Autoimmune disorders of gut and breastmilk

Yesterday in a class on human breast milk we discussed how it is considered a living tissue by some, because the breast milk contains living cells too. Many of these cells come from the gut associated lymphoid tissue(GALT), is what one of our professors said.
And surely that led me to the next possible question, what if the mother has an autoimmune disorder involving the GALT? How would that affect the type of cells in the breast milk? Would giving oral vaccines to the mother be a way of giving the baby protection against the disease in the first few months of life?

Let me know what you think.