Both Botulism and E. Coli make you sick due to potent toxins produced by the bacteria, not due to them taking over your gut flora. The bacteria doesn't even need to be alive to make you sick if it's already colonized your food.

Good thoughts! Botulism is caused by a toxin produced by Clostridium botulinum.

E. coli is a little more complicated: some E. coli spp. produce toxins, and other species are enteroinvasive and actually can outcompete the gut flora (confusingly enough, other species of E. coli are also in the normal gut flora).

The main reason that some species of E. coli can make it to your gut and cause disease are that they have a variety of pathogenic factors that definitely would not be found in bacteria in 'probiotic' foods.

(and I see who you are replying to just edited their response to add 'bad' E. coli)