It isn’t as neat and tidy to say breastfeeding gives infants (better) microbes for their gut marketplace and formula feeding gives infants (terrible) ones. Studies tend to contradict each other even as formula companies work harder and harder to produce a formula more like human milk, but one thing is clear: the microbes that thrive in the guts of infants fed formula differ from those who are breastfed. The gut structure and inhabitants directly respond to the nutrient energy flowing into it. That difference may or may not be better or worse; there are probably advantages and disadvantages to both just as in the case of H. pylori colonization in the stomach.
That said, distinct microbial species that have been associated with breastfed infants exhibit specific abilities to regulate host GI tract maturity and immune development such as some unculturable microbial species in mouse milk that can coordinate T-cell response in nursing rat pups[i]. Further, another study is showing in mice that T-cell development is not only vital for immune response but for cognitive ability[ii]. Every aspect of our holobiont is intricately connected and relies on the gut ecosystem’s being established from the very beginning of our lives. At the very least, the scientific community has accepted that the presence of specifically human-associated gut microbes in breast milk offers an incomparable education to the infant immune system as to what microbes are “friendly,” and many studies are attempting to replicate this education platform in formula[iii]. Finally, breast milk has other factors that influence tolerization like soluble pattern recognition receptors (PRR) and anti-inflammatory elements that recognize specific microbes and inform the maturing immune system just where their niche should be.
As our gut becomes established, many factors contribute to putting its occupants in their place. It is vital to the health of our holobiont to ensure that the microbial rabble function in diverse ways that will offer survival flexibility. The ecosystem of our gut is built upon the layers of niche structures that our initial occupants lay down as they scramble to survive, simultaneously educating our immune system and facilitating metabolic development.