Shouldn't there be a nearly infinite number of, for example, ecoli bacteria? Given mutation rates, wouldnt bacteria separated by something as simple as a river speciate within a thousand years or something? My genetics book keeps using examples from ecoli but I can't help but wonder how they can describe molecular processes so generally across all ecoli. Thanks!

Traditionally isolates are considered to be the same species within ~ 70% similarity using DNA-DNA hybridization.

E. coli is a species and of course there will be members with different DNA composition, just as any two humans will have differences, yet belong to the same species. Speciation is indeed faster in bacteria but if they accumulate sufficient changes (i.e. by convention above the threshold value) they would considered different species. Note that the the line between species in bacteria is even more arbitrary than in other organisms.

Also, as a consequence of more DNA sequencing numerous bacterial species have been reclassified.