Re: auto-immune bacterial nuisances...

 So it leads me to the next question - what about all these lists of foods that should be avoided, such as the nightshades for one?

Nightshades are only an issue for individuals with nightshade sensitivities.

Can these promote bacterial growth or supressed immunity?

The reactions to the nightshades are more allergy related.

And also, are some foods much more likely to have these bacteria (and therefore best avoided), like meats, handled nuts etc etc?

Not that I am aware of. I have not seen anything on the transmission of these particular bacteria. But I doubt if they are food contaminants.