Stoned rant:
Regarding the food / bacteria interaction, one thing helps me clarify things. Just about anything can be broken down by some strain of bacteria. If you pile up material X in a nice culture medium in the open air, sooner or later microbes will come along on the wind that just happen to love material X. They settle in, and multiply.
Same thing in our gut. Eat McDonalds daily and you'll start to encourage the growth of microbes that like McDonald's also. These McDonald Microbes are not natural for us. Prior to this point in our human existence, these compounds and the corresponding bacteria were not present in our guts.
All this is still fine and dandy, maybe, except that we don't know what by-products these bacteria may produce. Could have hormone-like behaviors, disrupt normal nutrient absorption, who knows? Likely they could displace beneficial bacteria who are performing a necessary function. We know beneficial microbes keep our immune system in tip-top shape. There's also links between autism and the immune system. There's a lot more connections here. We're literally swimming through oceans of microbes like something out of the Matrix.
So crazy that only 1 in 10 cells in / on us are human.