In general, researchers know what they'll find—Escherechia (including the ubiquitous microbial Everyman, E. coli) in the bowel, lactobacilli in the vagina and staphylococcus on the skin.
Also found on money: staphylococcus bacteria and fecal matter.
The most common bacteria isolated from the conjunctiva are small numbers of coagulase-negative staphylococcus and diphtheroids.
Most cases are due to Bacteria (including salmonella and staphylococcus) and their toxins (including Botulism).