Pharmacological Research 69 (2013) 137–143

Contents lists available at SciVerse ScienceDirect

Pharmacological Research
journal homepage: www.elsevier.com/locate/yphrs

Invited review

The oral microbiome in health and disease

William G. Wade ∗
King’s College London Dental Institute, Microbiology Unit, Floor 17, Tower Wing, Guy’s Campus, London SE1 9RT, UK

a r t i c l e i n f o a b s t r a c t

Article history: The human mouth harbours one of the most diverse microbiomes in the human body, including viruses,
Received 30 September 2012 fungi, protozoa, archaea and bacteria. The bacteria are responsible for the two commonest bacterial dis-
Received in revised form eases of man: dental caries (tooth decay) and the periodontal (gum) diseases. Archaea are restricted to
14 November 2012
a small number of species of methanogens while around 1000 bacterial species have been found, with
Accepted 15 November 2012
representatives from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, Spirochaetes, Syn-
ergistetes and Tenericutes and the uncultured divisions GN02, SR1 and TM7. Around half of oral bacteria
Keywords:
are as yet uncultured and culture-independent methods have been successfully used to comprehensively
Microbiome
Dental caries
describe the oral bacterial community. The human oral microbiome database (HOMD, www.homd.org)
Gingivitis provides a comprehensive resource consisting of descriptions of oral bacterial taxa, a 16S rRNA iden-
Periodontitis tification tool and a repository of oral bacterial genome sequences. Individuals’ oral microbiomes are
highly specific at the species level, although overall the human oral microbiome shows few geograph-
ical differences. Although caries and periodontitis are clearly bacterial diseases, they are not infectious
diseases in the classical sense because they result from a complex interaction between the commen-
sal microbiota, host susceptibility and environmental factors such as diet and smoking. Periodontitis, in
particular, appears to result from an inappropriate inflammatory reaction to the normal microbiota, exac-
erbated by the presence of some disease-associated bacterial species. In functional terms, there appears
to considerable redundancy among the oral microbiota and a focus on functional rather than phylogenetic
diversity may be required in order to fully understand host–microbiome interactions.
© 2012 Elsevier Ltd. All rights reserved.

Contents

1. Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
2. Composition of the oral microbiome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
2.1. Viruses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
2.2. Protozoa . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
2.3. Fungi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
2.4. Archaea . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
2.5. Bacteria . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
3. Role of oral microbiome in health . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
4. Oral microbiome-related oral diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
4.1. Dental caries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
4.2. Endodontic infections . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
4.3. Periodontal diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
4.3.1. Gingivitis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
4.3.2. Periodontitis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
4.4. The oral microbiome and non-oral diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
5. Functional aspects of the oral microbiome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
6. Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 141
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142

∗ Tel.: +44 20 7188 3872.

E-mail address: william.wade@kcl.ac.uk

1043-6618/$ – see front matter © 2012 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.phrs.2012.11.006
138 W.G. Wade / Pharmacological Research 69 (2013) 137–143

