Besides Yersinia, Mycobacterium and Treponema, which other pathogens might be expected to preserve in archaeological human skeletal remains and can be detected by molecular (aDNA) methods?
Staphylococcus aureus for example. The University of Göttingen had a master thesis about this bacterium and currently there is a phd thesis going on.
In theory you can detect every pathogen which is distributed by blood, to have a chance that it remains in the skeleton after death. But in practice it will depend on your methods. If you use the older PCR methods like you would do in DNA fingerprinting via autosomal STRs, you need a distinct and short locus.
I would suggest, that you look into the work of Johannes Krause (Max Planck Institute for the Science of Human History) and Kirsten Bos (same Institute). They are working on detecting pathogens in human bones.
Thank you Margarethe! We have also made some progress here in terms of figuring out exactly what we should be looking for.
Anything with a double-stranded DNA genome will persist best and be easiest to sequence (which sadly rules out many interesting viral pathogens, but still leaves evolutionarily important viruses like the herpesviruses and adenoviruses - adenovirus especially *might* be detectable in coprolite samples - as a number of intestinal parasites and microbes should be.
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