Microb Ecol (2017) 73:492–503

DOI 10.1007/s00248-016-0854-1

HUMAN MICROBIOME

The Oral Microbiome of Children: Development, Disease,

Received: 22 June 2016 / Accepted: 1 September 2016 / Published online: 14 September 2016
# Springer Science+Business Media New York 2016

Abstract In the era of applied meta-omics and personalized oral cavity. Indeed, Miller, in his seminal account of the mi-
medicine, the oral microbiome is a valuable asset. From bio- croorganisms of the human mouth BDie Mikroorganismen der
marker discovery to being a powerful source of therapeutic Mundhohle^ (1892) [1], suggests that a great number of bac-
targets and to presenting an opportunity for developing non- terial morphotypes obtained in the mouth could make their
invasive approaches to health care, it has become clear that classification impossible. Since then, microbiologists and mi-
oral microbes may hold the answer for understanding disease, crobial ecologists have come a long way—from targeting spe-
even beyond the oral cavity. Although our understanding of cific members of the Bculturable^ fraction of the oral cavity
oral microbiome diversity has come a long way in the past [2], to using cloning [3, 4], fingerprinting [5], and high-
50 years, there are still many areas that need to be fine-tuned throughput sequencing technologies—to reveal that this
for better risk assessment and diagnosis, especially in early microecosystem may harbor over 800 to 1000 different oral
developmental stages of human life. Here, we discuss the bacterial taxa (as sharing >98.5 % 16S ribosomal RNA
factors that impact development of the oral microbiome and (rRNA) sequence identity) [3], with varying abundance and
explore oral markers of disease, with a focus on the early oral diversity patterns across age and health status. Consequently,
cavity. Our ultimate goal is to put different experimental and this vast microbial diversity, which includes bacteria, archaea,
methodological views into perspective for better assessment viruses, phage, and various microeukaryotes, makes it a chal-
of early oral and systemic disease at an early age and discuss lenge for clinicians and microbial ecologists to look for valid
how oral microbiomes—at the community level—could pro- markers of oral health and disease, not to mention the hurdles
vide improved assessment in individuals and populations at risk. associated with the significant variation found between and
within (different oral cavity sites) subjects [6, 7]. Diversity
Keywords Microbial ecology . Oral microbiome . Children . surveys on healthy oral microbiomes do suggest a core group
Caries of phylotypes [8, 9], different from those found under diseased
conditions [5, 10]. Further, an extensive body of literature has
focused on reviewing and surveying the oral microbiome in
health and disease [3, 11–14]. However, finding consistent
Introduction
bacterial markers, across studies and cohorts, is still a daunting
task. Moreover, translating these findings into effective treat-
Leeuwenhoek’s microscope observations in his own dental
ment of oral and even systemic health is a significant
plaque, over three centuries ago, suggested an unprecedented
challenge.
diversity of microorganisms (or Banimalcules^) in the human
In this review, we attempt to dissect relationships between
oral bacteria and health by exploring the factors that shape the
* Andres Gomez human oral microbiome, with a focus on the early oral cavity.
agomez@jcvi.org Thus, we review studies on the oral microbiome of children
and the ecological and developmental aspects of this
1
Departments of Human Biology and Genomic Medicine, J. Craig microecosystem that relate to oral and systemic health. To
Venter Institute, La Jolla 92037, CA, USA accomplish these goals, we (1) examine the factors impacting
The Oral Microbiome of Children 493

development and maturation of the oral microbiome since maternal oral microbes and the seeding of the oral
birth, (2) explore biomarkers influencing oral health and dis- microbiome in newborns is potentially likely but needs
ease in children, and (3) inspect how oral microbial markers to be further tested using mechanistic, rather than associ-
affect health beyond the child’s oral cavity into adulthood. ation-type, models.
Finally, (4) we discuss the technical and analytical areas where Assembly of microbes in the oral cavity. After initial
the microbial ecology and clinical field should focus to trans- seeding, assemblage of the human microbiome seems to
late biomarker discovery into preventive therapeutics in oral be significantly influenced by environmental exposure. In
and systemic health in an individual’s lifetime. this scenario, specific body habitats create a set of physi-
cal, chemical, and biological conditions that Bfilter^ body
1. Development and maturation of the oral microbiome fol- microecosystems, to allow colonization by a very partic-
lowing birth ular set of environmentally derived bacteria [25]. In the
How we acquire our microbiome during pregnancy case of the oral cavity, it is likely that a specific set of
and after birth has been the subject of numerous research environmental stimuli and immune filtering, after initial
studies [15], the majority focusing on microbes populat- seeding, shapes the oral environment into adulthood, po-
ing the lower gastrointestinal (GI) tract, with far more tentially impacting oral health. In this regard, a combina-
limited information on the microorganisms populating tion of different mother microbiome sources including
of the oral cavity following birth. Interestingly, emerging gut, vaginal, skin, as well as breast milk and early foods,
evidence has pointed to a connection between the placen- may shape the early oral microbiome [26, 27]. For in-
tal environment and the oral microbiome. For instance, stance, just as it happens with the gut microbiome in in-
16S ribosomal RNA (rRNA) gene sequencing analysis fants, the early oral cavity is also influenced by mode of
has revealed the presence of several prominent oral com- delivery [15, 23, 28]. Specifically, vaginally delivered in-
mensals such as Streptococcus, Fusobacterium, fants tend to show increased abundances of taxa such as
Neisseria, Prevotella, and Porphyromonas in the human Prevotella, Bacteroides, and TM7, while C-section-
and murine placenta [16–18]. Indeed, close similarities delivered babies show increased colonization by
were found between the presumed placental microbiome Propionibacterium, Staphylococcus, Slackia, and
and that in the mother oral cavity, compared to any other Veillonella. The way these signals impact children oral
body site [18]. The hypotheses behind these findings pro- health later in life, as it has been suggested with gut mi-
pose that during pregnancy, oral commensals reach the crobial communities, requires further investigation.
amniotic fluid through blood (low-grade bacteremia), a Right after birth, the newborn oral cavity seems to be
condition that may be exacerbated during periodontal dis- rapidly dominated by Streptococcus (Streptococcus
ease and oral infection in mothers, with potential delete- mutans, Streptococcus epidermidis, and Streptococcus
rious consequences for term delivery [19–22]. Moreover, salivarius) and Fusobacterium [28–30]. Apparently, the
an association has been found between mode of delivery bloom of Streptococcus spp. (particularly S. salivarius)
and specific oral microbiome patterns in 3 to 6-month-old is associated with the first oligosaccharide stimuli in the
infants, specifically as far as the abundances of infant oral cavity [31]. Possibly, the metabolic products by
Streptococcus, Fusobacterium, and Slackia [23]. Streptococcus on dietary oligosaccharides in breast milk
Nonetheless, the hypotheses of a placental or formula (fermentation) pave the way for other oral
microecosystem of hematogenic origin and establishment commensals to thrive. Furthermore, different species of
of the newborn oral cavity influenced by mother-derived pioneer Streptococcus spp. isolated from both breast-fed
oral bacteria are controversial. The critiques mainly rely and formula-fed neonates have the metabolic capability to
on a lack of evidence that bacterial DNA found in amni- cleave immunoglobulin A1 (IgA1) [32], which would
otic fluid is that of live bacteria, as one would expect that suggest that Streptococci could bloom in an IgA1-rich
high-throughput sequencing technologies would detect environment, likely triggered by breast milk [33].
any bacterial DNA present regardless of cell viability, so However, it is unclear whether potential differential abun-
the signal obtained may be merely cell debris. dances in diverse Streptococci species arise in response to
Additionally, there is the possibility of contamination of formula or breast milk stimuli or if these differences could
placenta with maternal blood [24]. Despite these observa- impact oral health.
tions, it is a fact that both the placental and oral From the first months of life (3–4 months) into the first
microecosystems are particularly unique in diversity com- years and adulthood, the oral microbiome becomes sig-
pared to any other body site, including the vaginal nificantly more diverse and undergoes very particular suc-
microbiome [7], and that the microbial signal obtained cession mechanisms [34, 35]. For instance, at the genera
in the amniotic fluid includes bacteria not usually found and species levels, Escherichia coli, Staphylococcus, and
in the urogenital tract. Thus, the connection between Pseudomonas, as well as lactic acid-producing bacteria
494 A. Gomez, K. E. Nelson

