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A little bit of bleach can help kill any mold that may be growing in the bottle. Measure out about half a teaspoon of bleach, and pour it inside the bottle. Cool water helps bleach clean the bottle more effectively than warm or hot water. Pour water into the bottle up to its top line, and shake it to mix the solution together. If the mold is really bad, you may want to leave the solution in the bottle overnight to soak. Screw the cap on, and leave it until the next day. Sometimes just soaking the bottle will remove the mold, but in some cases, you may need to scrub to get all of the mold off.  Stick a dish or bottle brush in the bottle, and scrub the areas where there is mold. If there is any mold on the cap or threads, dip a rag or dish brush into the solution, and wipe it around the moldy parts. Pour out the bleach solution into a sink, and rinse with fresh water. If you are worried about ingesting bleach, you may want to rinse it again or put it through the dishwasher. Let it dry completely before using.

Summary:
Pour bleach into the bottle. Add cool water. Leave the bottle to soak overnight. Scrub away the mold. Rinse.