Chapter 9

The Oral Microbiome

Marcelle M. Nascimento
Associate Professor, Department of Restorative Dental Sciences, Division of Operative Dentistry, College of Dentistry, University of Florida,
Gainesville, FL, United States

INTRODUCTION
Untreated dental caries is the most common disease, and severe periodontitis is the sixth most common disease affecting
humans globally [1] (Figs. 9.1 and 9.2). Of great concern are the serious implications that these oral diseases can have on
general health [2]. Increasing evidence shows that oral bacteria may spread and be associated with infections in other parts
of the body [3,4]. For example, reports have identified transient bacteremia, which can be caused by poor oral hygiene,
periodontitis, dental procedures, and even tooth brushing, as the precursor of some cases of infective endocarditis [3].
Moreover, systemic conditions and their associated treatments may also affect oral health by reducing salivary flow and
affecting the ecological balance of the oral microbiome. Not surprisingly, there is growing interest on the composition and
metabolic activities of oral microbiome, as well as an evolving trend for dental and medical research to share knowledge on
the etiology and pathogenicity of human diseases.

ORAL BIOFILMS
Insights provided from the Human Microbiome Project reveals that ecological balance in biofilms play a significant role in
health [5]. As a result, an expanding area of research focuses on therapeutic interventions that modulate microbial ecology
to restore homeostasis of human biofilms and thus health [5,6]. It is well accepted today that dental caries and periodontitis
are closely related to a dysbiosis of the microbial consortia of oral biofilms driven by environmental changes, such as a
sugar-frequent and acidic-pH environment in caries and a protein-rich and alkaline-pH environment in periodontal disease
[7e9]. Conventional therapies for caries and periodontitis aim at controlling the development and metabolic activities of
supragingival and subgingival oral biofilms (also called dental plaque), respectively. Still, caries and periodontitis remain
as major public health problems worldwide.

COMPOSITION OF THE ORAL MICROBIOME

The oral microbiome comprises hundreds of microbial species, including bacteria, viruses, mycoplasmas, archaea, fungi,
and protozoa, that coinhabit and functionally interact in oral biofilms to maintain homeostasis or to cause disease [10e13].
Oral microbiology studies have traditionally focused on bacteria and bacterial infections, but the advances of OMICS
techniques (e.g., metagenomics, metatranscriptomics, metaproteomics, metabolomics, spectral imaging fluorescence,
in situ hybridization) are enabling the study of complex community interactions that includes members of the microbiota
from different kingdoms. One of the major challenges facing oral health researchers today is to distinguish which of the
potential microbialemicrobial and microbialehost interactions are critical for maintenance of dental health.
Following the advancement of gut microbiome research, genome databases specific to oral microorganisms were
developed, including the Human Oral Microbiome database (HOMD) [38] and the Core Oral Microbiome (CORE)
database [39], which are curated to remove contaminants and improve reliability of the analysis. Also important was the
sequencing of genomes of oral bacteria by the Human Microbiome Consortium [40]. This was particularly relevant to

Microbiome and Metabolome in Diagnosis, Therapy, and other Strategic Applications. https://doi.org/10.1016/B978-0-12-815249-2.00009-9 91
Copyright © 2019 Elsevier Inc. All rights reserved.
92 BLOCK | II Background Information

FIGURE 9.1 (A) Child with a healthy oral cavity; (B) Child with early childhood dental caries (ECC). Photography by Dr. Nascimento.

FIGURE 9.2 (A) Adult with a healthy oral cavity; (B) Adult with both dental caries and periodontal diseases. Photography by Dr. Nascimento.
 Mouth Microbiome Chapter | 9 93

reduce the number of unassigned reads in metagenomic analysis. Nevertheless, 40%e50% of the metagenomic reads still
remain unassigned or assigned as hypothetical proteins with unknown function; therefore, more work is needed in this area
[41e43].
To provide a more realistic picture of the complex interactions contributing to the compositional and functional stability
of the oral ecosystem, studies should also take place involving kingdoms other than bacteria, such as viruses, fungi,
archaea, and protozoa. It was recently demonstrated that bacterial viruses (bacteriophages) might assist in maintaining a
stable, healthy ecosystem compared with the dysbiosis of periodontal diseases [44]. OMICS approaches have been suc-
cessfully used to assess composition and functionality of complex communities grown in an in vitro biofilm model [45].
OMICS could also be used in search for optimal growth conditions of the so-called “unculturable” organisms, which may
grow in the presence of certain helper strains and/or compounds with siderophore activity [46].