such as Lactobacillus crispatus, Lactobacillus gasseri, development at an early age, and subsequent maturation,
and Streptococcus, all of which are associated with the including influence of oral disease markers.
gut, skin, or breast milk [15, 36–38], are prevalent in the
first months, even before tooth eruption. Conversely, Childhood oral diseases
Fusobacteria, Tenericutes, Synergistetes, TM7, and SR1 Caries, the most common chronic childhood dis-
start dominating the oral microecosystem toward the first ease, is of dietary/bacterial origin, and it occurs as a
years of life; specifically, Veillonella, Fusobacterium, result of cariogenic diets (sugar-related) and the me-
Neisseria, Prevotella, Rothia, Treponema, and tabolism of specific bacteria on dietary sugars in sus-
S. mutans, linked to more mature oral microbiomes and ceptible hosts [54, 55]. Thus, it is reasonable to ex-
with potentially cariogenic microbiomes, seem to emerge pect that the first dietary stimuli have a strong influ-
as infants transition into more mature stages and likely ence on the etiology of caries at later developmental
more exposure to the external environment [34, 35, stages. For instance, meta-analyses have shown evi-
39–42]. dence that bottle-fed children exhibit more early
Nonetheless, increasing attention has been given to childhood caries (p < 0.05), with additional
possible links between the host genetic factors and the supporting evidence to show that breastfeeding may
composition of the human microbiome [43–45], with prevent caries in early childhood [56]. Indeed, a sup-
some studies of this kind specifically targeting the oral pressive effect on cariogenic S. mutans has been ob-
cavity. For example, studies on healthy monozygotic served by Lactobacilli isolated only from the oral
and dizygotic infant twins using high-throughput se- cavity of breast-fed children but not from formula-
quencing and fingerprinting methods have shown that fed children [57], implying potential benefits of
host genetic background (as opposed to the shared envi- breast milk in the oral ecosystem. However, other
ronment) has no significant effect in shaping salivary or studies have suggested that a possible positive effect
plaque bacterial communities [46, 47]. These findings are of breastfeeding on the incidence of caries in children
in contrast to other twin cohort studies, in which checker- may be masked by other confounding
board assays point to taxa in saliva and plaque that are socioeconomical factors such as poverty, ethnicity,
potentially heritable and that may have role in the pathol- and maternal prenatal smoking [58].
ogy of caries (e.g., Mutans streptococci) [48, 49]. All in all, it seems that frequent sucrose consump-
Likewise, positive associations between some major his- tion at early age (from 1.5 to 3 years old) is one of the
tocompatibility complex (MHC) class II alleles and sali- leading causes influencing increased colonization
vary levels of culturable S. mutans and lactobacilli have with S. mutans, the main causing and predictive fac-
been found in caries-bearing adult women and young tor of oral caries [59–63]. During this process, par-
adults [50, 51]. Consequently, the extent to which the ticular community dynamics involving sucrose me-
shared environment and the host genetic landscape influ- tabolism, pH homeostasis, and biofilm formation im-
ence colonization of the early oral cavity is still unclear pacts oral disease development [55, 64]. For in-
and should be further investigated based on standardized stance, tooth decay and enamel demineralization
deep sequencing techniques. seem to be promoted by a community shift in biofilm
2. The oral microenvironment and biomarkers of oral dis- populations toward acidogenic (acid producing) and
ease in children aciduric (acid tolerant) cariogenic bacteria, likely
Thus, most evidence available shows that an early oral triggered by low pH after sucrose fermentation
environment, strongly shaped by maternal sources, rapid- [65]. Additionally, sucrose seems to be a substrate
ly transitions into a more complex, mature for the production of extracellular and intracellular
microecosystem influenced by the external environment. polysaccharides, two components that determine
A critical question then is to identify, at an early age, the biofilm formation and structure [66, 67]. Indeed,
factors that trigger oral disease later in life. For instance, children with nursing caries (12–48 months old with
healthy children (from 3 months old) already harbor po- primary dentition), who are also under increased su-
tentially cariogenic bacteria (S. mutans), which increase in crose exposure, not only have higher incidences of
abundance with age [35, 52]. Additionally, among 3- S. mutans but also an altered biofilm structure char-
month-old children, increased presence of Lactobacilli, a acterized low Ca, Pi, and F and higher levels of in-
taxon that tends to dominate carious lesions [41, 53], may soluble polysaccharides compared to caries-free chil-
be predictive of caries at 3 years [34]. These observations dren [68, 69].
suggest that a combination of extrinsic and intrinsic fac- Thus, a constant influx of fermentable sugars into
tors determine oral disease phenotypes later in childhood. the oral cavity results in increased carbohydrate fer-
Figure 1 offers a schematic view of oral microbiome mentation (lactic acid production), followed by
The Oral Microbiome of Children 495

Seeding community Established community

*
*

Early/Late childhood

Cariogenic meta-community *

pH
Caries
Maternal/External Birth/First months
Pasteurellaceae
Environment (Edentulous)
pH
Alkali
Direct transmission ? No Caries

Fig. 1 Oral microbiome development, maturation, and emergence of oral potentially cariogenic bacteria (e.g., S. mutans). Later in childhood, diet
disease markers. The early oral microbiome is mainly shaped by maternal and environment determine the mature oral microbiome, which increases
stimuli including a possible signal from the maternal oral cavity (via significantly in diversity including colonization with potentially
placenta), as well as her gut, skin, and vaginal microbiomes. During the cariogenic taxa. This stage is also critical for the emergence of oral
first months, diet further modifies the oral microecosystem, specifically as disease, with sugar consumption and fermentation by potentially
far as oligosaccharides present in formula and breast milk and cariogenic taxa (along with an acidic pH) being the main determinants.
immunoglobulin A1 from the later. These maternal and dietary stimuli However, the establishment of oral caries may be reversed by ureases
give rise to the seeding oral community of infants, which include encoded by certain commensals in plaque (e.g., Pasteurellaceae)

