No rhetoric intended — “Mycoprotein” can include regular mushrooms but in the meat replacement context, it’s usually used to mean microfungi like Fusarium venenatum. These are cultivated in big vats in roughly the same way you’d cultivate brewer’s yeast, rather than on more traditional farms like field mushrooms.
I’d be pretty surprised if the issues you raise were a serious problem. We have a huge amount of experience at preventing bacteria or pathogens getting into a whole range of industrial biotech processes, and in this case we can very tightly control the inputs and monitor conditions. Hell, if necessary, you could just include antibiotics as inputs into the process, though I doubt it’d come to that.
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There are lots of other large scale processes that have very high cleanliness standards and can’t use strong disinfectants, from brewing to mycoprotein cultivation. Honestly seems like one of the less difficult things to get right.
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