Native American civilizations were drastically weakened by European diseases like smallpox that they had previously zero exposure to. Was there much of this going on in the other direction?
You may be interested in our FAQ section on Native Americans and (European) Diseases.
The Native Americans didn't live in the same building as there live stock and were wise enough to live with there human and animals waste. Also the didn't have christian fear of nudity so they bathed fairly regularly.