The bacteria are in an environment very different than the human body. So while there may be a lot of bacteria, it's probably not going to do any harm to you because it's not adapted to infect you.

Speaking as someone who has done a decent amount of caving, I'd be much more worried about the CO2 and other gasses in the air (and I'm sure those scientists are as well). It's really rare for caves to have dangerous bad air. But sounds like this one could be an exception.

Hydrogen Sulfide is bad stuff. Friend did work for a tannery. One night the concrete lined cesspool they stored waste from leather manufacturing blurbled and turned over releasing CO2, Methane and Hydrogen sulfide. Killed two security guards in their guard shack 100 yards away.

I think like cyanide you lose your sense of smell as the concentration approaches lethal levels. That leads people to assume concentrations are falling instead of increasing.