Normal flora: We are all colonized with bacteria and fungi (we are buggy!). The organisms can be transmitted a via skin to skin contact. If your so had inflammation of the head of the penis (balnitis) this needs trestment; if he is uncircumcised he may well have a chronic asymptomatic low grade infection that needs treatment. You as we'll carry these organisms and may be translocating your own flora.
Answered 2/6/2016
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