Isolation of new periodontitis-associated bacterial species using culturomics – comparison with shotgun metagenome analysis

• Applicant: Professor Dr. Ali Al-Ahmad
• Subject Area: Dentistry, Oral Surgery
• Term: since 2025
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 567959569

Since periodontitis is associated with a shift of the subgingival microbiome, the subgingival biofilm sampling technique and the microbiological methods used are critical factors in the characterization of the oral periodontitis-associated microbiome. In this context, high-throughput next-generation sequencing (NGS) is the method of choice for studying periodontitis-associated bacteria at present, although the widespread use of NGS led to the detection of unculturable and unknown bacteria called the dark matter of metagenomics. While intensive culture methods (culturomics) have largely been used to characterize the gut microbiome, the subgingival oral biofilm has not been studied using culturomics to date. Furthermore, no studies describing the simultaneous application of culturomics and NGS for the analysis of periodontitis-associated bacteria are found in the literature. In the proposed project, periodontitis-associated biofilm and subgingival biofilm from healthy subjects will be analyzed using a combination of culturomics and NGS. The samples will be taken by an experienced periodontist using a standard protocol and bacteria will be isolated by plating the samples on different culture media that have not been used for culturing of periodontal bacteria to date. Concurrently, the metagenome of all samples will be analyzed by shotgun analysis. The proposed project comprises the following aims: culturing of novel bacterial species from the subgingival oral biofilm, increasing the knowledge of the dark matter of metagenomics, enhancing the current biodiversity and microbial database of oral bacteria, and comparing the limitations and strengths of culturomics and NGS. Furthermore, the Index for Measuring Subgingival Microbial Dysbiosis (SMDI), which was proposed in 2022, should be improved by the results of this project.

• DFG Programme: Research Grants
• Co-Investigators: Professor Dr. Harald Binder; Professor Dr. Fabian Cieplik; Privatdozentin Dr. Anne Kruse