How do I get it out? The top chamber is seemingly easy to clean with a flexible brush and some hot water but the lower chamber is a mf’er to clean and there are some spots of who knows what that are on the bottom. I’ve tried everything imaginable but without some sort of physical contact, i.e. scrubbing it with a brush or something, it has been a struggle. Surely someone else is as big of a germaphobe as me and wants theirs brand spankin’ new clean that has had this problem.
Bleach it out. Rinse with alternating hot and cold water.
Try tossing some hydrogen peroxide in there. It shouldn’t attack the plastic but will go after anything organic. Otherwise homebrewing stores sell B-Brite or C-Brite which are good cleaners for glass and plastic. 
Fill with a clorax, leave it overnight. Rinse clean and wash. Fill it with water and add a lot of baking soda (takes the clorax/bleech taste) leave it overnight and after wash you are good to go!
can’t you get some BB’s or similar into the lower chamber to thrash around with your cleaning solution?
Toss some rice in there (Dry)and shake vigorously like your making a martini. then add a little water / bleach / peroxide / soap, whatever cleaning solution you want, and repeat the shake (Keeping rice in still). Strain and enjoy. BBs aren’t small enough, the points of the rice chisel away at whatever is stuck. Just don’t leave the wet rice in overnight, you will need a spoon and a can opener then.
This also works during a race too. Just bring a 5LB sack of rice along and right as transition closes, fill everyones bottle up with a 1/2 cup of rice. by the time they get out of the water their bottles will be… I’m so evil. You will have no problem qualifying for Kona. (Unless they eat the rice. Don’t include a spoon.)
I’ve tried straight bleach and had no luck, suprisingly. I’m going to try the hydrogen peroxide as soon as I can find it. The rice idea is brilliant! Beyond brilliant. Thanks to the collective wisdom of ST for the answer to another conundrum.