I would like to point the following out:
Modern day extant species did not evolve for other modern day extant species. The bacteria you speak of would be very different genetically thousands, let alone millions, of years ago.
So how would a bacteria from millions of years ago and a bacteria from today differ? One is ready to evolve at a moments notice and the other isn't? That's not a statement backed by evidence. Sounds like a statement of faith to me.
Unless you can prove that bacteria of today are somehow at the top of the evolutionary ladder, it would seem that the mechanism of evolution "should" affect them as it always has, and therefore we should see more changes in 40,000 generations if that mechanism actually works.
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