Microbial community diversity analysis is commonly based on PCR-amplified sequences of 16S ribosomal ribonucleic acid (16S rRNA). However, the high degree of evolutionary conservation in the 16S rRNA gene can limit the determination of interspecific relationships. Here, I examine the utility of an alternate genetic marker, RNA polymerase subunit (rpoB), because it has been shown to enhance resolution of interspecific differentiation. However, no readily available software or database is configured to analyze rpoB data in oral bacterial communities. I will compare this rpoB data to the 16S rRNA to determine if the protein-coding gene rpoB can discriminate between closely related microbes in samples with different periodontal disease states. Here, I propose to develop a novel bioinformatics pipeline to analyze rpoB data in order to create a more accurate representation of species diversity, in particular for the classification of closely related bacterial species.