The strain itself (and its specific genome) can be patented. Not as it's found "in the wild", but with genetic modification. The thing is this "genetic modification" includes not just techniques like CRISPR, but also just letting the bacteria mutate in a vat.
I think it's total nonsense, but the law allows it. If wild bacteria growing on your skin happens to mutate into the exact same genetic code as a patented strain, you could technically be in infringement.