Interrogation of imaging-based interspecies dynamics in the oral microbiome

The oral cavity presents a highly dynamic environment where inter-microbial communications play a pivotal role. Understanding the spatial organization of microbial ecosystems has been highlighted on the microbiome and polymicrobial infection. Furthermore, cross-feeding and modulation by metabolites from the oral microbiota and host cells, such as lactate and reactive oxidative species, impact the stability and functionality of microbial communities. Traditional research focusing solely on the compositional aspects of these communities is insufficient to understand the sophisticated interactions.

We evaluated recent advancements in imaging technologies, bolstered by multi-omics analyses and artificial intelligence (AI)-driven approachesinsights, to provide an more integrated understanding of the dynamics and function of the oral microbiome.

Real time imaging and resolution-enhancing methods at the single-cell level have unraveled the ecology and dynamics of microbial communities, indicating unique three-dimensional architectures and biogeographical patterns associated with disease status in polymicrobial interplays. Emerging computational techniques can account for the spatial features of oral microbiome by creating image-like representations that capture the complex relationships between host tissues and microbial communities. Spatial multi-omics, help address the limitations of single-cell sequencing, deciphering molecular mechanisms between species in these biogeographical patterns. To process the massive volume of imaging-based data, AI-assisted analysis enables complex dataset integration, predictive capacity, and personalized treatment, bringing a whole new level of understanding of the oral microbiome and its relationships with the host.

In this review, we highlight recent imaging-based technologies used to study the spatial biogeography of interspecies and interkingdom relationships within oral microbial communities, focusing on how these interactions and functional/metabolic alterations associated with health and disease. We further outline limitations of AI-generated predictions and imaging-based observational data. Finally, we elaborate on potential biomarkers for early diagnosis and new effective therapeutic strategies to reshape microbial dynamics.