Journal of Oral Microbiology

Microenvironments in Oral Biofilms

Microenvironments in oral biofilms are increasingly recognized as key determinants of microbial behavior, resilience, and pathogenicity. Rather than being homogeneous layers of bacteria, dental biofilms are highly structured, spatially organized communities in which steep gradients of pH, oxygen, redox potential, nutrients, and signaling molecules develop over micrometer distances. These localized conditions shape microbial physiology, metabolic cooperation and competition, and ultimately the expression of virulence traits.

Advances in imaging, molecular ecology, and analytical chemistry now allow us to investigate these microhabitats with unprecedented resolution, revealing that what happens at the microscale often governs the emergent properties observed at the clinical level.

Understanding microenvironments in oral biofilms is crucial, because disease is never driven by single pathogens acting in isolation. Dental caries, periodontal diseases, and peri-implant infections develop when local ecological balances shift toward conditions that favor acidogenic, proteolytic, or inflammatory processes. Microscale acidification, oxygen depletion, or matrix remodeling can create protected niches that promote persistence despite mechanical disruption or antimicrobial exposure.

Traditional bulk analyses and broad-spectrum antibacterial strategies often fail to capture or counteract these localized processes. By focusing on microenvironments, researchers can better explain why clinically similar biofilms behave differently, why therapies succeed or fail, and how apparently minor ecological perturbations trigger irreversible disease trajectories. Insights at this scale are essential for moving oral microbiology beyond descriptive community profiles toward mechanistic, predictive, and ultimately preventive models of biofilm-associated diseases.

This Article Collection aims to highlight how chemical and biological heterogeneity within oral biofilms arises, how it is maintained, and how it influences health–disease transitions on tooth, mucosal and restorative surfaces. This article collection welcomes original research, reviews, and methodological papers that illuminate the spatial and chemical complexity of oral biofilms. We particularly encourage contributions employing chemical and physicochemical imaging approaches, including pH, oxygen, redox, and metabolite mapping. Studies using FISH and related spatial techniques to resolve microbiogeography and interspecies organization are strongly encouraged. We also invite work that dissects the composition, structure, and functions of the dental biofilm matrix, both as a determinant of microbial ecology and as an active driver of disease processes. Finally, we seek innovative therapeutic concepts that target microscale virulence—such as disrupting harmful niches, metabolic cross-feeding, or matrix integrity—rather than relying solely on nonspecific antibacterial agents. Together, these contributions will advance a more nuanced, ecology-driven understanding of oral biofilms.

Keywords

1. Oral biofilms
2. Extracellular matrix
3. Microenvironments
4. Microbiogeography
5. Biofilm-related oral disease

­­All manuscripts submitted to this Article Collection will undergo a full peer-review; the Guest Advisor for this Collection will not be handling the manuscripts (unless they are an Editorial Board member).

Please review the journal scope and author submission instructions prior to submitting a manuscript.

The deadline for submitting manuscripts is 31 March 2027.

Please contact Zhiyuan Zhang at [email protected] with any queries and discount codes regarding this Article Collection.

Please be sure to select the appropriate Article Collection from the drop-down menu in the submission system.

Guest Advisors

Prof. Sebastian Schlafer is a dentist by education and works as a Professor of Cariology at the Department of Dentistry and Oral Health, Aarhus University. His research focuses on the composition, architecture and metabolic activity of dental biofilms, with a particular focus on the biofilm matrix and its role in oral disease. He has expertise in quantitative microscopy, chemical and correlative imaging, as well as in the development and validation of novel approaches to biofilm control that preserve the benefits of the commensal microbiota.

Dr. Yumi C. Del Rey has a background in dentistry and is currently employed as a postdoctoral researcher at the Department of Dentistry and Oral Health, Aarhus University. Her work combines the development of correlative imaging methods to study the spatial organization, structure, and function of oral biofilms in health and disease with research on ecological strategies for caries prevention.