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Aggressive periodontitis (localized, and generalized) has had a controversial history in aligning its clinical to its biological features. This is partially due to the difficulty in procuring samples from such a patient population, differing methods that acquire samples from different subgingival compartments, and targeting a subset of the subgingival species at a time. The advent of whole genome sequencing and bioinformatics has allowed us to investigate these conditions in more detail than ever before. The purpose of this investigation was to examine the taxonomic and functional differences in localized aggressive periodontitis, generalized aggressive periodontitis, and chronic periodontitis. Cross-sectional and longitudinal study designs using both metagenomic and metataxonomic sequencing methodology were combined with a comprehensive systems biology approach to characterize the taxonomic composition, functional characteristics, and vertical inheritance patterns in health and disease. Gene and taxonomy-centric views of the dysbiotic shift from health to the 3 different disease phenotypes were illustrated. The investigation into parental contribution to the child's microbiome demonstrated a strong vertical transmission component. The child’s microbiome was also resilient to perturbation caused by supragingival prophylaxis which is the standard of care in this patient population. Differences in the sampling effort across different sampling methods (paper points, curettes, and tissue sampling) demonstrated differential sampling efficacy across each subgingival zone. Longitudinal studies with large population and investigations designed to understand host-bacterial interactions are warranted to understand the gradual move from eubiosis to dysbiosis in each disease phenotype to illustrate early disease biomarkers, and to devise a personalized risk assessment strategy in the future.