>> we need to find a way to cooperate with bacteria

We already do, unbeknownst to us, for centuries. [1]

OK maybe we did not decided to cooperate it but isn't that the point here.

"All the bacteria living inside you would fill a half-gallon jug; there are 10 times more bacterial cells in your body than human cells"

"The infestation begins at birth: Babies ingest mouthfuls of bacteria during birthing and pick up plenty more from their mother's skin and milk—during breast-feeding, the mammary glands become colonized with bacteria."

[1] http://www.scientificamerican.com/article/strange-but-true-h...