Acquisition of the Oral Microbiome

The oral cavity of a newborn baby is typically sterile. Right after birth, the oral cavity becomes a major point of entry of
microorganisms into the human body [10]. Oral microorganisms can be acquired from the birth canal, mother’s skin, air,
food, water, and other fluids, but saliva is the main route of microbial transmission. Salivary transmission occurs primarily
from the mother or main caregiver (vertical transmission), but it may also occur from other individuals in close contact with
the newborn or child (horizontal transmission). Notably, available evidence suggests that clinical and educational
interventions beginning during pregnancy are effective at reducing motherechild levels of cariogenic bacteria (e.g., mutans
streptococci) and thus transmission and caries in young children [14].

The Placenta and the Microbiome

The mode of delivery has been associated with specific oral microbiome patterns in 3- to 6-month-old infants [15]. Oral
commensals such as Streptococcus, Fusobacterium, Neisseria, Prevotella, and Porphyromonas have been detected in the
human placenta by 16 rRNA gene sequencing analysis, revealing that the oral microbiome may be a potential source of
intrauterine infection [16]. The placental microbiome was also shown to be more similar to the mother’s oral microbiome
compared with the microbiome of any other body site [17].
It has been suggested that oral commensals may reach the amniotic fluid through blood during pregnancy, which can
also be aggravated if the mother has periodontal disease [18]. In fact, significant evidence supports an association between
adverse outcomes of pregnancy (e.g., preterm birth and preeclampsia) and the virulence properties of periodontal
pathogens, such as Fusobacterium nucleatum, Porphyromonas gingivalis, Filifactor alocis, Campylobacter rectus, and
others [19].

THE ORAL MICROBIOME OF THE INFANT AND CHILD

The diversity of the oral microflora increases during the first months of life. The pioneer oral bacterial species are mainly
streptococci, particularly Streptococcus salivarius, Streptococcus mitis, and Streptococcus oralis. These early colonizers
are followed by gram-negative anaerobes, including Prevotella melaninogenica, Fusobacterium nucleatum, and Veillo-
nella spp. Bacterial species such as mutans streptococci and Streptococcus sanguinis begin to colonize the oral cavity at the
time of teeth eruption, when they are able to attach to the nonshedding hard dental tissues and initiate the development and
maturation of oral biofilms [17]. From the first months of life into the first years and adulthood, the oral microbiome
becomes significantly more diverse and undergoes specific succession mechanisms that are mostly influenced by the
environmental factors and immune filtering [20].

The Oral Environment

The oral cavity is moist and warm (35 e37 C), which is suitable to the growth of a broad range of microorganisms. The
oral cavity also not only provides abundant and continual influx of nutrients for microbial growth, such as salivary
proteins and glycoproteins, but also provides dietary components such as carbohydrates [21,22]. As a result, the mouth
harbors over 700 bacterial species and a range of viruses, archaea, fungi, and protozoa [10]. Genome sequencing
techniques have identified some of these oral microorganisms, but several others (about one-third of oral bacteria) are yet
to be isolated from oral samples and cultivated in the laboratory by using conventional methods. Bacterial cultivation
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may be challenging because some bacteria have specific requirements for nutrients, while others may be inhibited by
substances in the culture media or produced by other bacteria [23].

