The oral microbiome is a rather complex environment that is home to several thousands of bacterial types. It is known that the oral biome is highly variable and almost unique for each individual. However, little research has been conducted in the area of the oral microbiome's functional genomics, and specifically the metabolic pathways that play an important role in the progression of periodontal disease. The majority of previous research articles investigated bacterial diversity by traditional sequencing of the 16S rRNA gene but discarded information taken from "unknown" organisms. In this research proposal we use metagenomic-sequencing methods to analyze the distribution of functional pathways and the bacterial diversity of 12 metagenomic samples before and after periodontal treatment. These samples were divided into two categories: six individuals were characterized as improved after periodontal treatment and the remaining six were characterized as worsened. We demonstrate a significant shift in bacterial diversity that occurs after treatment in healthy patients and diseased states and, furthermore, we study the underlying difference between functional pathways. In addition we define additional oral bacterial species and suggest that these species are correlated with the state of periodontal disease. Together with dental records, these findings indicate the effectiveness of metagenomic sequencing and provide a basis for further understanding of this complex disease.