Yes, there are some species that are only symbiotic in the right circumstances, but are very harmful if they escape their niches. But there are also thousands of species that are evolved for very specific niches with in our bodies and cannot survive outside of those niches. When in those niches, they are helpful. When outside of them, they are harmless. Immunocompromised or not.
But you're right, I don't actually have the evidence to say whether the bacteria discussed with in the article are of the sort that are always harmless or of the sort that can be very harmful in the wrong circumstance. I'll edit the comment. I do think it is likely that they are largely harmless, because of the ammonia based metabolism. That would be pretty limiting. Also, their apparent fragility.
But you're right, I don't actually have the evidence to say whether the bacteria discussed with in the article are of the sort that are always harmless or of the sort that can be very harmful in the wrong circumstance. I'll edit the comment. I do think it is likely that they are largely harmless, because of the ammonia based metabolism. That would be pretty limiting. Also, their apparent fragility.