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I wonder why it does not happen naturally if they outcompete normal bacteria, though.

Bacteria has great speed of evolution.



Because there's no downside to the current system they use. They only out-compete if you modify them in other ways to make them more successful in addition to the change you want.


The added genetic factors may, themselves, be exogenous and genetically modified. Your argument does make sense over thousands of years, however.




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