Oral Microenvironments
The physical and biological properties of each oral habitat can be very distinct from one another, and this results in diverse
site-specific microbial communities that have likely adapted to their unique oral environmental niche [24,25]. While some
communities colonize the shedding surfaces of the oral mucosa (tongue, cheek, gingiva, and palate), others colonize the
hard and nonshedding surfaces of teeth and prosthetic devices [26]. Other factors affecting the communities’ composition
at the oral sites include differences in nutrient availability and redox potentials, competition among species for binding
sites, interspecies antagonism or cooperation, differences in species-specific receptors on different tissues, pH, atmospheric
conditions, salinity, and access to saliva [24].
The microbial load on mucosal surfaces is relatively low due to constant desquamation; however, colonization is
augmented on the nonshedding surfaces of the oral cavity. More specifically, oral biofilms develop and mature over time in
oral sites that are relatively protected from the mechanical actions of the tongue, cheeks, abrasive foods, and tooth brushing
[27]. To persist in the oral cavity, oral microorganisms must adhere to a surface or to other organisms. This coadhesion
process facilitates nutritional cooperation and food chains, gene transfer and cellecell signaling, and ultimately the for-
mation of multispecies biofilms [28].
Oral microorganisms gain substantial advantages by growing as a biofilm and by functioning as a microbial com-
munity. Biofilms are inherently more tolerant to environmental stresses, host defenses, and antimicrobial agents compared
with growth as single microbial cells.

BIOFILM ARCHITECTURE AND COOPERATION

The complex spatial organization or biogeography of supragingival oral biofilms was revealed by spectral imaging
fluorescence in situ hybridization (CLASI-FISH) and metagenomic sequence analysis [29]. Corynebacterium was shown
as the cornerstone of supragingival plaque architecture with long filaments that serve as anchor sites for many other
microorganisms [29]. If these findings are confirmed, it could imply that Corynebacterium, rather than Fusobacterium
species, are the bridging bacteria in biofilms.
This study also revealed that individual taxa are localized at the micron scale, in ways suggestive of their functional
niche in the biofilm consortium. For example, anaerobic taxa tend to be in the interior, whereas facultative or obligate
aerobes tend to be at the periphery of the consortium. Consumers and producers of certain metabolites, such as lactate, tend
to be near each other.
Another example of synergistic relationship occurring within oral biofilms is related to oxygen tolerance and meta-
bolism. Despite the fact that the oral cavity is overtly aerobic, obligate anaerobes and facultative anaerobic bacteria
comprise the most numerous group of oral bacteria. Survival mechanisms of oral anaerobes include the ability to express a
range of enzymes, whose function is to scavenge low levels of oxygen in the environment and the ability to persist in close
partnership with oxygen-consuming species [26,30].

PATHOGENESIS OF SUPRAGINGIVAL BIOFILMS

The pH and carbohydrate availability are key environmental factors affecting the physiology, ecology, and pathogenicity
of the oral biofilms colonizing the teeth [31]. Many beneficial oral bacteria can tolerate brief conditions of low pH, but their
growth is inhibited by prolonged or frequent exposures to acidic conditions. In this context, the buffering activity of saliva
plays a major role, in maintaining the intraoral pH at around neutrality, which is optimal for the growth of most members of
the oral microbiome [32].
Changes in environmental pH occur following consumption of dietary sugar. Specifically, organic acids produced by
the fermentation of dietary carbohydrates by cariogenic bacteria elicit demineralization of tooth enamel. These periods of
acid challenge to the tooth are followed by periods of alkalinization, which neutralizes plaque pH and promotes remi-
neralization and enamel surface integrity [31]. Whereas many factors contribute to the alkalinization of oral biofilms
(e.g., buffers in saliva, diffusion of acids out of biofilms), alkali generation by oral bacteria plays a major role in pH
homeostasis in oral biofilms and inhibits the initiation and progression of dental caries [31,33,34] (Fig. 9.2).
 Mouth Microbiome Chapter | 9 95

Is It Symbiosis or Dysbiosis?
The most abundant members of the oral microbiota are commensal organisms beneficial for oral health, but pathogens
responsible for oral disease also exist. Commensal communities function to maintain the normal development of host
tissues and defenses by providing colonization resistance and downregulation of damaging host inflammatory responses.
However, the homeostasis or symbiotic relationship between the oral microbiome and the host is highly dynamic, as the
composition and metabolic activities of microbial communities fluctuate according to the environmental changes in pH,
nutrient availability, oxygen tension and redox environment, shedding effects of oral surfaces, and composition of salivary
and crevicular fluids [35].
In addition, both health-associated and disease-associated bacteria display remarkable phenotypic plasticity. Specif-
ically, they can morph rapidly in response to oral environmental changes [35]. Constant changes in the environment can
disturb the symbiotic interactions between microbeemicrobe and microbeehost and lead to ecological dysbiosis, which is
characterized by the outgrowth of pathogens and increased risk of disease development (Fig. 9.3) [26].

