Either that article is terribly written or the study cited says exactly the opposite of what is implied. “Substituted processed red meat protein for that found in nuts….” means eliminated the plant protein and replaced it with red meat protein. They almost certainly mean “substituted… with”, but as written that’s not what they say.

EDIT: the original scientific paper uses a similar awkward construction, but in context it is clearer than in the popular article. Most of the papers’ authors appear to be non native English speakers, but their co-authors, the journal editors or the reviewers should have corrected that. Ambiguity in scientific papers is bad.