longer periods of oral exposure to low pH (Stephan However, in epidemiological experiments or animal
curve [70]) and the selection of bacteria able to models of oral disease, it is not immediately clear
thrive on these conditions (aciduric taxa), such as whether the bloom in the aforementioned cariogenic
S. mutans, Lactobacilli, and Bifidobacteria [71, taxa occurs in response to increased sugar availability
72]. These taxa constitute some of the main bio- or if low pH after sugar metabolism creates an
markers in caries lesion biofilms. For instance, acidogenic environment that displaces non-aciduric,
S. mutans can trigger pH conditions as low as 3.0 health-associated taxa [75]. In this regard, controlled
after sugar stimuli through fermentation, a scenario culture systems of defined mixed inoculum have shown
that has been linked to enamel demineralization [73, that constant glucose influx, while maintaining neutral
74]. In contrast, other species within the pH, keeps the bacterial community in balance and the
Streptococcus genus, such as S. salivarius and proportions of potentially cariogenic taxa at low levels
Streptococcus mitis, are associated with an increase (e.g., S. mutans and Lactobacillus rhamnosus) [76]. In
of pH through alkali-generating pathways and there- contrast, allowing the pH to drop, proportional to glu-
fore are linked to a protective effect against caries cose fermentation, results in significant blooms of
[64, 65]. caries-associated (aciduric) taxa, at the expense of
496 A. Gomez, K. E. Nelson

health-associated bacteria [77]. Thus, low pH due to Additionally, adopting a system-level approach to
sugar catabolism, rather than substrate availability profile microbe-microbe and microbe-metabolite in-
alone, is a determining factor in promoting the rise of teractions in the early oral ecosystem should improve
potentially cariogenic taxa in the oral cavity [75]. our understanding of microbial function in disease,
These observations denote the high complexity of beyond taxonomic characterizations [65, 83].
caries as far as the physicochemical triggers and taxa As far as meta-community dynamics, we are
involved and suggest the adoption of an ecology- starting to realize that it is a dysbiotic oral ecosystem
wise approach to understand oral disease [71, 72]. (microbial imbalance), rather than the detection of a
For example, despite the traditional central role of few bugs, that characterizes and triggers oral disease.
S. mutans in childhood caries, oral bacteria belong- For instance, early studies using culture-based and
ing to other genera such as Granulicatella, fingerprinting approaches (denaturing gradient gel
A c t i n o m y c e s , A c t i n o b a c u l u m , S c a rd o v i a , electrophoresis (DGGE)) demonstrated a higher lev-
A t o po b i u m , A gg re g a t i b a c t e r, S l a c k i a , el of microbial diversity in the dental plaque of
Bifidobacteria, and Prevotella have also been asso- healthy children (2–8 years old) over those with se-
ciated with early childhood caries and severe early vere dental caries [84]. These results contrast with
childhood caries (S-ECC, an extremely destructive the microarray detection of higher bacterial diversity
form of early childhood caries involving multiple in saliva of caries-affected 6 to 8 year olds with
teeth) [10, 34, 78, 79]. Interestingly, however, the mixed dentition compared to healthy controls [85].
role of Lactobacilli on childhood caries seems am- Likewise, although S. mutans has been the central
biguous. On the one hand, there is not only the po- subject of microbe connections to caries, cloning ap-
tential suppressive effect of Lactobacilli isolated proaches to analyze the microbiome of children (pri-
from the oral cavity of breast milk-fed 3-month-old mary and permanent teeth) and young adults have
infants on cariogenic Streptococci [57] but also the suggested that other taxa such as Atopobium,
predicted high incidence of caries at 3 years of age in Propionibacterium, and Lactobacillus are more
3-month-old infants with higher proportions of abundant in S. mutans—caries-bearing subjects,
Lactobacilli [34]. Furthermore, Lactobacillus is while other Lactobacillus spp., Bifidobacterium,
dominant in deep lesions on permanent dentition of and non-mutans streptococci were predominant on
children with S-ECC, suggesting an even more affected subjects not harboring S. mutans [82].
prominent potential role than S. mutans [80]. Altogether, these observations highlight the non-
Other conflicting results have shown similar bac- specific source, polymicrobial nature, and complex
terial genera in caries-positive (n = 10; 19.1 metabolic and community dynamics of oral disease
± 3.5 months) and caries-free (n = 9; 19.3 [71, 86].
± 3.2 months) children previous to eruption of sec- In this regard, analyses of metabolic homeostasis
ondary primary molars, with a few major genera and community ecology (454-pyrosequencing) in
making up more than 60 % of the total microbiota the early oral environment (3–6 year olds) have re-
in both groups [81]. Furthermore, although the group vealed that urease activity and alkali production is
of children positive for caries showed higher preva- significantly associated with the bacterial composi-
lence of Streptococcus, Neisseria, and Veillonella, tion of dental plaque [87]. It seems that urease-alkali
compared to higher levels of Leptotrichia, activity by certain commensals (e.g.,
Actinomyces, Prevotella, and Porphyromonas in the Pasteurellaceae family) positively impacts the oral
caries-free children, these differences were not statis- acid-base homeostasis to inhibit aciduric and caries-
tically significant [81]. Additional inconsistent re- associated taxa (e.g., Leptotrichia and S. mutans) in
sults suggest windows of infectivity, strong interper- plaque under low sugar consumption [88]. However,
sonal differences, and many different bacteria as be- the opposite scenario characterizes saliva, in which
ing responsible for disease onset [82]. These appar- increased urease activity is associated with high car-
ent incongruences may correspond to known differ- ies incidence and levels of S. mutans [89]. This sce-
ences in microbial diversity coverage provided by nario poses a very complex framework to understand
culture-based and molecular methods and by diverse community and metabolic interactions in the early
molecular methods (e.g., cloning, fingerprinting, and oral cavity and to implement valid biomarkers of
high-throughput sequencing). Thus, it is necessary to caries risk in children in relation to alkali balance.
improve and standardize microbial community pro- A useful approach would be to characterize microbi-
filing in early oral disease by refining diversity at al communities using shotgun metagenomic se-
deeper taxonomic levels (e.g., species and strains). quencing in addition to enzymatic activity profiling.
The Oral Microbiome of Children 497

