For the most part, yes. But also, I think if you dig into the details, it's less that bacteria have the upper hand, and more that we've reached a truce with the bacteria.

A lot of bacterial species need us to provide the environment for them to live, and our immune systems are pretty paranoid with our gut bacteria, especially if they getting too close to the intestinal walls. Also, our bodies are pumping out bacterial-killing compounds constantly.

I would describe the situation as that our bodies can't kill every bacteria, and bacteria can't kill us (not easily, anyways), so we've reached an agreement that as long as the bacteria stay in their lane, they can stay, and we might consider doing some trading at a distance