Depends on the organism. Them (organisms) depend on certain nutrients to live and many are the same ones we need, so it presents a problem in that we may be assisting them but at the same time weakening our own bodies. These nutrients are vital for immunity, detoxification and provide energy at the cellular level (Krebs Cycle).
Different organisms require different nutrients, for example there are reports about limiting the use of cysteine in Autistic patients. Cysteine is a critical nutrient (amino acid) for humans but also can be used by organisms.
I don't think there is an easy answer except to monitor the intake of nutrients and try to correlate if you are making progress or regressing.