I am no religious fundemantalist (I'm actually an atheist), and care very little for the notion of purity of humanity. The idea of 'human DNA' vs 'non-human DNA' seems suspect to me, as in some trivial sense, anything that is in the genome of a human being is by definition human DNA, and on the other hand, you can find large swaths of human DNA that are identical to most mammals, and probably a few that are common to virtually all eukaryotes. I also know that viruses can leave long-lasting changes to your DNA, that may even be heritable I think.

Still, related to the importance of bacteria, while I don't doubt that, as we learn more, we will discover that they have a bigger role than even dreamed 50 years ago, you still can't compare it to the basic roles of human organs. We have actually created microorganism-free mice and other organisms, and while they are not very healthy, they are fully functional (with bad digestion and big immune problems): https://en.m.wikipedia.org/wiki/Germ-free_animal