The majority of cells in the human body are bacterial; most of which are commensal, however, some species are pathogenic. One question facing microbiology is how do different indigenous microbial communities affect health. It is known that there are many different microbial community compositions present in the vaginas of healthy women and they may provide different levels of protection from pathogenic organisms. We test the colonization by the pathogen Staphylococcus aureus encoding toxic shock syndrome toxin 1. To test this we examined the community compositions of the vaginas otherwise healthy women colonized with S. aureus and compared these communities to those not colonized. We were unable to demonstrate an association between the presence of the pathogen S. aureus and the community structure which suggests no difference in the ability of the community to exclude the pathogen.