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Ughh, this is my favorite science mystery. Why do microbes go so much better in nature than in the lab? If I ever end up in grad school, I would love to put my focus on that.
My guess has always been lack of some micronutrients and harsh transitions (freeze/thaw etc). E.g. If you need to be able to report the exact composition of your LB broth, they won't be putting in anything more than strictly necessary.
Some recent new discoveries and new antibiotics have been found by growing and analyzing bacteria in their native soil in the lab.