1. Introduction 2.3. Fungi

The human mouth is heavily colonised by microorganisms, Candida species are carried symptomlessly by around half of
including viruses, protozoa, fungi, archaea and bacteria. In contrast individuals with the prevalence increasing with age, and also
to the commensal microbiota found at other body sites, which typ- cause a wide range of acute and chronic infections [8]. A culture-
ically live in harmony with the host, the normal microbiota of the independent survey of the oral mycobiome in healthy individuals
mouth is responsible for the two commonest diseases of man – found 85 fungal genera in the mouths of 20 healthy individuals
dental caries and the periodontal diseases. Because of this, humans, [9]. The predominant genera were Candida, Cladosporium, Aureoba-
particularly in developed countries engage in regular oral hygiene sidium, Saccharomycetales, Aspergillus, Fusarium, and Cryptococcus.
practices, typically brushing with toothpastes and/or rinsing with Whether the detection of these, and the more rarely found gen-
mouthwashes. Why this should be necessary remains unknown era, represents colonisation by the vegetative forms of the fungi
although it is likely that soft and sugar-rich diets are largely respon- is unclear. It is possible that the method used detected airborne
sible. The bacterial communities found in the mouth are highly spores or transient colonisation from food.
complex with around 1000 species present [1] and has been shown
to be the second most complex in the body, after the colon [2]. 2.4. Archaea
The use of culture-independent methods of determining the com-
position of the oral microbiome, allied with next generation DNA The Archaea make up only a minor component of the oral micro-
sequencing methods is providing a far deeper analysis than hitherto biome and the archaeal community is restricted to a small number
possible. Species-level identification may not be sufficient how- of species/phylotypes, all of which are methanogens. They can be
ever, because of the genetic heterogeneity of bacterial species and detected in health but their prevalence and numbers are raised
the strong influence of the environment on phenotype. A combi- in subjects with periodontitis. The species found are Methanobre-
nation of phylogenetic, metagenomic, transcriptomic, proteomic vibacter oralis and two un-named Methanobrevibacter phylotypes,
and metabolomic approaches may be required to fully dissect oral Methanobacterium curvum/congolense and Methanosarcina mazeii
host–microbiome interactions relevant to health and disease. In [10,11].
this review, the progress made towards this goal will be described
and discussed. 2.5. Bacteria

Initial knowledge of the composition of the oral bacterial

biome came from microscopy with the well-known observations
2. Composition of the oral microbiome
of Leeuwenhoek [12], who showed a diverse collection of bacte-
rial morphotypes in dental plaque. Following the development of
2.1. Viruses
bacterial culture media by Koch, Pasteur and others, the character-
isation of the cultivable component of the mouth’s microbiota was
A range of viruses can be found in the mouth, which are primar-
effected and found to comprise a diverse collection of organisms,
ily disease-associated. For example, the mumps and rabies viruses
including obligate aerobes and facultative and obligate anaerobes
infect the salivary glands and thus those viruses will be found in
and a wide range of metabolic potential including the ability to
saliva in affected individuals. Similarly, blood-borne viruses such
degrade sugars and proteins, and complex substrates derived from
as the hepatitis viruses and HIV can enter the mouth via gingival
them. This culture-based work led to the identification of specific
crevicular fluid and viruses causing upper respiratory tract infec-
organisms thought to play a causative role in caries and periodon-
tions will clearly be present in the mouth during the acute phase.
titis and which could be treated with antimicrobials [13]. Culture
Herpes simplex causes gingivostomatitis or a sub-clinical infection
alone gives a highly distorted view of the composition of the oral
in the majority of neonates and the virus can subsequently enter a
microbiome, however.
dormant state in the trigeminal ganglion. The virus can reactivate
It has long been known that a substantial proportion of bac-
in response to external factors such as stress, cold weather or other
terial life on earth cannot be cultivated in the laboratory [14]. In
virus infection, and cause herpes labialis (cold sores) [3]. Human
the mouth, approximately half of the bacteria present have yet
papilloma virus HPV is responsible for a number of oral conditions,
to be cultured [15]. Complex bacterial communities such as the
including papillomas, condylomas and focal epithelial hyperplasia
oral microbiota have been characterised by culture-independent
[4] and has also been implicated in head and neck squamous cell
methods based on the analysis of the sequences of conserved
carcinoma [5].
housekeeping genes directly isolated from samples of saliva or oral
A survey of the oral virome in five subjects revealed that the
biofilms. The gene most commonly used for this purpose has been
majority of virus sequences detected had homology with bacterio-
that encoding the 16S rRNA [16]. The 16S rRNA itself can be isolated
phages which is perhaps not surprising, given the dense and diverse
directly and sequenced [17] but more typically the gene encoding
community of bacteria found in the mouth [6].
the 16S rRNA is amplified by PCR using “universal” primers tar-
geting the ultra-conserved regions of the gene and then cloned by
incorporation into a plasmid vector [18]. The use of this method
2.2. Protozoa has allowed the comprehensive description of the oral bacterial
biota [1]. The method is time-consuming and relative costly, how-
Two protozoon species are found as part of the normal micro- ever, and typically only around 100 cloned genes are sequenced per
biome: an amoeba, Entamoeba gingivalis, and the more structured sample, a relatively shallow analysis of a highly complex commu-
Trichomonas tenax. The numbers of these organisms is raised nity.
in subjects with poor oral hygiene and gingival disease and A major advance to this technique has been the adoption of
were once considered as potential pathogens. They are currently high-throughput next generation sequencing methods such as
regarded as harmless saprophytes and the apparent link with dis- pyrosequencing. In the 454 system (Roche) [19], 16S rRNA genes
ease is nutritional, in that poor oral hygiene leads to increased are amplified by PCR from samples with universal primers and
amounts of food debris and bacteria, both food sources for protozoa then mixed in equal proportions. The mixture is then amplified in
[7]. an emulsion and distributed among wells on a plate to which are
 W.G. Wade / Pharmacological Research 69 (2013) 137–143 139

