Tolerization of the GALT to microbes in the gut is an ongoing, dynamic process. Every individual is exposed to different microbes at different times. However, just as when early man laid down the first irrigation canals that would change the landscape of the Fertile Crescent forever, the first few years of our lives are possibly the most important in gut development. Most of us get our initial dose of microbes from our mothers. The most common way for any mammal to give birth is through the vagina, ensuring that all formerly sterile prenatal offspring are given a big mouthful of microbes as they pass through the birth canal. Scientists like to call this process a vagina-anal to oral inoculum, and all mammals including humans have been introduced to their microbes in this manner. In our first-world focus of hygiene, the idea of swallowing microbes in any way sounds a bit gross, but these initial inoculations are possibly vital to healthy GI and immune system development.
With advances in technology, most humans now survive caesarian births, a process which introduces yet another way to acquire our miniature inhabitants: from the grubby hands of those handling us. Research has shown that children born vaginally have markedly different microbial populations than children born via caesarian. In the former, they are colonized with more vaginal microbes such as Lactobacillus and Bifidobacterium; while in the case of the latter, more skin associated microbes predominate such as Staphylococcus and Clostridia[i].
But before you rub your next kid’s face in vaginal fluids, we should note that many respected scientists argue that babies don’t spend enough time in the vaginal canal (though as a mother, it felt like forever to me) for it to be a major source of inoculation. However, all agree that that sucking on mother’s nipples is one of the best sources of our initial microbes. Piglets allowed to suckle on manure-coated (which means microbe-coated) teats have larger Peyers patches than formula fed piglets, indicating a healthy immune system[ii]. They also have more complex villi structures so that their pig epithelial cells in the small intestine have more surface area to access nutrient energy. Piglets fed formula from a sterilized bottle have a delay expansion of lymphocytes and display characteristics of crypt hyperplasia—enlarged crypts in response to immune stress. Again, studies like this one show that microbes—even before we begin eating solid food—are shaping the environment (i.e. our gut) where they live. Even recent human studies are confirming these studies in pigs, linking initial inoculation of an infant to things like risk for type 1 diabetes, obesity, and asthma[iii]. Thus the ecosystem of our body has adapted to coexist with a myriad of microbes and even parasites.