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So, just to clarify…. They take all those precautions to prevent an infection, because…. There is a risk of infection… right?
While certainly far from perfectly analogous, my experience with sourdough starter (which is a yeast culture,) says that when it goes off (specifically serratia marcescens) the entire starter needs to be scrapped; and the “bioreactor” (that would be a mason jar, heh.) needs to be sterilized in the dish washer.
As one scales the reactors to comercially-viable size, the risks and costs increase- simply by the mere increase of inputs increasing the risk that something is missed.
As for antiboitic use in cattle, this is certainly common, but it’s also far from universal. My big-box grocery store sells antibiotic-free meat and antibiotic free dairy; and the chain butcher sells it exclusively.
I’m not trying to defend natural meat, but dealing with and preventing infection is a necessity; the largest drawback is scaling. Incidentally, a solution nobody seems to consider here is scaling the other direction- towards smaller, in-home bioreactors.
If they became small enough, maintenance free enough and inexpensive-to-operate enough; people would start adopting them. Like how people frequently grow their own veggies.