added beads containing the sequencing reagents. Nucleotide incor- identification for the members of many genera. Indeed, it is
poration is detected by a CCD camera imaging system and around unfortunate that even full-length 16S rRNA sequences have
0.8 million sequences, up to 750 base pairs long can be obtained insufficient resolution for confident identification of species com-
in a single run. To enable multiple samples to be sequenced in the prising some of the important and predominant oral genera
same run, primers with unique barcodes are used, typically 8–12 such as Actinomyces, Streptococcus, Neisseria, Veillonella, Porphy-
nucleotides, incorporated into the initial PCR primer. These bar- romonas and Selenomonas. In part, this is due to genetic exchange
codes are then incorporated into the final sequences obtained and between members of these genera which have led to recom-
can be easily sorted and assigned to source samples after sequenc- bination within the 16S rRNA gene, making the interpretation
ing. of phylogenetic relationships derived from this gene difficult
The use of pyrosequencing and alternative high through- [29].
put methods such as the Illumina system, which provides even Because of these limitations, the Ribosomal Database Project
higher numbers of sequences, although of shorter length, has Classifier [30], one of the most commonly used analysis pipelines,
revolutionised culture-independent analyses and has been the cor- only allows identification of sequences to genus level. This may be
nerstone of that part of the Human Microbiome Project devoted informative when applied to highly diverse bacterial communities
to determining the composition of the microbiomes at different but for a well-studied microbiome such as the oral microbiome, it
human body sites [2]. These studies have shown that each body is a severe limitation. Thus, genera such as Porphyromonas, Aggre-
site studied was colonised by a microbiome characteristic of that gatibacter and Tannerella all include some species that are strongly
site but that the individual was the primary factor influencing the associated with disease and others that are health-associated. Data
composition of the microbiome i.e. each individual is colonised from next generation sequencing studies targeting the 16S rRNA
by a unique microbiome. Within the mouth, samples from seven gene should therefore be interpreted with caution to avoid drawing
different surfaces were found to be colonised by three distinct bac- erroneous inferences because of the deficiencies of current analysis
terial communities: the buccal mucosa, gingivae and hard palate pipelines. For the oral microbiota, it is possible to use the mothur
had similar microbiota while the saliva, tongue, tonsils and throat, analysis suite [31] in conjunction with the HOMD reference set to
and supra- and sub-gingival plaque each had distinctive communi- obtain species-level identifications for most oral bacterial genera
ties [20]. The oral microbiota was found to be only second to that of [32]. An alternative approach is used in the SpeciateIT programme,
the colon in terms of species-richness and, while there are similar- based on the construction of hidden Markov models, and has been
ities between individuals oral microbiomes at the genus level [21], shown to improve species-level identification of the endodontic
at the species level, the composition of the microbiota is more vari- and vaginal microbiota [33,34].
able in different individuals with, in one study, 47% of species-level The bacterial community of the mouth is dominated by the phyla
OTUs shared between three individual [22]. There appears to be Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, Spirochaetes
some evidence, then, for a core oral microbiome common to most and Fusobacteria which account for 96% of species detected [1]. The
individuals. key features of the predominant bacterial taxa have been described
Interestingly, a study of 120 individuals from 12 worldwide loca- previously [1] and are available from the Human Oral Microbiome
tions found no significant geographical differences between their Database website at www.homd.org [35].
