A strain of E. coli is a sub-group within the species that has unique characteristics that distinguish it from other E. coli strains. These differences are often detectable only on the molecular level; however, they may result in changes to the physiology or lifecycle of the bacterium. For example, a strain may gain pathogenic capacity, the ability to use a unique carbon source, the ability to inhabit a particular ecological niche or the ability to resist antimicrobial agents. Different strains of E. coli are often host-specific, making it possible to determine the source of fecal contamination in environmental samples.
But, lets do the maths, the Lenski experiment showed a mutation happen in 25,000 generations - on average, E.Coli reproduce every 233 minutes. There have been about 1077300000000000 minutes since Bacteria first became Eukaryotic. Thus we could expect about 4623605150214 generations in that time, which, with a uniform mutation rate would be around 184944206 mutations. Do you think that 184944206 additions to the genes of a microbe could result in a dog? (Of course, this maths is flawed because the reproduction rate between microbes is shorter than later mutations, such as dogs - nonetheless, we should expect a significantly large number of mutations, or additions to genetic code, to be available to bring the genetic code from 500,000 base pairs in bacteria to 300,000,000 base pairs in humans).
But, perhaps the biggest problem for theists is not mutation and change in characteristics between bacteria and dogs. Their incredulity comes from the fact that they cannot accept this line of mutations and changes:-