Hi Dan,
 
Rabies and histoplasmosis are the two things to be most concerned about in bat caves.  Contact the National Speleological Society in Huntsville, Alabama and Bat Conservation International in Austin, Texas.  They can give you  the latest recommendations and protective measures.
 
George 
 
George H. McCluskey
Senior Archeologist
Department of Arkansas Heritage
Little Rock, Arkansas
 
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