salivary microbiota [23]. This suggests that diet and the environ- Defining the precise composition of the oral microbiome is
ment do not significantly influence the composition of the oral difficult because the mouth is an open system and frequently
microbiome and that the host species is the primary determinant. exposed to exogenous bacteria in food, in water, in air and the
Some novel taxa were found, however, in a study of the oral micro- normal microbiota of other mammals including humans via social
biota in South American Amerindians living in a remote village contact and kissing. It is often difficult to determine whether
[24], although the lack of a control group makes interpretation of long-term colonisation with a particular species occurs. However,
these data difficult. The primary source of nutrients for oral bacte- most non-oral bacteria are not routinely isolated from the mouth.
ria is endogenous in the form of saliva and gingival crevicular fluid. Why this should be so is unclear but exogenous bacteria may lack
When food is placed in the mouth and chewed, saliva production is adhesins and receptors that would enable them to bind to oral
increased and the food is quickly swallowed, which may explain surfaces or co-aggregate with other bacteria. There may also be
why, in general, diet has little effect on the composition of the immune exclusion. Evidence for this is provided by the observation
oral microbiota. One exception is fermentable carbohydrate; some that gut coliforms are rarely found in health but often found in
oral bacteria are adept in taking up sugars and fermenting them to immunocompromised individuals and those with reduced salivary
produce acid, resulting in dental caries, as described below. Sus- flow [36,37]. Another group of organisms that fall into this category
tained high intake of dietary carbohydrates can result in an altered is the methylotrophs that can use 1-carbon substrates for growth.
microbiota, dominated by aciduric species [25], and the salivary By performing enrichment culture of oral samples using a range
microbiome in caries-active subjects differs from that found in of 1-carbon substrates, representatives of a number of genera
caries-free subjects [26]. including known methylotrophs such as Methylobacterium and
Next generation sequencing methods undoubtedly have the Hyphomicrobium and other organisms including Brachybacterium,
potential to revolutionise our view of the composition of the Gordonia, Leifsonia, Microbacterium and Micrococcus were isolated,
microbiomes but do suffer from some disadvantages compared in which methylotrophy had not previously been demonstrated
to conventional Sanger sequencing. Early data suffered from a [38,39]. Most of these organisms had not previously been isolated
high error rate due to the formation of heteroduplexes and from the mouth and were not among those detected in 16S rRNA
homopolymeric tracts during sequencing which led to the detec- gene clone libraries. They are frequently found in tap water and
tion of spurious diversity and excessively high estimates of species the environment, so it is possible that when applying the powerful
richness in saliva and plaque [27]. This problem has now been suc- selection of enrichment culture, organisms that were only present
cessfully addressed bioinformatically [28] and estimates of species in the mouth transiently, but were not permanent colonists, were
richness from recent studies are now of the same order as hitherto, isolated. These species are also all mainly obligate aerobes. These
with the advantage that the depth of coverage that can be achieved are a rare group in the mouth because of the highly anaerobic
for each individual sample has been greatly increased. nature of oral bacterial biofilms after a short period of develop-
Another significant issue is that, at present, only relatively ment. It is possible that methylotrophic bacteria could transiently
short sequences can be obtained which precludes species-level but repeatedly colonise the exposed aerobic surfaces of the mouth
140 W.G. Wade / Pharmacological Research 69 (2013) 137–143

