Saliva is safe to apply to the sexual organs. While it is true that the mouth contains lots of micro-organisms, the same varieties are also commonly thrive elsewhere in the body, and are all harmless against a normally functioning immune system. Saliva also contains antibacterials, has skin-like acidity, and acts as a pH buffer.
The only concern is that it may also contain anything that has recently been in your mouth. For example, using saliva as a sexual lubricant may be risky if you—
have a topical infection around your mouth or lips, or have recently licked a location of such an infection,
have recently eaten a food that can irritate sensitive skin or mucous membranes (e.g. vinegar, salt, or anything abrasive), or
have recently kissed or had oral sex with anyone who might have a sexually transmissible illness.
In cases that you're unsure, other water-based lubricants sold in supermarkets and pharmacies are a safe alternative.