Nature Reviews Microbiology (subscription. Sorry!) has a cool article on Paleomicrobiology , the science of identifying little beasties from very old material. I have to admit it: what I'm really interested in is the Indiana Jones aspect of what must be a very painstaking and artifact-prone discipline. Among the highlights, in the tables of discoveries: successfully culturing enteric bacteria from the bowels of a mastadon corpse found in permafrost (evidence reliability level C/II); and microscopic identification of crab lice from the pubic hair of a 2,000 year old mummy (level B/II). Cool!
There's also a very serious discussion that some of these microbes might still be viable. People are advised to be really careful when going into graves where smallpox is suspected. The Spanish flu virus of 1918 might still be kicking around somewhere as well.
The authors themselves have been able to confirm that the Justinian Plague (Wiki; see also the comment) in the late Roman empire was due to Y. Pestis (i.e. the Black Death) of the same biovar as the medieval and modern plagues. So it likely originated in China as well. See Plagues and Peoples for more on this.