and use 1-carbon substrates while there. However, further work is there are a large number of species naturally present in the oral
needed to confirm this. plaque biofilm that produce acid from dietary carbohydrate and
An additional problem in the interpretation of data from that the consequent caries-associated microbiota is complex [51].
culture-independent surveys is that PCR reagents are frequently In addition to S. mutans and lactobacilli, members of the genera Bifi-
contaminated with DNA from environmental bacteria which can dobacterium, Propionibacterium and Scardovia have been found to
then be amplified by the universal primers used in such studies [40]. be caries-associated [52–55]. In addition to acid production, some
Pre-treatment with ultra-violet light has been found to be effective bacteria can raise pH by producing ammonia from urea and arginine
in the reduction of such contamination [41]. [56], which provides a mechanism for balancing acid production
from dietary sugars by other bacteria and thus maintaining homeo-
stasis. There is a wide variation in the metabolic activity of strains
3. Role of oral microbiome in health
within species, however, and the environment has a marked effect
on bacterial phenotype. Species-level identifications may therefore
The commensal microbiota plays an important role in maintain-
not be of value in understanding the disease process; functional
ing oral and systemic health. Commensals in the gut are known
characterisation is required which takes environmental influences
to be essential for the development of the structures of the gut
into account [57].
and for appropriate development of local and systemic immunity.
Lymphoid follicles do not develop in the small intestine of germ-
4.2. Endodontic infections
free mice and mucosal IgA is produced only in the presence of the
microbiota [42,43]. The simple presence of the oral microbiota in
If dental carious lesions are left untreated, the lesion can
the mouth inhibits colonisation by pathogens, the phenomenon of
progress through dentine and into the pulp where the pulp
colonisation resistance [44]. Because all surfaces of the mouth are
becomes infected and dies. The microbiota associated with
colonised by commensals there are few binding sites available for
untreated endodontic infections are primarily anaerobic proteo-
pathogens. The importance of this effect can be seen when the com-
lytic bacteria [41]. Interestingly, endodontic infections that persist
mensal microbiota is disrupted, for example by antimicrobials [45].
after treatment frequently include enterococci which are not nor-
Infections by opportunistic pathogens such as Candida species and
mally found in the mouth in health. The source of these organisms
Staphylococcus aureus can occur.
has long been debated but it has been recently shown that are found
Some health-associated bacteria have been shown to be antag-
in cheese, both pasteurised and unpasteurised, and can persist in
onistic to oral pathogens. For example Streptococcus salivarius
the mouth for some time after cheese has been eaten [58]. In an
strain K12 produces a bacteriocin which inhibits the growth of
in-vitro model, it was shown that enterococci could gain access to
Gram-negative species which are associated with periodontitis and
the root canal via microleakage through the type of temporary fill-
halitosis in vitro [46], and has been shown to have beneficial effects
ings that are placed between visits during endodontic therapy [59].
on halitosis in vivo [47].
It is possible then that cheese, and perhaps other dairy and fer-
An interesting property of the oral microbiome relates to
mented meat products, are the source of the enterococci that can
nitrate metabolism and cardiovascular health. Around a quarter of
cause endodontic infection once the root canal has been opened for
ingested nitrate is returned to the mouth via an entero-salivary cir-
treatment. It appears that enterococci can colonise the root canal
cuit. Oral bacteria reduce nitrate to nitrite which is taken up into
and cause infections there but are not able to compete with the
the bloodstream via gastric absorption, and converted into nitric
normal microbiota away from this habitat, elsewhere in the mouth.
oxide. Nitric oxide is essential for vascular health, and helps to keep
Patients receiving endodontic treatment should be advised to avoid
blood vessels pliant and supple and thus has an anti-hypertensive
consumption of foods known to be colonised by enterococci.
effect. Dietary nitrate supplements lower blood pressure by stim-
ulating this mechanism [48]. The central role of oral bacteria has
4.3. Periodontal diseases
been confirmed by the observations that the increase in plasma
nitrite following nitrate ingestion is markedly reduced by the use
4.3.1. Gingivitis
of an antimicrobial mouthrinse [49], and, in rats, antimicrobial use
Gingivitis is perhaps the most common bacterial disease of man
abolishes the blood pressure lowering effect of ntirate [50]. This
with a prevalence in adults of over 90% [60]. Dental plaque forms
may, then, have implications for oral hygiene. Over-zealous oral
continuously on tooth surfaces. Salivary glycoproteins are selec-
hygiene could have negative implications for what appears to be
tively adsorbed onto the teeth to form the salivary pellicle. Oral
an important natural mechanism for maintaining cardiovascular
bacteria then attach to the tooth surface by adhering to epitopes
health.
in the pellicle [61,62]. Primary colonisers can then co-aggregate
with other bacteria joining the developing biofilm via coaggrega-
4. Oral microbiome-related oral diseases tion interactions [63]. In general, primary colonisers tend to be
Gram-positive aerobes and facultative anaerobes such as strepto-
4.1. Dental caries cocci and Actinomyces species [64], while among the predominant
anaerobic organisms in mature plaque are Gram-negatives such
Dental caries, or tooth decay, is the dissolution of tooth structure as Fusobacterium, Treponema and members of the phylum Syner-
by acid produced as a result of the fermentation of dietary car- gistetes [65]. A variety of oral hygiene measures have been used
bohydrates by oral bacteria. In individuals who repeatedly ingest throughout human history to remove dental plaque [66]. Brush-
high levels of carbohydrates, the frequency of acid production leads ing with a toothpaste is the primary method in industrialised
to the erosion of the buffering capacity of saliva and frequent and countries but the use of chewing sticks is perhaps the most com-
sustained reductions in pH. In turn this changes the composition monly used method of oral hygiene worldwide. If tooth cleaning
of the oral microbiota to one that favours aciduric species [25]. is practised regularly, dental plaque is kept in an immature state
These species, particularly Streptococcus mutans and lactobacilli, and in relatively small amounts. If an individual does not practice
continue to produce acid under acidic conditions and thus exac- oral hygiene, then the proportion of Gram-negative and anaero-
erbate the damage to the dental hard tissues. S. mutans has been bic species increases and endotoxin and other enzymes pass into
studied intensively for its cariogenic properties and has even been the gingivae and cause irritation and inflammation by activating
regarded as a specific pathogen. It is now recognised, however, that pro-inflammatory pathways. The clinical signs of gingivitis are
 W.G. Wade / Pharmacological Research 69 (2013) 137–143 141

