Bacteria were used to be classified based on physical appearance. In the last decades however, the genetic material of bacteria was analysed, and the entire classification had to be remade, because the research showed diffrent things.
For example, expression of genes. just because this of this factor, two bacteria that dont seemb alike at first sign, actually had extremely much in commen..
Another thing, is the use of metabolic molecules. Like proteins. Some genetically closely related species, use the the D form of a certain amino acide as a signalling molecule, where others use a diffrent protein or amino acid for the same purpose.
in further relatives, a same amino acid or protein, or any signalling molecule, can be used for a diffrent function. this because trough evolution and adaptation, it was no longer neccecary to use it for the previous function. however like allways, new spontane mutations, that could actually benefit from this molecule, can give it a new purpose.
a more interesting discovery has been done in more recent years . In 2003 the entire human genome was entirely mapped. Offcourse we know only extremely small bits of what sequences translate into what action. this mapping has also been done in other organisms, tho significantly less complex.
When researching the patterns of the discovered genomes, certain "nonsense" dna sequences that have no use, have been found in closely related species. This proves they come from the same ancestor.
So far, its only done on micro organisms, because of the large knowledge of their genome, and the MUCH shorter lengt.