Deworming products do not affect gut bacteria.

There's no distinction between the quality or composition of processed diets other than prescription diets being discussed as having an increased association. Prescription diets are only fed if there's an issue, so being fed a prescription diet as a puppy is a suggestion that there's a GI issue present before the diet is fed, and therefore there can't be a causal relationship like they are suggesting.

The wide range in quality and composition of different diets available should also be considered. They looked at the ingredient components of non-kibble diets but not the composition of kibble diets. If berries are considered protective then would a processed diet containing berries also be of benefit?