Oral Diseases
The factors driving dysbiosis in caries differ from those of periodontal disease. In caries, continuous acid production from
the metabolism of dietary carbohydrates results in the emergence of acid-producing and acid-tolerant organisms in
supragingival biofilms, a selective process that alters the pH homeostasis of biofilms and shifts the demineralizatione
remineralization equilibrium toward loss of tooth minerals. Microbial diversity appears to be lower in caries than health,
which may reflect the ecological pressure of low environmental pH [13].
Accumulation of subgingival plaque leads to inflammation of the gum tissues, or gingivitis, which may progress to
periodontitis. In periodontitis, certain members of the microbial community can destabilize the host immune response,
which may result in destruction of periodontal tissues in susceptible individuals. Contrasting with caries, periodontal
diseases are associated with an increase in microbial diversity, which could be the result of impaired local immune
function, increased availability of nutrients, or a reflection of the diverse environmental niches at the periodontal pocket
[36,37].

The Caries Microbiome

The microbiome that naturally colonizes teeth in health is a biofilm community that can counterbalance acid production
from dietary intake of carbohydrates to maintain an intact tooth surface, for example, by ammonia production from
arginine or urea [31]. Dysbiosis of the biofilm, with change of the bacterial composition, occurs when excessive and
frequent intake of carbohydrates exceeds the buffering capacity of the healthy microbiome [47].

FIGURE 9.3 The dynamic relationship between the oral microbiome and the host environment in health (A) and disease (B) [26].
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The renowned Keyes’s diagram of dental caries describes three main pillars as responsible for the disease: host features
(e.g., immune system, genetic nature that predisposes the enamel structure, salivary composition and buffering effect),
environmental components (e.g., dietary sugars, fluoride, oral hygiene habits, as well as personal factors influenced by
socioeconomic status and lifestyle), and microbiological features (e.g., acidogenicity of dental plaque, presence of pH-
buffering bacteria, levels of pathogenic microorganisms). Numerous oral microbial taxa exhibit association with dental
health or caries activity [48e50]. The use of next-generation sequencing (NGS) technologies have revealed the high
complexity of the oral microbiome [41,43], metatranscriptome [42,51], metaproteome [52,53], and metabolome [54,55].

Bacterial Signature in Childhood Caries

The microbiome of healthy tooth surfaces differs substantially from that found in caries activity [41,48,49,56]. Changes in
the microbial profile with the progressive stages of early childhood caries were observed when supragingival plaque of
healthy tooth surfaces was compared with those of enamel and then dentin carious lesions [13]. In particular, plaque
communities from dentin carious lesions of caries-active children (CA-PD) showed a very distinctive bacterial profile.
Moreover, communities from healthy tooth surfaces of caries-active children (CA-PF) were shown to be more similar to
those from enamel carious lesions (CAE-PE and CA-PE) than to those of healthy teeth from caries-free children (CF-PF),
suggesting that CA-PF sites appear to be at greater risk of caries development than CF-PF sites (Fig. 9.4). This finding is
concordant with previous risk factor studies for childhood caries [57] and highlights the interconnectedness of plaque
communities, in which these communities are part of a larger ecosystem, where changes in the structure of one community
may eventually affect others.

NEWLY IDENTIFIED BENEFICIAL AND PATHOGENIC MICROBES

One of the most significant findings from OMICS studies was the identification of previously unknown, thus “new”
bacterial genera/species, which appeared to be associated with dental health or caries. Such was the case for Streptococcus
A12 [58] and Streptococcus dentisani [59], which were both isolated from supragingival plaque of caries-free individuals.
A12 is able to inhibit the growth and intercellular signaling of the caries pathogen Streptococcus mutans and to buffer pH

(A) (B)

