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Even with health store varieties, there's no guarantee that one batch of brewers yeast is of the same quality (or even yeast species) as another batch from the same company. Some of the variations can be attributed to what the yeast was fed, strain of yeast used, temperature of fermentation, etc. The nutritional contents is based on averages - it is not absolute like it is in purified supplements. The health supplement market is horribly regulated... but that's a long rant we don't need to get into now.
Basically, brewer's yeast is just the dried up crud they filter out of alcoholic beverages (usually beer). The reason it is used as a vitamin b-complex (including niacin) supplement is because:
1) brewer's yeast is efficient at producing b-complexes which are very readily bio-available (easy to absorb) (actually almost all forms of yeast are which is why bread is a good source of b vitamins)
2) it's a cheap waste product of fermentation
Main difference between brewer's yeast, baker's yeast, torula yeast, and "nutritional" yeast as a supplement is that those yeasts have much lower amounts of chromium available (assuming of course chromium was available in what the yeast was feeding on...). Since it's the b-complex vitamins that we care about for ducks, any yeast should provide the desired extra nutrition. I wouldn't be concerned whatsoever if the co-op yeast is the "same" as the health store stuff.
The high prices for health store varieties comes from the need to package it for human consumption (sterilization, processing into tablets, packaging, etc) and more importantly, the
HUGE mark up put on supplements. People that believe they need particular supplements are willing to pay a lot more for them than they are actually worth and companies know that.
I'd wager that the brewer's yeast from the co-op is likely coming from microbreweries or home brewers that are more than happy to give it away for free or cheap. It's possible that the cheaper stuff is actually better for the ducks as it probably doesn't contain unnecessary chemicals used as tablet binders, fillers, coloring, flavor, etc. (purely conjecture on my part). Main risk would be if the yeast went bad... (should be obvious by the smell- it should smell like yeast, not rotten garbage)
Is unprocessed yeast safe to eat? Considering that you ingest some every time you eat leavened bread, unfiltered alcoholic beverages, and many fresh fruits (that dull color on grape skind is yeast), I'd say it's reasonably safe (barring allergies or contamination of course).