I hate to even speculate. But if I were I would say that anytime you eliminate certain types of pathogens and concentrate other types. Or create an unnatural or extraordinary situation we are not acclimated or accustomed to.
Weather internal inside our bodies or externally in our environment. There is the potential for a wide range of problems to develop. And I think that is nasa's concern.
Of course there are exceptions like where liability is involved than any amount of imbalance is safe. (sarcasm)