swollen and inflamed gums which bleed on probing or spon- entirety on their own but consortia of bacteria can work together to
taneously. The disease is entirely reversible if oral hygiene is degrade complex substrates to the benefit of the whole community
reinstated [67]. There are no specific bacteria associated with gin- [82]. For example, it has been shown that certain streptococci have
givitis but the amount of plaque present, the plaque load, and its both glycosidic and endopeptidase activity and are thus able both to
maturity are correlated with disease severity [68]. remove the oligosaccharide sidechains and attack the protein core
of glycoproteins [83,84]. Many Gram-negative anaerobic bacte-
4.3.2. Periodontitis ria such as members of the genera Prevotella and Porphyromonas
In susceptible individuals, attachment is lost between the gin- also have endopeptidase activity which results in the cleavage of
givae and the teeth with the formation of a periodontal pocket, proteins to peptides [85]. Many frequently detected oral bacte-
which becomes heavily colonised with anaerobic bacteria. The host ria including Fusobacterium and Peptostreptococcus and relatives
response is ineffectual and actually contributes to the development have aminopeptidase activity [86,87], and can ferment amino acids
of the lesion with host proteases making a significant contribution producing short chain fatty acids. The connective tissue found in
to tissue damage [69]. The alveolar bone which supports the teeth the periodontium is rich in sulphur-containing glycosaminoglycans
resorbs ahead of the infection, the teeth become mobile in their [88] and sulphate accumulates as a result of tissue breakdown in
sockets and are eventually lost. Dental plaque-associated periodon- disease. Bacterial species regarded as terminal degraders are found
titis is classified into two main categories – chronic and aggressive, in periodontal pockets. For example the methanogens use short
with the latter being characterised by increased severity and rate chain fatty acids in the production of methane [10], and a number
of progression and generally earlier onset [70]. These general of species of sulphate-reducing bacteria, including Desulfobulbus,
descriptions are likely to encompass a spectrum of related diseases, Desulfomicrobium and Desulfovibrio can be found [89,90].
however, which are clinically difficult to differentiate. A specific Oral bacteria vary widely in their sensitivity to oxygen. There
microbiota is associated with advanced periodontitis [13], although are relatively few species of obligate aerobes in the mouth. The
whether certain species are responsible for the initiation of the dis- principal aerobic genera are Neisseria and Rothia species which
ease or the inflammation and pocket formation create conditions are among the earliest colonisers of tooth surfaces [91]. Many are
that periodontitis-associated bacteria prefer remains unclear. Host facultative anaerobes including Streptococcus and Actinomyces, the
susceptibility is clearly of primary importance and tobacco smok- two most numerous genera found. As oral biofilms develop, they
ing is a strong environmental factor [71]. Species associated with rapidly become anaerobic which explains the high proportions and
periodontitis include Porphyromonas gingivalis, Treponema denti- large number of species of obligate anaerobes that are found in
cola and Tannerella forsythia which were originally associated with the mouth. Interestingly, it has been shown that members of the
the disease in culture-based studies and subsequently confirmed oral bacterial community can cooperate to protect each other from
with whole-genomic DNA probes [72]. Culture-independent stud- atmospheric stresses. It has been shown that the presence of the
ies have expanded the range of disease-associated organisms to obligate aerobe Neisseria enables obligate anaerobes to grow in a
include Anaeroglobus geminatus, Eubacterium saphenum, Filifactor mixed-culture biofilm under aerobic conditions [92].
