I think the explanation of germs went a little too smoothly, or if Nobunaga decided to let it slide because it just gives more credence to his suspicion she's more likely something like a Heavenly maiden (I would be really really annoyed if he guesses she's from the future, given how much of this series was given over to establishing a working concept of marking time).
If I had been in her place, I would have asked what he thinks causes disease, and see if I could work from that to explain the idea of nearly invisible particles/animals in the blood and tissue. Hell, the idea that demons/monsters cause sickness isn't too bad a place to start.