My polluted water storage has considerable food poisoning. I was setting up a chlorine area to purify it when I noticed my output going through the sieve and into the clean water storage has no germs. I assume this is a bug as in previous versions the sieve or pump would not remove germs. In response to other posters I have added a germ overlay. There is no food poisoning of any kind in the final water chamber. This has run for several cycles and the line has completely emptied multiple times. The middle water pocket has food poisoning from some dupe urine which happened many cycles earlier and is still contaminated with a reported half life of 20 cycles for those germs. There is nothing in the system that should drop the food poisoned water from over 200k germs to none in that distance unless the sieve has been changed to clear these out. The only other thing on the line is the thermo aquatuner and the polluted water in that area is ~65 degrees but I do not see why that short little run there would eliminate 200k germs in water. The rest of the water is all ~20-40 degrees so there should not be an insta kill of the food poisoning germs. I know in prior versions the final water tank would have germs in this type of setup. If this is intended then fine but based on playing the game for over a year now and reading about it germs have not been removed by this method previously. Maybe they did amp up the death rate for food poisoning but the middle pocket of water at 26 degrees would not seem to suggest so.
Just setup the system and see if the germs are cleared out.