One of the coolest things scientists can do now is figure out which genes are turned on or off in a living person. (They look at the RNA that the DNA in a particular cell produces.) These researchers found that different genes are activated in the guts of breast-fed babies than in formula-fed babies. We can't say yet what the specific effects of those differences are, but you have to start with the guess that formula fails to start some normal epigenetic process. The genes they found differently expressed mostly have to do with gut development, which is not surprising, since they did the study with cells exfoliated from the gut and pooped out.
The researchers suggest it has something to do with all those health issues that differ between breast-fed and bottle-fed babies.