However, up to date, no studies exist on the enamel [98]. In children, healthy permanent and de-
metagenome of the early oral cavity. ciduous teeth also harbor different supragingival mi-
As far as whole-metabolome analyses in the early crobial profiles [99]. Furthermore, analyses of tooth
oral cavity, studies have shown that the saliva of decay in children have shown that caries in a given
caries-bearing children with primary, mixed, and per- tooth not only impacts the microbial ecology and
manent dentition exhibits different metabolomic pro- health onsite but also on nearest teeth [78, 80, 100].
files (nuclear magnetic resonance) and increased Likewise, studies on temporal and spatial
levels of lactate, n-butyrate, and acetate compared microbiome variation in preschool children show
to healthy matches [90]. Furthermore, the salivary that both plaque and saliva acquire distinct
metabolome of caries-affected children after a 3- microbiome configurations with age and transitions
month treatment with composite resin exhibits sig- to cariogenic stages [101]. These observations dem-
nificant changes that correlate with a reduction in onstrate that targeting single sites in the early oral
propionate, acetate, n-butyrate, and saccharides cavity to assess oral disease may only offer a partial
along with decreased levels of cultured S. mutans view of disease biomarkers.
and Lactobacillus sp. [91]. These observations cor-
relate with the proposed links between bacterial me- 3. Bacterial markers of early oral health and disease and
tabolism of sugars (glycolysis), fermentation, and an implications for systemic health
increased abundance of acidogenic taxa (e.g., The associations between periodontal and systemic
Propionibacterium and Lactobacillus) in early oral disease have been the subject of numerous studies includ-
disease [71, 92, 93]. Other saliva metabolome anal- ing oral marker links to cardiovascular, respiratory, im-
yses (gas chromatography mass spectrometry mune, metabolic, osteopathic, and obstetric complications
[GCMS]) on children with tooth decay highlighted [102–106]. The proposed mechanisms of these oral-
a prominent role of metabolites involved in the argi- systemic links include the spread of infection from the
nine and proline metabolic pathway and connected oral cavity in the form of bacteremia or circulating bacte-
arginine to alkali production and hence acid-base rial toxins, triggering increased circulating pro-
balance [64, 94]. inflammatory cytokines and a weakened immune system,
Indeed, a metaproteomic analysis of oral biofilm as well as cross-reactivity (molecular mimicry) between
in caries-bearing and healthy adults identified pro- bacterial and self-antigens [104, 107]. Although associa-
teins involved in the L-lactate dehydrogenase and tions between oral disease markers and systemic health in
arginine deiminase systems. These systems aid in children are scarce, some studies have provided important
pH buffering and show the highest expression in insights.
the supragingival dental plaque of healthy individ- For instance, children with juvenile idiopathic arthritis
uals [64, 95]. Interestingly, in these studies, the over- (13 years old in average), who typically resemble adults
expression of the L-lactate dehydrogenase and argi- with rheumatoid arthritis, have increased antibody re-
nine deiminase systems correlated negatively with sponse to Porphyromonas gingivalis, one of the main
high abundance of sugar transporters (ATP-binding taxon involved in periodontal disease [108, 109], and
cassettes and phosphotransferase systems) and other higher incidence of symptoms related to periodontal dis-
sugar-degrading proteins from Actinomyces, ease [110]. Likewise, children with celiac disease
Corynebacterium, Rothia, and Streptococcus. Thus, (1.4 years old in average) under gluten-free diets show a
the combined power of meta-omics and high- less diverse salivary microbiome compared to healthy
throughput approaches to community ecology could controls and increased abundance of oral caries-related
provide a clearer, system-like picture of early oral taxa (e.g., Rothia, Porphyromonas, Gemellaceae,
disease and potential marker discovery in early diag- Prevotella, Streptococcus, and Lachnospiraceae) [111].
nostics. These approaches are also key to determine The abundances of these taxa also correlated with higher
how early oral disease provides clues to understand levels of organic volatile compounds in the saliva and
systemic health from childhood into adulthood. fecal samples of affected children detected through GC-
Finally, meta-OMIC integration analysis and MS [112]. A similar scenario takes place in the tongue
system-level approaches should also take into ac- microbiome of children with Crohn’s disease, who exhibit
count biogeographical aspects of early oral disease. reduced diversity and decreased abundance of
For example, in adults, there is a distinct microbial Fusobacteria and Firmicutes compared with healthy con-
composition between different healthy tooth surfaces trols [113]. However, it is unclear whether these apparent
and different tooth types in a single individual [96, dysbiosis leads to more susceptibility to oral disease (e.g.,
97] and between carious lesions in dentine and caries) in Crohn’s patients. Therefore, these findings,
498 A. Gomez, K. E. Nelson

which mirror what takes place in the intestinal mucosa metabolome) [123, 124]. This view is essential to
during Crohn’s, have more important implications for de- shift current disease models from focusing on
veloping diagnostic tools of systemic disease based on pathobiomes rather than on pathogens [125]. Thus,
oral biomarkers. a complete understanding of early oral disease may
As such, the assessment of oral risk factors in children not be accomplished by applying one of these tech-
could provide important information on current and future niques but by combining two or more, an approach
systemic health status; however, further understanding of that is seldom implemented in early oral community
directionality in these mechanisms and caution in diag- ecology assessment (but see [126]).
nostics are necessary. For instance, it is likely that a gen- (ii) Effective meta-omic integration to extrapolate/
erally weakened immune system compromises oral translate the data to ecosystem (host) phenotype:
health, as it is the case of HIV-infected children [114]. Likewise, the use of one or more Bomic^ tech-
Likewise, bacteremia can be the result of periodontal trau- niques requires effective models to integrate these
ma in children (teeth extraction) [115], with potential det- datasets and predict host phenotype and potential
rimental consequences for cardiovascular disease (platelet disease risks. This view takes into account that sys-
aggregation induced by oral commensals) and endocardi- tem components (modules, layers) cannot be con-
tis in adulthood [102, 116]. Thus, although multiple ave- sidered from isolated perspectives [127]. In this re-
nues are open to use oral disease biomarkers in the diag- gard, meta-OMIC modeling and network-view ap-
nosis of chronic disorders such as cancer and liver disease proaches are just beginning to emerge to character-
[117–119], several technical, methodological, experimen- ize oral microbiome dynamics and predict health
tal, and therapeutic challenges remain. and disease states [64, 126, 128]. However, there is
4. Challenges: techniques, analyses, biomarker discovery, a clear necessity for more applications of such
and translational preventive therapeutics in oral and sys- models into risk assessment in the early oral cavity.
temic health Moreover, given the difficulty of implementing
Even though the application of molecular-based tech- mechanistic views of disease onset in the early oral
niques in the last 20 years has allowed us to have a better cavity, meta-OMIC network modeling becomes an
understanding of the complex oral microecosystem, we attractive tool to understand ecosystem functioning
are just beginning to unravel the role that multiple intrin- and potential causal factors [129]. In this regard,
sic and extrinsic layers play in oral disease. This aware- efforts in assessing disease biomarkers in the early
ness requires knowledge of a multi-system approach that oral cavity are already exploiting machine learning
integrates different techniques to characterize the host- models for disease risk prediction [101]. However,
microbe entity [120] and analyses that extend into an in- these efforts have been so far limited to microbial
dividual’s or population’s environment (socioeco- community composition analyses.
nomics)—a challenge that is most relevant in childhood (iii) Studies that not only include cross-sectional but also
health [83]. We propose that such framework should build longitudinal data in larger cohorts:
on four main stakes to guarantee more effective risk as- Most of the molecular and meta-OMIC-based
sessment, bring precision at the individual level, and min- reports on the oral microbiome in health and disease
imize population-level health disparities [121] (Fig. 2). have traditionally relied on small cohorts. This sce-
nario may improve as sequencing and other high-
(i) High-resolution tools to study the oral microbiome at throughput techniques decrease in cost, which will
the compositional and functional levels: result in improved resolution power. Likewise, effi-
As characterizations of oral microbiomes move cient risk assessment for individuals and specific
from strictly culture-based methods to using the vulnerable populations may require longitudinal ap-
Human Oral Microbiome Identification Microarray proaches [83], which is key to identify valid bio-
(HOMIM) [122] and, lately, whole community pro- markers of disease in real time (pre and post disease)
filing using high-throughput 16S rRNA sequencing [130, 131]. In this regard, the use of larger cohorts,
and shotgun metagenomics, the concepts of the Beco- in combination with longitudinal sampling, has re-
logical plaque hypothesis^ [71] and a super complex vealed the corresponding weight-shared environ-
oral ecosystem have become more relevant. This ment and genetics on the early oral microbiome
complexity, however, has also pointed out that under- [46]. Furthermore, despite the realization that there
standing microecosystem functioning requires a may be little geographic structure in global diversity
multi-level view that includes taxonomic assessment patterns in the human salivary microbiome [4],
(composition), potential (metagenome-tran- global surveys of diverse human populations at a
scriptome), and encoded functions (proteome and larger scale may provide important clues to better
The Oral Microbiome of Children 499