FIGURE 9.4 (A) Ordination analysis: distance-based redundancy analysis (db-RDA) of plaque bacterial communities. (B) Neighbor joining phylogeny
based on pairwise PERMANOVA variance components for beta diversity. Branch lengths represent the degree to which bacterial communities are
differentiated. Groups shaded in green showed no significant differences in beta diversity. CF, caries-free children; CAE, caries-active, with enamel
carious lesions, children; CA, caries-active, with dentin carious lesions, children; PF, supragingival plaque samples from caries-free tooth surfaces; PE,
plaque from active, enamel carious lesion; PD, plaque from active, dentin carious lesions [13].
 Mouth Microbiome Chapter | 9 97

through the arginolytic pathway. Similar to A12, S. dentisani presents antimicrobial activity on S. mutans and is capable of
metabolizing arginine. Current evidence supports the role of arginine metabolism in caries prevention [60e65].
Given their beneficial and health-associated properties, A12 and S. dentisani are currently being tested as probiotic
strains for caries prevention. Other newly identified species are yet to be characterized, such as Schlegelella species, which
were detected by high-throughput 16S rRNA gene sequence analysis of carious dentin samples. In some subjects,
Schlegelella represented a high proportion of the total microbiota detected in the carious samples [66]. Scardovia wiggsiae
was significantly associated with severe early childhood caries [67].
Lactobacillus species have long been associated with late stages of caries progression [68]. In a metagenome analysis of
the bacterial communities found at the different stages of caries development, Lactobacillus species were detected only in
deep carious dentin [43].

ACTIVE VERSUS INACTIVE BACTERIA

OMICS studies also underpinned a pivotal aspect of the caries processdthe presence of bacteria does not necessarily
indicate metabolic activity. Specifically, the prevalence of bacteria revealed by metagenome analysis may not correlate
well with the patterns of the active microbial community revealed by metatranscriptome analysis of the same oral sample.
Actinomyces, Corynebacterium, and Neisseria were the three most abundant taxa in the RNA-based community of a 24-h
plaque sample, whereas Veillonella, Streptococcus, and Leptotrichia were the most prevalent in the total DNA-based
metagenome of the same sample [51]. This underlines the dynamic nature of microbial activity in biofilms by indi-
cating that some genera were especially active at 24 h of biofilm development, whereas others were less active, albeit being
present at higher proportions at that point of sampling.

Gum Microbiome
In periodontitis, an inflammatory response is triggered if biofilm accumulates around the gingival margin beyond levels
compatible with oral health. The flow of gingival crevicular fluid (GCF) is increased to deliver components of the host
defenses (e.g., immunoglobulins, complement, neutrophils, cytokines) in response to the microbial challenge. This
response will inhibit the growth of susceptible species, but a number of subgingival organisms (including P. gingivalis) can
use specific mechanisms to disturb host defenses, such as by degrading complement, interfering with neutrophil function,
and blocking phagocytosis. The increased flow of GCF also provides other host molecules that can serve as nutrients for
some of the proteolytic members of the subgingival microbiota.
Early studies linked advanced periodontitis with the presence of the “red complex,” which was composed by
P. gingivalis, Treponema denticola, and Tannerella forsythia. Other consortia termed the “orange complex,” which
included Fusobacterium nucleatum, Eubacterium nodatum, and various Prevotella and Campylobacter species, often
preceded the presence of the “red complex.” However, there is currently no great consistency in defining the predominant
species implicated in disease, and generally inflammation is associated with diverse polymicrobial communities.
Like in other polymicrobial infections, no single bacterial species has been implicated as a principal pathogen in
periodontal disease. The prevalent taxa in periodontal disease fall into eight bacterial phyla: Firmicutes, Proteobacteria,
Spirochaetes, Bacteroidetes, Actinobacteria, Synergistetes, Fusobacteria, and TM7 [10]. The genera Peptostreptococcus,
Veillonella, and Selenomonas are prevalent in chronic periodontitis, while the genera Streptococcus, Eubacterium,
Selenomonas, Treponema, Porphyromonas, and Capnocytophaga were more common in subjects with aggressive
periodontitis. It remains uncertain whether phylotypes identified by 16S rDNA as associated with chronic and aggressive
periodontitis (Filifactor alocis), or chronic and refractory periodontitis (TM7 and Synergistetes), have a meaningful role as
periodontal pathogens [24].

