Defining a minimal oral microbiome (MinOroBiome)

• Applicants: Professor Dr. Fabian Cieplik; Professor Dr. Johannes Hertel
• Subject Area: Dentistry, Oral Surgery ; Microbial Ecology and Applied Microbiology
• Term: since 2026
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 573622698

Approximately 700 species-level taxa are adapted to colonize the surfaces of hard and soft tissues in the human oral cavity. Oral hygiene measures such as brushing and flossing remove biofilms from the smooth surfaces of teeth, but microorganisms recolonize them within minutes. If left undisturbed, relatively mature dental biofilms will form within hours. Over this stage, saliva provides the key nutrient source for the growth and division of attached microorganisms. Individual species cannot grow effectively on saliva alone, and interspecies interactions are essential for efficient growth in the oral cavity. Laboratory models are essential to understand the processes involved in growth and biofilm formation in saliva. However, very few models available at present use saliva as the sole nutrient source for in vitro growth, partly due to the challenges associated with identifying microbial communities that can grow on this substrate. This project will combine microbiome, metagenome, metatranscriptome and metabolome analysis with bioinformatics and statistical modelling to select synthetic microbial communities that can efficiently grow on saliva. The aim is to develop standardized, clinically relevant models that can be used in future to explore biofilm growth, resilience and transitions towards oral diseases. We will take a top-down approach starting with total salivary bacteria to converge experimentally on the key taxa that need to be included within minimal oral microbiomes. This selection will be guided by 16S rRNA amplicon sequencing in saliva-fed batch culture models, after which the communities will be transferred to a more advanced biofilm model that mimics salivary flow. Community selection will also be accompanied by culture-based techniques. The resulting minimal microbial communities will be analyzed using multi-omics to provide an in-depth characterization of the microbiome, metatranscriptome and metabolome, with the aim of elucidating the key functions of these microbial communities. Data from laboratory models will provide a basis for the development and refinement of metabolic models that will be used for statistical modelling of microbial community interactions. This will provide insights into the overall metabolic capabilities of our minimal oral microbiomes, allowing iterative development of communities if required. The computational modelling will also provide insights into the potential resilience of minimal oral microbiomes against challenges such as the invasion of new species. This project will provide key resources for the oral health research community in terms of new laboratory and computational models for studying biofilm development and transitions to oral disease and a new understanding of the key metabolic interactions that shape oral microbial communities.

• DFG Programme: Research Grants
• International Connection: United Kingdom
• Co-Investigators: Professor Dr. Ali Al-Ahmad; Professor Dr. Harald Binder
• Cooperation Partners: Professor Nicholas Jakubovics; Professor Dov Stekel, Ph.D.