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 is not routinely needed but it may be helpful in complicated or refractory infections and in differential diagnostics.
Headlines
The oral microbiome consists of a high number of cultured and as yet uncultured species of bacteria, fungi, viruses, Archae, and protozoa
Microbiological diagnostics is still mainly performed by culture for bacterial and fungal infections
Nucleic acid detection methods are used for identification of periodontitis-associated bacteria and viruses
Thanks to high-throughput sequencing technologies, we now realize that the oral microbiota is far more diverse than previously expected. This has profound implications for treatment of oral infections, especially with regard to using antimicrobials. The purpose of this review is to provide the reader with the recent advances in the concept of the oral microbiome and to present an overview of the indications and methodologies used in diagnostic microbiology today.
The oral microbiome
Microbiome is the term used to refer to our resident microbiota (). The oral microbiome consists of bacteria, fungi, Archae, viruses, and protozoa (). Throughout the 20th century improvements in cultivation and biochemical analyses revealed an increasingly diverse microbiota but the introduction of sequencing technology caused an explosion in microbial diversity because it enables detection of both cultivable and as yet uncultured species (). In 2007, the Human Microbiome Project was launched () and in 2010 the Human Oral Microbiome Database was established (). Bacteria have been predominantly identified by sequencing the 16S ribosomal RNA (16S rRNA) gene that contains regions conserved in all bacteria and regions that vary between species (). This far, over 700 species of bacteria have been identified in the oral bacteriome and about half of them are as yet uncultured
Microbiome studies have revealed that the microbiome may differ significantly between individuals and different oral niches. This has led to the definition of a 'core' oral microbiome consisting of the microorganisms found in all or the vast majority of individuals and a 'variable' part that has a lower prevalence (). Three studies based on high-throughput sequencing of 16s rRNA genes from oral samples of up to 200 individuals have shown that the predominant oral taxa belong to the phyla Firmicutes (genus Streptococcus, Veillonella, Granulicatella), Proteobacteria (genus Neisseria, Haemophilus), Actinobacteria (genus Corynebacterium, Rothia, Actinomyces), Bacteroidetes (genus Prevotella, Capnocytophaga, Porphyromonas), Fusobacteria (genus Fusobacterium) and Spirochaetes (genus Treponema . Frequently detected as yet uncultured phyla are GN02, SR1, and TM7 Although we now have an understanding of the core oral microbiome, it is important to bear in mind that for example poor oral hygiene, wearing dentures, immunosuppression, use of antimicrobials, hospitalization and being bedridden all significantly alter the composition of the oral microbiome with for example opportunistic respiratory pathogens and staphylococcal species being introduced
Over 75 fungal genera have been detected in the oral mycobiome by high-throughput sequencing using fungal internal transcribed spacer (ITS) primers In these studies, Candida species have been the most frequent finding (75 %-100 % of healthy individuals). Other common genera detected were Cladosporium, Aureobasidium, Aspergillus, Fusarium, Cryptococcus and Malassezzia ().
The oral virome consists of both eukaryotic viruses and bacteriophages (). Metagenomic studies on the oral virome are still rare. In a recent study, members of the virus families Herpesviridae and Papillomaviridae were found to be the most common of the human DNA viruses detected ().
How has high-throughput sequencing affected to our understanding of the oral microbiota?
The main contribution of high-throughput sequencing is the revelation of the immense diversity of the oral microbiota (). In addition, the microbiota of a specific oral site may differ between individuals (). Thus, it is necessary to define the microbiota associated with health and to follow the transition from health to disease in longitudinal studies. This can disclose microbial changes associated with disease. A cross-sectional study of a limited number of individuals most likely will reflect differences in the microbiota between health and disease but due to the large inter-individual differences it is far from certain that this indicates a significance of the microorganisms found only in the diseased subjects.
The Human Genome Project revealed that our genome does not contain all genes necessary for the functions of the human body (). The resident microbiota of man provides far more genes necessary for the well-being of man than hitherto anticipated. Through evolution man has coevolved with the members of the resident microbiota and together they form a 'superorganism Because of the coevolution, the immune system has developed immune tolerance towards the res
