Question

what is the best way to classify organisms

Answer 1

When use genetic info to compare the relatedness of species by sequencing DNA from both organisms and comparing it. The more the two sequences resemble each other, the more closely related the organisms are. The less the two sequences resemble each other, the more distant the relationship between the organisms.

You should approach a prob like this with process of elimination:

The DNA of all organisms (bacteria included) are made out of DNA; the DNA of bacteria can be easily distinguished from the DNA of its host (grow a colony of bacteria from a single bacterium and get the sample to be sequenced from that instead) and the mutation rates of bacteria, though different in some cases than the mutation rates in other organisms, can certainly be tracked. That leaves...

Answer 2

Yup, exactly. :D