Single-cell profiling of the subgingival bacteria reveals transcriptional heterogeneity and niche-specific programs

Periodontitis is a chronic inflammatory disease driven by subgingival dysbiosis. Despite progress in characterizing microbial diversity, functional heterogeneity at the single-cell level remains poorly understood, mainly due to challenges from low microbial biomass and host contamination. Here, we present a single-cell RNA sequencing framework for profiling subgingival bacteria, enabling high-resolution analysis of these communities in health and periodontitis. Using 16 subgingival samples, we generated an atlas spanning 133,458 cells across 285 species, including 57 core active species grouped into eight functional clusters. Health-associated subpopulations specializing in adhesion and polysaccharide degradation decline in periodontitis, coinciding with hypoxia and elevated amino acid availability. The keystone pathogens T. denticola and P. gingivalis display species-specific tendencies in amino acid metabolism-related transcriptional profiles, while P. intermedia harbors a proteolytic subpopulation enriched in periodontitis. These insights deepen our understanding of periodontitis pathogenesis and inform precision diagnostics and therapeutic strategies.