There was a substantial amount of contaminating human DNA in our samples: about 9% of the Smithsonian sample and 4% of the Stockholm sample. The human DNA in the Smithsonian sample appeared to have been introduced relatively recently, because it was in longer pieces than most of the DNA fragments, and breakage is believed to increase over time.
To determine what bacteria and viruses were present, we compared the DNA in our samples with that in the GenBank public sequence database. The two specimens had quite different collections of these microbes. Once these surveys of microbial species are done for many museum specimens, we may learn how to tell which ones inhabited the living animal, and which were added when the specimen was collected, prepared, or stored in the museum. Both cases will be interesting.
One intriguing possibility is that we might be able to determine which microbe caused an epidemic that killed many thylacines around 1900. According to the book by Robert Paddle (page 203), 16 of 17 thylacines in the Melbourne Zoo succumbed to this disease during 1901-1903.
Another application of these studies will be to guide museum curators toward specimen preparation and storage procedures that reduce the level of microbial contamination, and thereby obtain specimens that will last longer and will be better candidates for future DNA analysis.