Microbial, especially bacterial taxonomy, is dominated by the comparative analysis of a small stretch of their genomes called 16S rDNA. Since Carl Woese separated Archea as the 'third form of life', ribosomal RNAs have been the major decider of bacterial grouping systematics. In almost every major field related to microbial taxonomy and genomics, it is advisable to compare their ribosomal sequences rather than the whole genome. No doubt it is easy and rapid as compared to the whole genome comparison, but still, it has certain limitations that need to be highlighted.
In the case of bacteria, 16S rDNA is a ~1500 base pair nucleotide stretch in the non-coding region of their genome, and have nine variable regions within it. Moreover, these variable regions are also prone to nucleotide substitution, deletion depending upon their position, and susceptibility to natural forces. Though the ribosomal RNAs are essential for translation purposes and supposed to be conserved in all the microbes. Additionally, they are less prone to mutations as compared to other parts of the genome. But that does not mean they are also efficient in classifying the microbes. However, it is ok to restrict the 16S rDNA sequence analysis for genus-level classification, but there are so many reports where the authors have used this stretch to classify the microbes up to the strain also. Which is in my opinion, not a rational approach.