This is actually really interesting, thanks for sharing.

They talk about mother's milk/breast milk being a source of microbes for babies at birth. I have heard this before and I wonder if it could be an alternative to this pill/fecal transplants?

It depends what you're using the feces to accomplish. Usually FMT is done for people suffering from CDiff infections. The healthy gut flora outcompete the CDiff, causing the infection to go away.

Mother's milk is mostly viruses, so it's unlikely this would work against CDiff. For other users is sounds interesting though!