Oral Mycobiome
Recent molecular studies revealed a diverse array of fungi as potential oral residents [72]. Candida albicans is the most
commonly cultivated and studied fungus, and Candida species, especially C. albicans, have been unequivocally linked to
the etiology of oral thrush (candidiasis). Despite considerable research in oral candidiasis, it is not clear why some subjects
develop the condition, while others with similar risk factors remain disease-free.
Oral candidiasis can present clinically as a pseudomembranous condition or as erythematous and/or hyperplastic lesions
[73]. Most cases of oral candidiasis are associated with C. albicans, although some have been linked to Candida
dubliniensis, Candida glabrata, Candida krusei, and Candida tropicalis, commonly as mixed infections including
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C. albicans. Aspergillus, Fusarium, and Cryptococcus are other fungi reported to be colonizers of the oral cavity of healthy
individuals. While the mechanisms that prevent these pathogenic fungi from causing disease in healthy individuals are
unknown, there is evidence that oral bacteria provide a natural defense through the production of antifungal compounds.
Components of saliva, such as lactoferrin, also inhibit growth of Candida and Aspergillus [24].
Recent studies have shown that C. albicans may play a role as a secondary agent in the caries process [74]. C. albicans
and other members of the fungal kingdom have also been recovered from periodontal pockets of patients with chronic and
aggressive periodontitis. C. albicans can express both cell surfaceebound and secreted proteinases capable of degrading
major extracellular matrix and basement membrane components such as collagens and fibronectin, as well as promoting
strong, chronic, and compact inflammatory cell infiltrates in the periodontal tissue [75,76]. Moreover, these C. albicans
proteinases can enhance the tissue-destructive host cell proteinase network, in the same way as the proteases expressed by
periodontopathic bacteria. However, the role played by C. albicans in periodontal diseases is unclear, and further studies
are needed to demonstrate the clinical significance of the findings.

Oral Microbiome Associated With Systemic Disease

Severe forms of oral disease may result in systemic repercussions at different body sites, including cardiovascular disease,
pneumonia, preterm birth, and diabetes. Chronic inflammatory periodontal diseases, which are among the most prevalent
of chronic infections in humans, are thought to constitute a significant inflammatory burden that contributes to cardio-
vascular disease (e.g., atherosclerosis, myocardial infarction, and stroke). Bacteria that colonize the oropharynx, including
Streptococcus pneumoniae, Haemophilus influenzae, and Mycoplasma pneumoniae, are recognized as a source of
community-acquired pneumonia. Streptococcus gordonii, a pioneering colonizer of the oral environment and commensal
microorganism, is an opportunistic pathogen associated with endocarditis [24].
Of importance, oral diseases share common risk factors with other chronic, systemic diseases/conditions including (1)
Western-type diet (risk factor for dental caries, coronary heart disease, stroke, diabetes, cancer, obesity); (2) tobacco
smoking/chewing (oral and other cancers, periodontal disease, coronary heart disease, stroke, respiratory diseases,
diabetes); (3) alcohol consumption (oral and other cancers, cardiovascular disease, liver cirrhosis, trauma); (4) poor
hygiene (periodontal disease and other bacterial and inflammatory conditions); (5) injuries (trauma, including dental
trauma); (6) stress (periodontal disease and cardiovascular disease); and (7) socioeconomic status (underlying determinant
of other risk factors; information available from: https://www.dentalhealth.ie/dentalhealth/causes/general.html).

CONCLUSIONS
Even though the healthy oral microbiome appears to be more stable than those of other body niches like the gut, there is
evidence for substantial degree of within-individual variability in the oral microbiome [69,70].
Genetic diversity and complexities in the adaptive strategies of oral bacteria to fluctuating biofilm conditions diminish
the utility of taxa-level correlation of the microbiome with health especially, but also with caries and periodontal disease.
The relevant questions may be answered by elucidating what the microbes are doing, rather than focusing primarily on who
is performing those actions [9]. Also deserving more attention are the microbial interactions with the host, e.g., adhesion
mechanisms between microbes and salivary proteins [71] and the recognition patterns with the oral immune system [66].
Future microbiome and metagenome analysis will certainly contribute to the development of more effective therapeutic and
diagnostic techniques and, ultimately, to personalized medicine and personalized dental medicine [77].

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