i
Saliva
Taxon (16S rRNA, high-throughput sequencing) iv Standardized Plaque
methods/techniques
Metabolite (GC/MS, NMR - metabolomics) Swab
Function (metagenomics/transcriptomics/proteomics) Sample
collection

ii

Interaction
Oral disease
Individual/population
risk assessment/prediction

iii Cohort selection: cross-sectional and longitudinal

Host genotype
Time A Time B Time A Time B
Unaffected Affected

Fig. 2 Biomarker discovery and translational preventive therapeutics in statistical models to integrate various omic datasets and algorithms that
oral and systemic health. Effective risk assessment of oral disease and allow risk prediction based on meta-omic integration networks); (iii)
diagnostics precision at the individual level and specific populations at studies that not only include cross-sectional but also longitudinal data in
risk may be accomplished by implementing a framework that builds on larger cohorts (valid biomarkers of oral disease in real time (pre and post
four main stakes: (i) high-resolution tools to study the oral microbiome at disease) and at a global scale); and (iv) standardization of methods
the compositional and functional levels (Bomic^ techniques that (sample storage methods, standardization of phylogenetic markers and
simultaneously unravel community composition, potential and encoded sequencing techniques, building of comprehensive oral microbe
functions); (ii) effective meta-omic integration modeling to extrapolate/ databases)
translate the data to ecosystem (host) phenotype (computational and

understand the influence of cultural and genetic fac- significant progress toward standardization of
tors in impacting health and disease [132]. methods, the chances for better risk assessment
(iv) Need for standardization of technical methods: an and prediction of oral disease in children will im-
issue that spans all areas of microbiome research in prove significantly.
general:
The necessity to find reproducible results and the
ability to compare different datasets are huge chal-
lenges that the microbiome field faces today [133]. Conclusion
These concerns have increased efforts to evaluate
better sample storage methods [134–137], to select The Future of Microbiome Studies for Oral Health
appropriate phylogenetic markers and techniques and Childhood Diseases
and effectively assess microbial community compo-
sition [138] and build comprehensive databases for As the challenges mentioned above are surpassed,
the vast number of uncharacterized and uncultured microbiome research on early oral health and disease should
oral organisms (e.g., the Human Oral Microbiome move beyond profiling oral community patterns in cross-
Database (HOMD) [139] and the Core Oral sectional and longitudinal cohorts. For instance, as we stan-
Microbiome Database (CORE) [140]). As all dardize techniques to find valid oral disease biomarkers, ef-
microbiome fields (and researchers) make forts should be focused on using biomarker information to
500 A. Gomez, K. E. Nelson

apply effective therapeutics in specific individuals and popu- 12. Wade WG (2013) The oral microbiome in health and disease.
Pharmacol Res 69:137–143
lations at most risk. Specially, the concept of precision medi-
13. Costalonga M, Herzberg MC (2014) The oral microbiome and the
cine has been proposed to minimize health disparities in the immunobiology of periodontal disease and caries. Immunol Lett
most vulnerable populations, taking into account subject- 162:22–38
specific variability in genes and environment [83]. Along 14. Paster BJ, Olsen I, Aas JA, Dewhirst FE (2006) The breadth of
bacterial diversity in the human periodontal pocket and other oral
these lines, we are already making efforts to identify oral
sites. Periodontol 42:80–87
microbial markers at increased taxonomic depth and diversity 15. Dominguez-Bello MG, Costello EK, Contreras M et al (2010)
coverage, a particularly relevant issue in oral disease. For in- Delivery mode shapes the acquisition and structure of the initial
stance, the improved Human Oral Microbiome Identification microbiota across multiple body habitats in newborns. Proc Natl
Acad Sci U S A 107:11971–11975
using Next-Generation Sequencing (HOMINGS), from the
16. Bearfield C, Davenport ES, Sivapathasundaram V, Allaker RP (2002)
Forsyth Institute (http://forsyth.org) [122], harbors a well- Possible association between amniotic fluid micro-organism infection
curated collection of sequences from oral bacteria at the spe- and microflora in the mouth. BJOG 109:527–533
cies level, allowing researchers to accurately expand marker 17. Fardini Y, Chung P, Dumm R et al (2010) Transmission of diverse
oral bacteria to murine placenta: evidence for the oral microbiome
identification in the highly diverse oral ecosystem. Likewise,
as a potential source of intrauterine infection. Infect Immun 78:
more rigorous studies on infant twin cohorts and by using 1789–1796
genome-wide analyses, host gene expression levels, and deep 18. Aagaard K, Ma J, Antony KM, et al. (2014) The placenta harbors
sequencing in the oral cavity could provide clues on the extent a unique microbiome. Sci Transl Med 6:237ra65.
to which oral disease in children is explained by heritable or 19. Goldenberg RL, Hauth JC, Andrews WW (2000) Intrauterine in-
fection and preterm delivery. N Engl J Med 342:1500–1507
environmentally acquired taxa. Finally, researchers involved 20. Han YW, Redline RW, Li M et al (2004) Fusobacterium
in oral microbiome research should visualize the value of oral nucleatum induces premature and term stillbirths in pregnant
samples beyond the oral cavity—a key concept in the era of mice: implication of oral bacteria in preterm birth. Infect Immun
applied meta-omics and personalized medicine. 72:2272–2279
21. Han YW, Ikegami A, Bissada NF et al (2006) Transmission of an
uncultivated Bergeyella strain from the oral cavity to amniotic
Acknowledgments Research supported in this publication was sup- fluid in a case of preterm birth. J Clin Microbiol 44:1475–1483
ported by the National Institute of Dental and Craniofacial Research of 22. Han YW, Shen T, Chung P et al (2009) Uncultivated bacteria as
the National Institutes of Health under Award Number R01DE019665. etiologic agents of intra-amniotic inflammation leading to preterm
The content is solely the responsibility of the authors and does not nec- birth. J Clin Microbiol 47:38–47
essarily represent the official views of the National Institutes of Health. 23. Lif Holgerson P, Harnevik L, Hernell O et al (2011) Mode of birth
delivery affects oral microbiota in infants. J Dent Res 90:1183–1188
24. Kliman HJ (2014) Comment on BThe placenta harbors a unique
References microbiome.^ Sci Transl Med 6:254le4–254le4.
25. Costello EK, Stagaman K, Dethlefsen L et al (2012) The applica-
1. Miller WD (1892) Die Mikroorganismen der Mundhöhle. DMW- tion of ecological theory toward an understanding of the human
Deutsche Medizinische Wochenschrift 18:1016–1018 microbiome. Science 336:1255–1262
2. Kligler IJ, Gies WJ (1915) A biochemical study and differentia- 26. Isolauri E (2012) Development of healthy gut microbiota early in
tion of oral bacteria with special reference to dental caries. J Allied life. J Paediatr Child Health 48(Suppl 3):1–6
Dental Soc 10:445–458 27. Munyaka PM, Khafipour E, Ghia J-E (2014) External influence of
3. Dewhirst FE, Chen T, Izard J et al (2010) The human oral early childhood establishment of gut microbiota and subsequent
microbiome. J Bacteriol 192:5002–5017 health implications. Front Pediatr 2:109
4. Nasidze I, Li J, Quinque D et al (2009) Global diversity in the 28. Hegde S, Munshi AK (1998) Influence of the maternal vaginal
human salivary microbiome. Genome Res 19:636–643 microbiota on the oral microbiota of the newborn. J Clin Pediatr
5. Ling Z, Kong J, Jia P et al (2010) Analysis of oral microbiota in Dent 22:317–321
children with dental caries by PCR-DGGE and barcoded pyrose- 29. Merglova V, Polenik P (2016) Early colonization of the oral cavity
quencing. Microb Ecol 60:677–690 in 6- and 12-month-old infants by cariogenic and periodontal path-
ogens: a case-control study. Folia Microbiol . doi:10.1007/s12223-
6. Bik EM, Long CD, Armitage GC et al (2010) Bacterial diversity
016-0453-z
in the oral cavity of 10 healthy individuals. ISME J 4:962–974
30. Wan AK, Seow WK, Purdie DM et al (2001) Oral colonization of
7. Human Microbiome Project Consortium (2012) Structure, function Streptococcus mutans in six-month-old predentate infants. J Dent
and diversity of the healthy human microbiome. Nature 486:207–214 Res 80:2060–2065
8. Zaura E, Keijser BJF, Huse SM, Crielaard W (2009) Defining the 31. Carlsson J, Grahnén H, Jonsson G, Wikner S (1970) Early estab-
healthy Bcore microbiome^ of oral microbial communities. BMC lishment of Streptococcus salivarius in the mouths of infants. J
Microbiol 9:1–12 Dent Res 49:415–418
9. Keijser BJF, Zaura E, Huse SM et al (2008) Pyrosequencing analysis 32. Cole MF, Evans M, Fitzsimmons S et al (1994) Pioneer oral strep-
of the oral microflora of healthy adults. J Dent Res 87:1016–1020 tococci produce immunoglobulin A1 protease. Infect Immun 62:
10. Becker MR, Paster BJ, Leys EJ et al (2002) Molecular analysis of 2165–2168
bacterial species associated with childhood caries. J Clin 33. Hanson LA, Söderström T (1981) Human milk: defense against
Microbiol 40:1001–1009 infection. Prog Clin Biol Res 61:147–159
11. Zarco MF, Vess TJ, Ginsburg GS (2012) The oral microbiome in 34. Lif Holgerson P, Öhman C, Rönnlund A, Johansson I (2015)
health and disease and the potential impact on personalized dental Maturation of oral microbiota in children with or without dental
medicine. Oral Dis 18:109–120 caries. PLoS One 10:e0128534
The Oral Microbiome of Children 501

