The main purpose of this systematic narrative review is to determine the difference in abundance of bacteria and bacterial genes of subgingival microflora of human periodontal pockets compared to healthy sites, via Metagenomic and Metatranscriptomic analyses. Databases EMBASE and MEDLINE were searched for articles, with earliest records from 1978. Main outcome measures included: 1) Bacterial genera and/or species significantly increased 2) Most prevalent or significantly upregulation of genes. Ten studies met selection criteria and were included in the study. Nine studies were cross-sectional, and one was longitudinal. Main results showed trends of specific bacteria and genes found in periodontal pockets. However, within the limitations of this narrative review, trends of abundant bacteria and genes does not imply these specific species or genes are actively participating in disease progression. Nine of ten included studies were cross-sectional in design with eight studies being metagenome based and not able to measure gene expression.