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The reference to wearing gloves when touching or penetrating the anus or vagina is about the STIs that can be passed by skin to skin contact. These are Herpes, Syphilis, and HPV. If you wore gloves that covered your skin, you would be protected from those STIs. Keep in mind that while it is possible to pass STIs through this kind of contact, it not common for them to be passed this way.
Gonorrhea, HIV and Chlamydia are not passed through touching or penetrating the anus or vagina with fingers. Generally, it is always a good idea to cover broken skin when you have sexual contact. Covering broken skin protects you from other bacteria that can be present on the skin or in the body.
You might want to check out our chart called "Know Your Chances" to get more information about the chances of passing or getting STIs with different ways of having sex.
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This answer was posted on October 10, 2013