35. Cephas KD, Kim J, Mathai RA et al (2011) Comparative analysis 57. Holgerson PL, Vestman NR, Claesson R et al (2013) Oral micro-
of salivary bacterial microbiome diversity in edentulous infants bial profile discriminates breast-fed from formula-fed infants. J
and their mothers or primary care givers using pyrosequencing. Pediatr Gastroenterol Nutr 56:127–136
PLoS One 6:e23503 58. Iida H, Auinger P, Billings RJ, Weitzman M (2007) Association
36. Ward TL, Hosid S, Ioshikhes I, Altosaar I (2013) Human milk between infant breastfeeding and early childhood caries in the
metagenome: a functional capacity analysis. BMC Microbiol United States. Pediatrics 120:e944–52.
13:116 59. Alaluusua S, Mättö J, Grönroos L et al (1996) Oral colonization by
37. Martín R, Langa S, Reviriego C et al (2003) Human milk is a more than one clonal type of mutans streptococcus in children
source of lactic acid bacteria for the infant gut. J Pediatr 143: with nursing-bottle dental caries. Arch Oral Biol 41:167–173
754–758 60. Burt BA, Eklund SA, Morgan KJ et al (1988) The effects of sugars
38. Jost T, Lacroix C, Braegger C, Chassard C (2013) Assessment of intake and frequency of ingestion on dental caries increment in a
bacterial diversity in breast milk using culture-dependent and three-year longitudinal study. J Dent Res 67:1422–1429
culture-independent approaches. Br J Nutr 110:1253–1262 61. Naidu R, Nunn J, Kelly A (2013) Socio-behavioural factors and
39. Yang F, Zeng X, Ning K et al (2012) Saliva microbiomes distin- early childhood caries: a cross-sectional study of preschool chil-
guish caries-active from healthy human populations. ISME J dren in central Trinidad. BMC Oral Health 13:30
6:1–10 62. Kanasi E, Dewhirst FE, Chalmers NI et al (2010) Clonal analysis
40. Struzycka I (2014) The oral microbiome in dental caries. Pol J of the microbiota of severe early childhood caries. Caries Res 44:
Microbiol 63:127–135 485–497
41. Rôças IN, Alves FRF, Rachid CTCC et al (2016) Microbiome of 63. Harris R, Nicoll AD, Adair PM, Pine CM (2004) Risk factors for
deep dentinal caries lesions in teeth with symptomatic irreversible dental caries in young children: a systematic review of the litera-
pulpitis. PLoS One 11:e0154653 ture. Community Dent Health 21:71–85
42. Crielaard W, Zaura E, Schuller AA et al (2011) Exploring the oral 64. Edlund A, Yang Y, Yooseph S et al (2015) Meta-omics uncover
microbiota of children at various developmental stages of their temporal regulation of pathways across oral microbiome genera
dentition in the relation to their oral health. BMC Med during in vitro sugar metabolism. ISME J 9:2605–2619
Genomics 4:22 65. McLean JS (2014) Advancements toward a systems level under-
43. Goodrich JK, Waters JL, Poole AC et al (2014) Human genetics standing of the human oral microbiome. Front Cell Infect
shape the gut microbiome. Cell 159:789–799 Microbiol 4:98
44. Goodrich JK, Davenport ER, Beaumont M et al (2016) Genetic 66. Leme AFP, Koo H, Bellato CM et al (2006) The role of sucrose in
determinants of the gut microbiome in UK twins. Cell Host cariogenic dental biofilm formation—new insight. J Dent Res 85:
Microbe 19:731–743 878–887
45. Blekhman R, Goodrich JK, Huang K et al (2015) Host genetic 67. Krzyściak W, Jurczak A, Kościelniak D et al (2014) The virulence
variation impacts microbiome composition across human body of Streptococcus mutans and the ability to form biofilms. Eur J
sites. Genome Biol 16:191 Clin Microbiol Infect Dis 33:499–515
46. Stahringer SS, Clemente JC, Corley RP et al (2012) Nurture 68. Nobre dos Santos M, Melo dos Santos L, Francisco SB, Cury JA
trumps nature in a longitudinal survey of salivary bacterial com- (2002) Relationship among dental plaque composition, daily sug-
munities in twins from early adolescence to early adulthood. ar exposure and caries in the primary dentition. Caries Res 36:
Genome Res 22:2146–2152 347–352
47. Papapostolou A, Kroffke B, Tatakis DN et al (2011) Contribution 69. Mattos-Graner RO, Smith DJ, King WF, Mayer MP (2000) Water-
of host genotype to the composition of health-associated insoluble glucan synthesis by mutans streptococcal strains corre-
supragingival and subgingival microbiomes. J Clin Periodontol lates with caries incidence in 12- to 30-month-old children. J Dent
38:517–524 Res 79:1371–1377
48. Corby PM, Bretz WA, Hart TC et al (2007) Heritability of oral 70. Stephan RM, Miller BF (1943) A quantitative method for evalu-
microbial species in caries-active and caries-free twins. Twin Res ating physical and chemical agents which modify production of
Hum Genet 10:821–828 acids in bacterial plaques on human teeth. J Dent Res 22:45–51
49. Corby PMA, Bretz WA, Hart TC et al (2005) Mutans streptococci 71. Marsh PD (1994) Microbial ecology of dental plaque and its sig-
in preschool twins. Arch Oral Biol 50:347–351 nificance in health and disease. Adv Dent Res 8:263–271
50. Acton RT, Dasanayake AP, Harrison RA et al (1999) Associations 72. Marsh PD (2016) Dental biofilms in health and disease. In:
of MHC genes with levels of caries-inducing organisms and caries Goldberg M (ed) Understanding Dental Caries. Springer
severity in African-American women. Hum Immunol 60:984–989 International Publishing, pp 41–52
51. Ozawa Y, Chiba J, Sakamoto S (2001) HLA class II alleles and 73. Matsui R, Cvitkovitch D (2010) Acid tolerance mechanisms uti-
salivary numbers of mutans streptococci and lactobacilli among lized by Streptococcus mutans. Future Microbiol 5:403–417
young adults in Japan. Oral Microbiol Immunol 16:353–357 74. Forssten SD, Björklund M, Ouwehand AC (2010) Streptococcus
52. Gizani S, Papaioannou W, Haffajee AD et al (2009) Distribution mutans, caries and simulation models. Nutrients 2:290–298
of selected cariogenic bacteria in five different intra-oral habitats 75. Marsh PD (2003) Are dental diseases examples of ecological ca-
in young children. Int J Paediatr Dent 19:193–200 tastrophes? Microbiology 149:279–294
53. Kianoush N, Nguyen K-AT, Browne GV, et al. (2014) pH gradient 76. Bradshaw DJ, McKee AS, Marsh PD (1989) Effects of carbohy-
and distribution of streptococci, lactobacilli, prevotellae, and drate pulses and pH on population shifts within oral microbial
fusobacteria in carious dentine. Clin Oral Investig 18:659–669. communities in vitro. J Dent Res 68:1298–1302
54. Takahashi N, Nyvad B (2011) The role of bacteria in the caries 77. Bradshaw D, Marsh PD (1998) Analysis of pH-driven disruption
process: ecological perspectives. J Dent Res 90:294–303 of oral microbial communities in vitro. Caries Res 32:456–462
55. Burne RA, Marquis RE (2000) Alkali production by oral bacteria 78. Jiang W, Zhang J, Chen H (2013) Pyrosequencing analysis of oral
and protection against dental caries. FEMS Microbiol Lett microbiota in children with severe early childhood dental caries.
193:1–6 Curr Microbiol 67:537–542
56. Avila WM, Pordeus IA, Paiva SM, Martins CC (2015) Breast and 79. Tanner ACR, Kent RL Jr, Holgerson PL et al (2011) Microbiota of
bottle feeding as risk factors for dental caries: a systematic review severe early childhood caries before and after therapy. J Dent Res
and meta-analysis. PLoS One 10:e0142922 90:1298–1305
502 A. Gomez, K. E. Nelson

