The king is gone but he's not forgotten
The more recent explosion in technical sophistication and high-speed sequencing should not belittle the work of dedicated microbiologists over 50 years in characterizing new species of cultivable oral bacteria, and correlating disease conditions with individual or groups of microorganisms. Although the number of oral microbial species is estimated to be approximately 700 (there are 624 taxa in HOMD) (Dewhirst et al., 2010), there remains debate as to what constitutes a normal oral species. If a cut-off is applied, such that the likelihood that a species will be found in 99.5% of genomes sequenced, then the potential species count rises to about 1200. Because the oral cavity is the portal through which most microorganisms enter the body, it is also possible to identify genomes associated with food, e.g. Rhizobium, drink, e.g. Saccharomyces carlsbergensis, and air, e.g. Legionella.
Back to the present, the main questions now raised by the oral microbiome data relate to fathoming microbial functions in the contexts of health or disease conditions (Xie et al., 2010). In a recent study of oral bacterial communities in healthy subjects it was found that each individual's mouth houses a unique collection of bacterial species. However, about 15 bacterial genera were conserved among the individuals (Bik et al., 2010) showing that communities tend to be more similar when classified at the level of genus, and raising the possibility of defining a core microbiome (Zaura et al., 2009). On top of this, every site in a mouth has a non-random subset of bacteria, the make-up of which varies according to whether the site is basically healthy or diseased (Jenkinson and Lamont, 2005). This is very apparent from studies comparing the microbiota of teeth from children with or without dental caries (Gross et al., 2010; Kanasi et al., 2010); subgingival microbial communities of adults presenting with periodontitis compared with healthy periodontal status (Colombo et al., 2009); the oral microbiotas of HIV-infected subjects (Aas et al., 2007); and the root canal microbiotas from subjects with different types of endodontic infections (Siqueira and Rôças, 2009). Typically, microbiotas found at diseased sites are more structurally complex than those at corresponding healthy sites, suggesting that it might be easier to define microbial community activities at these latter sites.
Historically, the quest has been to identify cultivable microorganisms that were regularly associated with different oral diseases. Studies of caries-free versus caries-positive subjects, and data from in vivo experimental models, have suggested that mutans streptococci, e.g. S. mutans, Streptococcus sobrinus, were major causative agents of dental caries (Takahashi and Nyvad, 2011). Other studies have shown that three species of bacteria, so-called the red group, were consistently associated with adult periodontal disease (Socransky et al., 1998). However, molecular methodology has come up with some interesting discoveries that challenge dogma (Table 1). For example, the anaerobic Gram-positive bacillus Scardovia wiggsiae has been designated a new caries pathogen (Tanner et al., 2011). This organism was found in plaque from carious lesions in children in the presence or absence of S. mutans. Future studies on S. wiggsiae are anticipated to determine pathogenic potential in experimental in vivo models, characterize virulence factors and assess usefulness as a risk indicator for dental caries.
Table 1. Changing concepts in oral disease aetiologies.
|Dental caries||Streptococcus mutans, S. sobrinus, S. downei, Lactobacillus acidophilus, L. casei, L. fermentum, L. rhamnosus, Actinomyces naeslundii, A. odontolyticus||Bifidobacterium dentium, S. mutans, Scardovia wiggsiae, B. longum, B. adolescentis, Prevotella spp., Selenomonas spp., Lactobacillus spp.|
|Root caries||Actinomyces gerencseriae, A. israelii, Streptococcus spp., Lactobacillus spp., A. naeslundii||Actinomyces spp., Lactobacillus spp., Prevotella denticola, Pseudoramibacter spp., Enterococcus faecalis|
|Pulpitis||E. faecalis, Porphyromonas endodontalis, A. odontolyticus, Parvimonas micra (Peptostreptococcus micros), Prevotella intermedia||Bifidobacterium spp., S. intermedius, Lactobacillus spp., A. israelii, Treponema denticola, P. micra, Prevotella baroniae, Dialister invisus, Olsenella uli, Prevotella spp.|
|Gingivitis||Fusobacterium spp., Actinomyces spp., P. micra, P. gingivalis||Eubacterium nodatum, Eikenella corrodens, Fusobacterium nucleatum, P. micra|
|Aggressive periodontitis||Aggregatibacter actinomycetemcomitans, Capnocytophaga spp.||Selenomonas spp., Prevotella spp., A. actinomycetemcomitans, Filofactor alocis, Tannerella forsythia, T. denticola, P. gingivalis|
|Chronic periodontitis||P. gingivalis, T. forsythia, T. denticola, Fusobacterium spp.||P. micra, Campylobacter gracilis, E. nodatum, Eubacterium saphenum, T. forsythia, P. gingivalis, Prevotella spp., Treponema spp., Selenomonas noxia E. corrodens|
|Halitosis (oral malodour)||Prevotella spp., P. gingivalis, Actinomyces spp.||Atopobium parvulum, Dialister phylotype, Eubacterium sulci, TM7 phylum, Solobacterium moorei, Prevotella spp.|
Another potential cariogenic pathogen recently identified is Bifidobacterium dentium (Ventura et al., 2009). This is closely related to gut commensal bifidobacteria, but has acquired genes for survival in dental plaque at low pH, and does not colonize the edentulous mouth (Mantzourani et al., 2010). These various discoveries widen viewpoint of the causative agents of dental caries past the mutans streptococci. In a similar way, molecular methods have identified Dialister invisus, Olsenella uli and Synergistes spp. as prevalent in persistent root canal infections (Siqueira and Rôças, 2005), questioning a previously held belief that Enterococcus faecalis often played a significant role in the disease process (Siqueira and Rôças, 2009). Another potential paradigm shift results from the revelation that periodontitis-associated microbial communities are hugely more complex than previously believed, with possibly new pathogens, e.g. Eubacterium saphenum being implicated in periodontitis (Abiko et al., 2010) in addition to P. gingivalis and Tannerella forsythia (Table 1). Of note is that genomic analyses have revealed the presence of multiple phylotypes of Treponema within periodontal pockets (Moter et al., 2006) and it is suggested that members of this genus are almost always found within oral soft tissue lesions (Table 1).
Recent molecular genomic studies have thus confirmed some of the previous correlations made between the presence of bacterial species and specific disease conditions, but have identified some new and potentially significant associations. However, the discussion up until now has exclusively involved bacteria. The oral cavity is also home to more than 100 species of fungi (Ghannoum et al., 2010), and untold numbers of protozoan species. While fungi seem often to be omitted from microbiomics, yeasts such as Candida albicans clearly contribute to a wide range of oral infections, e.g. denture stomatitis, periodontitis, and interact specifically with some of the oral bacteria (Bamford et al., 2009). Protozoa, as well as undiscovered bacteriophage, would be continuously depleting the bacterial communities, while the bacteria themselves indulge in molecular war games between each other. Now that components of oral microbial communities have been identified, the objectives are to better understand the architectural, metabolic and genetic activities of these communities. For this, the new molecular taxonomic information has to be integrated with more conventional genetic, biochemical and physiological approaches, and it will then become evident how these communities function. The physical and chemical interactions that occur between the microorganisms determine how the community grows and survives, and influences the niche. The interactions can be studied through the employment of metabolomics, which characterize the metabolic product profiles of the community (Takahashi et al., 2010), proteomics (Rudney et al., 2010) and transcriptomics. Ultimately, it will be possible to incorporate all of this information into generating microbial community interactomes, essentially describing the functional consequences of the microbiome.