Oral microbiology in the microbiome era – when, how and why to perform microbiological diagnostics
Knowledge about the oral microbiota has increased greatly during the past decade after the introduction of high-throughput sequencing technologies. These culture-independent technologies have enabled the detection of the as yet uncultured bacterial species that make up about half of the 700 species identified in the oral microbiome. Similarly, the oral mycobiome has been shown to be much more diverse than previously expected. Currently, studies are underway to clarify the differences between the microbiome in health and disease with regard to both the species involved and the functional properties of the microbiome. The implications for disease management and diagnostics still remain undetermined.
Culture is still the preferred diagnostic method both for bacterial and fungal infections. The benefit of using culture is that it enables identification of multiple species and antimicrobial susceptibility testing. Nucleic acid detection methods have become increasingly available for detection of a number of suspected periodontal pathogens as well as for diagnostics of viral infections. Microbiological diagnostics are not routinely needed but may be helpful in complicated or refractory infections and in differential diagnostics.
High-throughput sequencing studies have expanded our knowledge about the diversity of the oral microbiome by detecting a great number of as yet uncultured species both in health and disease. However, the clinical significance of these findings remains undetermined. In clinical practice, culture methods are still preferred for diagnostics of bacterial and fungal infections because culture allows susceptibility testing. In addition, nucleic acid detection methods have become available for detection of periodontitis-associated pathogens and viral infections.