Long list of great questions:
Here are some answers
1.[edited out for convenience and perfectly understandable answer]
2. Probiotic bacteria needs a food source to stay alive. Yeast as a live culture is a great food source for this live bacteraia. Yeast is not a fungus but is also a great food source for fungus. That is why milling is done at 200- 280 degrees. This is hot enough to kill mold spores but not hot enough to kill the yeast or the probiotics. Yeast infections are different. They are a yeast/fungal colony that grows on dead or necrotic tissue. Definitely not a good food source.
3. Very true in regards to digestive track. Studies of these fish on a 20% protein vegetable only diet vs our 67% protein diet show a 250% increase in bio-mass growth conversion. How ever using formulations that have 50% protein made up of gluten only yielded a 40% increase in bio-mass conversion. This mean that the amino acids from both fish and plant proteins are more digestible than the gluten proteins.
4. Live food is always best from a nutritional standpoint. Processed foods like our are mostly for convenience. The are also free from parasites or other unknown bacteria issues. Once the bone a scale is rendered into feed most of the value from it becomes inert. Some minerals and calcium are still needed to help with fish growth, but in all levels of pellet food we have tested this has never been an area that is lacking. The ones that do tent to lack these are flake food as a direct result of their manufacturing process.
2. Um...maybe I'm missing something here, but my AP Biology class this year was taught that yeast is a eukaryotic, single-celled fungus. Additionally, how would you feed yeast to bacteria (which I would assume would be smaller than the yeast)? Are you saying that you add yeast to the fish food, which are eaten by the bacteria in the packaging? In that case, wouldn't there be a sterilization problem, in case of the probability that a non-probiotic bacterium or spore entered the package and proceeded to outcompete the probiotic bacteria?
3. As you are probably aware, different fish have different requirements. For the fish you did your comparison to, which fish were studied? Were they more open water herbivorous fish like pacu or possibly tilapia? Or were they mainly grazing fish, such as mbuna, and plecos? Or would these be micro-invertebrate hunters who incidentally happen to ingest large amounts of plant matter due to feeding technique like tangs and Poeciliid livebearers? Would you be able to provide comment on exactly which fish species you used? Additionally, wouldn't said study be flawed, as you fail to specify exactly which proteins are in your "67% protein diet" which could be any mix of terrestrial/aquatic plant/animal proteins, as well as failing to match the %protein in both diets? And aren't you also flawed in using vegetable protein, rather than cultured algae protein, which could incidentally be a more readily utilized protein due to the availibility of the wild to the fish?
4. Wouldn't the bone/scale already be chemically inert, due to it being comprised of (mostly) calcium carbonate? Unless you were heating the fish food mixture in an oxygen rich environment at high temperatures which would burn the scales and bones into Ca(OH)2 and CO2, but at that point, would you not be damaging the nutrition content of the food?