There are many reasons breastfeeding can be beneficial. A reason they talk about in this article is that it promotes good gut bacteria.
“‘These changes in the developing microbiome could explain susceptibilities to a variety of conditions later in life,’ such as obesity, diabetes, and GI conditions.”
They say C-section, formula fed babies have the poorest gut flora.
http://www.medpagetoday.com/OBGYN/Pregnancy/37304
Our guts have been expecting two things for a long time. An “inoculation with bacteria from the mother” during vaginal delivery, and mothers milk. This has been the norm for hudreds of thousands of years.
The study is small and there were a bunch of other factors which couldn’t be accounted for, like the anti-biotics the mother took during pregnancy or at delivery, or if the baby had any soon after birth. They do say “species richness was higher in formula-fed infants,” but they seem to have an “over-representation” of “bad” bacteria.
There still a lot to figure out, but it’s good to know that the “simple route” is a good option for lots of babies.