alocis, Porphyromonas endodontalis, Prevotella denticola and un- Although oral bacteria can be grouped by function in this way,
named Bacteroidetes and Fretibacterium phylotypes [73]. there must still be a reason for the extreme diversity and variability
within species. Presumably, this diversity lends versatility to the
4.4. The oral microbiome and non-oral diseases community and the ability to respond to environmental stresses
in the most appropriate way. Recently developed genetic meth-
The oral microbiome has long been known to be a reservoir for ods are allowing the functional potential of the oral microbiome to
infection at other body sites. Oral bacteria easily and frequently gain be assessed. Firstly, metagenomic sequencing using next genera-
access to the bloodstream via the gingival crevice and untreated tion sequencing methods can be used to sequence large amounts
carious lesions and are a significant cause of infectious endocardi- of DNA from oral sites without the need to culture the microbiota.
tis [74], and brain and liver abscesses [75,76]. Oral bacteria have For example, the metagenomes associated with periodontitis and
been detected in the lungs in cystic fibrosis patients [77], and can caries have been found to be significantly different from those seen
cause a variety of soft tissue infections following bites and clenched in oral health and to include sequences coding for a variety of viru-
fist injuries [78,79]. In addition, it has been suggested that the com- lence factors [93,94]. Combined metagenomic and 16S rRNA based
position of the oral microbiome may be linked to diseases at other analyses have allowed correlations between the community struc-
body sites either in a causative way or as a reflection of systemic ture and metabolic activity to be determined for a variety of sites
changes in the body [80,81]. In the latter case, oral microbiomic from the adult digestive tract [20]. Further clues as to the function
profiles could be used as diagnostic biomarkers for other diseases. of oral bacteria and archaea in health and disease will be obtained
from metaproteomic and transcriptomic studies. For example, the
5. Functional aspects of the oral microbiome metaproteome of salivary sediments has been successfully studied,
with peptides identified from over 100 oral bacterial and success-
The complexity of the oral bacterial community is so great that fully mapped to metabolic pathways [95].
it might be considered an impossible task to assign a role for each
organism within the community. What is important, however, is
the functional role of each organism and it is likely that the range 6. Conclusion
of such functions is more limited than the phylogenetic range of
species present. Within each habitat, and depending on the health The use of recently developed molecular methods has greatly
status of the site, a restricted range of functions may be needed expanded our knowledge of the composition and function of the
and could be provided by a number of organisms. Arguably, the oral microbiome in health and disease. Much remains to be done,
most important functions are nutritional. The primary substrates however. Bacterial species are far from homogeneous and compar-
for growth in the mouth are not derived from the food ingested isons of genomes of strains from the same species have revealed
by the human host since this is removed quickly by the combined the high genetic diversity of most species studied, particularly
actions of salivary flow and swallowing, but are derived from saliva in relation to the presence or absence of virulence factors. As
and gingival crevicular fluid in the form of glycoproteins. There discussed above, diseases associated with the commensal micro-
are probably no bacteria that can digest oral glycoproteins in their biota are not caused by a single pathogen but result, in part, from
142 W.G. Wade / Pharmacological Research 69 (2013) 137–143

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