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After that I filter the air and wait for all the germs it contains to die off.
Third stage would be to transfer all the contaminated slime in a wee over-pressurized chlorine chamber. Once it is disinfected, I then proceed to transform it into sterile polluted water and algae in situ. I have no particular use for slime, so I have no interest in storing it long term.
It's tedious but still the fastest way I found to clear said biome.
During this whole process, the biome is sealed off with a water lock, the dupes go in with suits, the slime does not get out of the biome, and there are plenty of sinks and disinfectant stations nearby the suit station. And once everything is in containers, I disinfect the staircases manually with a vengeance.
You just can't trust those dupes ...
Your best bet? Don't let your dupes touch it at all. Send the material straight to automation. The automation system can check ore for germs and pass it through chlorine rooms as needed.
You can keep slime in chlorine to stop it from releasing germs but as soon as it gets out of the chlorine the slime stars to release germs again because it's made of germs.
This is false. Once disinfected; it can still release polluted oxygen, but not germy polluted oxygen.
I've got you covered, OP. Now, diseases can actually be a big deal again.
https://steamcommunity.com/sharedfiles/filedetails/?id=1911357229&searchtext=diseases+restored
But it is VERY easy to have some germs transfer around, e.g. to and from ladders, then re-infect previously sterilized slime. And then they'll very rapidly multiply out of control again. This is exceedingly likely to account for your observations.