No one said we know everything about our biology. But we're made up of particles, just like everything else. We don't fully understand those particles either, but it doesn't make them not real or not subject to the rules reality seems to follow. They actually make little pills you can swallow to take samples at certain locations a long your digestion, so I suppose I could, given the knowledge and resources. Surgical sampling is also possible. But I don't see why it matters because all of the bacteria and archaea present in the body are made up of subatomic particles.