, but remains a solid piece of work on the subject.

The flora of the vagina does change in the months prior to parturition (cite: Rosebury's classic Life on Man). However, how these changes come about is unknown. Certainly before the days of hospital births, there was greater exposure to the mother's feces which would result in inoculation. Whether or not the mother's vaginal flora is changed by the ingestion of probiotics via the anus- I don't know. Some women claim their yeast infections may be cleared up with oral yogurt, so perhaps it's possible.

As to whether the 1-2-3 (or as many as 10-15) organisms in encapsulated probiotics- many of which do not survive transit through the acid environment of the stomach- are even healthy for newborns- I doubt there are any good data on that.