80. Gross EL, Leys EJ, Gasparovich SR et al (2010) Bacterial 16S 101. Teng F, Yang F, Huang S et al (2015) Prediction of early childhood
sequence analysis of severe caries in young permanent teeth. J caries via spatial-temporal variations of oral microbiota. Cell Host
Clin Microbiol 48:4121–4128 Microbe 18:296–306
81. Xu H, Hao W, Zhou Q et al (2014) Plaque bacterial microbiome 102. Li X, Kolltveit KM, Tronstad L, Olsen I (2000) Systemic diseases
diversity in children younger than 30 months with or without caused by oral infection. Clin Microbiol Rev 13:547–558
caries prior to eruption of second primary molars. PLoS One 9: 103. Beck JD, Slade G, Offenbacher S (2000) Oral disease, cardiovas-
e89269 cular disease and systemic inflammation. Periodontol 23:110–120
82. Aas JA, Griffen AL, Dardis SR et al (2008) Bacteria of dental 104. Seymour GJ, Ford PJ, Cullinan MP et al (2007) Relationship
caries in primary and permanent teeth in children and young between periodontal infections and systemic disease. Clin
adults. J Clin Microbiol 46:1407–1417 Microbiol Infect 13(Suppl 4):3–10
83. Divaris K (2015) Predicting dental caries outcomes in children: a 105. Iacopino AM, Cutler CW (2000) Pathophysiological relationships
Brisky^ concept. J Dent Res. doi:10.1177/0022034515620779 between periodontitis and systemic disease: recent concepts in-
84. Li Y, Ge Y, Saxena D, Caufield PW (2007) Genetic profiling of the volving serum lipids. J Periodontol 71:1375–1384
oral microbiota associated with severe early-childhood caries. J 106. Shen H, Ye F, Xie L et al (2015) Metagenomic sequencing of bile
Clin Microbiol 45:81–87 from gallstone patients to identify different microbial community
85. Luo AH, Yang DQ, Xin BC et al (2012) Microbial profiles in patterns and novel biliary bacteria. Sci Rep 5:17450
saliva from children with and without caries in mixed dentition. 107. Slots J, Rams TE (1991) New views on periodontal microbiota in
Oral Dis 18:595–601 special patient categories. J Clin Periodontol 18:411–420
86. Theilade E (1986) The non-specific theory in microbial etiology of 108. Tanaka S, Murakami Y, Seto K et al (2003) The detection of
inflammatory periodontal diseases. J Clin Periodontol 13:905–911 Porphyromonas gingivalis, Prevotella intermedia, and
87. Morou-Bermudez E, Rodriguez S, Bello AS, Dominguez-Bello Actinobacillus actinomycetemcomitans in the supragingival
MG (2015) Urease and dental plaque microbial profiles in chil- plaque of children with and without caries. Pediatr Dent 25:
dren. PLoS One 10:e0139315 143–148
88. Morou-Bermudez E, Elias-Boneta A, Billings RJ et al (2011) 109. Merchant AT (2012) Periodontitis and dental caries occur together.
Urease activity in dental plaque and saliva of children during a J Evid Based Dent Pract 12:18–19
three-year study period and its relationship with other caries risk 110. Lange L, Thiele GM, McCracken C et al (2016) Symptoms of
factors. Arch Oral Biol 56:1282–1289 periodontitis and antibody responses to Porphyromonas gingivalis
in juvenile idiopathic arthritis. Pediatr Rheumatol Online J 14:8
89. Morou-Bermudez E, Elias-Boneta A, Billings RJ et al (2011)
111. Francavilla R, Ercolini D, Piccolo M et al (2014) Salivary micro-
Urease activity as a risk factor for caries development in children
biota and metabolome associated with celiac disease. Appl
during a three-year study period: a survival analysis approach.
Environ Microbiol 80:3416–3425
Arch Oral Biol 56:1560–1568
112. Di Cagno R, De Angelis M, De Pasquale I et al (2011) Duodenal
90. Fidalgo TKS, Freitas-Fernandes LB, Angeli R et al (2012)
and faecal microbiota of celiac children: molecular, phenotype and
Salivary metabolite signatures of children with and without dental
metabolome characterization. BMC Microbiol 11:219
caries lesions. Metabolomics 9:657–666
113. Docktor MJ, Paster BJ, Abramowicz S et al (2012) Alterations in
91. Fidalgo TKS, Freitas-Fernandes LB, Almeida FCL et al (2014)
diversity of the oral microbiome in pediatric inflammatory bowel
Longitudinal evaluation of salivary profile from children with
disease. Inflamm Bowel Dis 18:935–942
dental caries before and after treatment. Metabolomics 11:
114. Hicks MJ, Carter AB, Rossmann SN et al (1998) Detection of
583–593
fungal organisms in saliva from HIV-infected children: a prelimi-
92. McLean JS, Fansler SJ, Majors PD et al (2012) Identifying low pH nary cytologic analysis. Pediatr Dent 20:162–168
active and lactate-utilizing taxa within oral microbiome commu- 115. Roberts GJ, Holzel HS, Sury MR et al (1997) Dental bacteremia in
nities from healthy children using stable isotope probing tech- children. Pediatr Cardiol 18:24–27
niques. PLoS One 7:e32219 116. Joshipura K, Ritchie C, Douglass C (2000) Strength of evidence
93. Takahashi N, Washio J, Mayanagi G (2012) Metabolomic ap- linking oral conditions and systemic disease. Compend Contin
proach to oral biofilm characterization—a future direction of bio- Educ Dent Suppl 12–23; quiz 65.
film research. J Oral Biosci 54:138–143 117. Fábián TK, Fejérdy P, Csermely P (2008) Salivary genomics, tran-
94. Foxman B, Srinivasan U, Wen A et al (2014) Exploring the effect scriptomics and proteomics: the emerging concept of the oral eco-
of dentition, dental decay and familiality on oral health using system and their use in the early diagnosis of cancer and other
metabolomics. Infect Genet Evol 22:201–207 diseases. Curr Genomics 9:11–21
95. Belda-Ferre P, Williamson J, Simón-Soro Á et al (2015) The hu- 118. Gao S, Li S, Ma Z et al (2016) Presence of Porphyromonas
man oral metaproteome reveals potential biomarkers for caries gingivalis in esophagus and its association with the clinicopatho-
disease. Proteomics 15:3497–3507 logical characteristics and survival in patients with esophageal
96. Simón-Soro A, Tomás I, Cabrera-Rubio R et al (2013) Microbial cancer. Infect Agent Cancer 11:3
geography of the oral cavity. J Dent Res 92:616–621 119. Nakajima M, Arimatsu K, Kato T et al (2015) Oral administration
97. Sato Y, Yamagishi J, Yamashita R et al (2015) Inter-individual of P. gingivalis induces dysbiosis of gut microbiota and impaired
differences in the oral bacteriome are greater than intra-day fluc- barrier function leading to dissemination of enterobacteria to the
tuations in individuals. PLoS One 10:e0131607 liver. PLoS One 10:e0134234
98. Simón-Soro A, Guillen-Navarro M, Mira A (2014) 120. Ibrahim R, Pasic M, Yousef GM (2016) Omics for personalized
Metatranscriptomics reveals overall active bacterial composition medicine: defining the current we swim in. Expert Rev Mol Diagn
in caries lesions. J Oral Microbiol 6:25443 16(7):719–722
99. Shi W, Qin M, Chen F, Xia B (2016) Supragingival microbial 121. Lee JY, Divaris K (2014) The ethical imperative of addressing oral
profiles of permanent and deciduous teeth in children with mixed health disparities: a unifying framework. J Dent Res 93:224–230
dentition. PLoS One 11:e0146938 122. Mougeot J-LC, Stevens CB, Cotton SL, et al. (2016) Concordance
100. Afroughi S, Faghihzadeh S, Khaledi MJ, Motlagh MG (2010/5) of HOMIM and HOMI N GS technologies in the microbiome
Dental caries analysis in 3–5 years old children: a spatial model- analysis of clinical samples. J Oral Microbiol. doi:10.3402/jom.
ling. Arch Oral Biol 55:374–378. v8.30379
The Oral Microbiome of Children 503

