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True enough. Hawaii authorities introduced mongooses to control the rat population. Just one problem, rats are nocturnal and mongooses are not, so they never meet. They also introduced a fish in hopes of boosting sports fishing but Hawaiians won't eat them - they appear very similar to a fish they consider sacred. Time will tell what will happen with probiotics being introduced to aquaria.
Although Hans Werner spoke of prebiotics (food for beneficial organisms), and you mention probiotics (the actual organisms themselves), I think you do have a valid point there. Perhaps it is more interesting for the hobby to consider if there are valid means of 'human manipulation' that do not introduce new unknowns but instead enable tanks to better mimic a natural reef from a probiotic standpoint. For example looking at current husbandry methods to see if they are getting in the way of a more natural system as seems to be shown by the articles I linked to.