To remove bacteria, first kill as much of it as possible, not just in the bowl but in the bowl's rim and rim holes. Pour a mixture of 1 part household bleach and 10 parts water directly into the tank's overflow tube. Just lift the tank lid, and direct a cup or more of the bleach solution into the overflow. Allow the bleach to work for a few minutes; then flush the toilet, and carefully ream the rim holes with a pen knife or a piece of wire. Use a pocket mirror to check your progress. Scour any bacteria stains from the underside of the rim, using bowl cleaner and an abrasive pad. Add a final does of bleach through the overflow; wait a few minutes; and flush the toilet. To clear a clogged siphon jet, ream it thoroughly with a stiff wire. You'll probably have to do this all-out ream-and-scour cleaning only once or twice a year if you add one or two tablespoons of bleach to the overflow tube periodically.
Step 1: To kill a bacteria buildup in and under the toilet bowl's rim, pour a bleach solution directly into the overflow tube. A good mix has one part household bleach to 10 parts of water.
Step 2: Clear bacteria from the rim holes using a length of insulated electrical wire. Approach each hole from several angles. The wire coil serves as a handle to manipulate the end of the wire.
Step 3: Clear bacteria from the siphon jet(opposite the trap hole) at the bottom of the bowl. Use a piece of insulated wire and turn it with a cranking motion. Clean the bowl with household cleanser.