123. Duran-Pinedo AE, Frias-Lopez J (2015) Beyond microbial com- 133. Hamady M, Knight R (2009) Microbial community profiling for
munity composition: functional activities of the oral microbiome human microbiome projects: tools, techniques, and challenges.
in health and disease. Microbes Infect 17:505–516 Genome Res 19:1141–1152
124. Wong DTW (2012) Salivaomics. J Am Dent Assoc 143:19S–24S. 134. Nunes AP, Oliveira IO, Santos BR et al (2012) Quality of DNA
125. Vayssier-Taussat M, Albina E, Citti C et al (2014) Shifting the extracted from saliva samples collected with the
paradigm from pathogens to pathobiome: new concepts in the Oragene\texttrademark DNA self-collection kit. BMC Med Res
light of meta-omics. Front Cell Infect Microbiol 4:29 Methodol 12:1–6
126. Hart TC, Corby PM, Hauskrecht M, et al. (2011) Identification of 135. Rogers NL, Cole SA, Lan H-C et al (2007) New saliva DNA
microbial and proteomic biomarkers in early childhood caries. Int collection method compared to buccal cell collection techniques
J Dent 2011:196721 for epidemiological studies. Am J Hum Biol 19:319–326
127. Gehlenborg N, O’Donoghue SI, Baliga NS et al (2010) 136. Ng DPK, Koh D, Choo SGL et al (2004) Effect of storage condi-
Visualization of omics data for systems biology. Nat Methods 7: tions on the extraction of PCR-quality genomic DNA from saliva.
S56–S68 Clin Chim Acta 343:191–194
137. Quinque D, Kittler R, Kayser M et al (2006) Evaluation of saliva
128. Dimitrov DV, Hoeng J (2013) Systems approaches to computa-
as a source of human DNA for population and association studies.
tional modeling of the oral microbiome. Front Physiol 4:172
Anal Biochem 353:272–277
129. Bartel J, Krumsiek J, Schramm K et al (2015) The human blood 138. Ahn J, Yang L, Paster BJ et al (2011) Oral microbiome profiles:
metabolome-transcriptome interface. PLoS Genet 11:e1005274 16S rRNA pyrosequencing and microarray assay comparison.
130. Ferreira Zandoná A, Ando M, Gomez GF, et al. (2013) PLoS One 6:e22788
Longitudinal analyses of early lesions by fluorescence: an obser- 139. Chen T, Yu W-H, Izard J, et al. (2010) The Human Oral
vational study. J Dent Res 92:84S–9S. Microbiome Database: a web accessible resource for investigating
131. Härkäne T, Larmas MA, Virtanen JI, Arjas E (2002) Applying oral microbe taxonomic and genomic information. Database
modern survival analysis methods to longitudinal dental caries 2010:baq013.
studies. J Dent Res 81:144–148 140. Griffen AL, Beall CJ, Firestone ND et al (2011) CORE: a
132. Nasidze I, Li J, Schroeder R et al (2011) High diversity of the phylogenetically-curated 16S rDNA database of the core oral
saliva microbiome in Batwa Pygmies. PLoS One 6:e23352 microbiome. PLoS One 6:e19051