Establishment and Development of Oral Microflora in 12-24 Month-Old Toddlers Monitored by High-Throughput Sequencing

Characterization of the unique oral microbiome of children harboring Helicobacter pylori in the oral cavity

Objective

Helicobacter pylori infection is acquired in childhood via the oral cavity, although its relationship with the characteristics of the oral microbiome has not been elucidated. In this study, we performed comprehensive analysis of the oral microbiome in children and adults with or without H. pylori in the oral cavity.

Methods

Bacterial DNA was extracted from 41 adult and 21 child saliva specimens, and H. pylori was detected using PCR. 16S rRNA gene amplification was performed for next-generation sequencing. Bioinformatic analyses were conducted using Quantitative Insights into Microbial Ecology 2 (QIIME 2).

Results

Faith's phylogenetic diversity analysis showed a significant difference between H. pylori-negative adult and child specimens in terms of α-diversity (p < 0.05), while no significant difference was observed between H. pylori-positive adult and child specimens. There was also a significant difference in β-diversity between H. pylori-positive and negative child specimens (p < 0.05). Taxonomic analysis at the genus level revealed that Porphyromonas was the only bacterium that was significantly more abundant in both H. pylori-positive adults and children than in corresponding negative specimens (p < 0.01 and p < 0.05, respectively).

Conclusion

These results suggest unique oral microbiome characteristics in children with H. pylori infection in the oral cavity.

Impact of breastfeeding and other early-life factors on the development of the oral microbiome

The oral cavity is home to the second most diverse microbiome in the human body. This community contributes to both oral and systemic health. Acquisition and development of the oral microbiome is a dynamic process that occurs over early life; however, data regarding longitudinal assembly of the infant oral microbiome is scarce. While numerous factors have been associated with the composition of the infant oral microbiome, early feeding practices (breastfeeding and the introduction of solids) appear to be the strongest determinants of the infant oral microbiome. In the present review, we draw together data on the maternal, infant, and environmental factors linked to the composition of the infant oral microbiome, with a focus on early nutrition. Given evidence that breastfeeding powerfully shapes the infant oral microbiome, the review explores potential mechanisms through which human milk components, including microbes, metabolites, oligosaccharides, and antimicrobial proteins, may interact with and shape the infant oral microbiome. Infancy is a unique period for the oral microbiome. By enhancing our understanding of oral microbiome assembly in early life, we may better support both oral and systemic health throughout the lifespan.

The role of Actinomyces spp. and related organisms in cervicofacial infections: Pathomechanism, diagnosis and therapeutic aspects

Members of the Actinomyces genus and Actinomyces-like organisms (ALOs; namely Actinotignum, Arcanobacterium, Schaalia and Varibaculum) are Gram-positive, non-spore-forming rods that are commensal members of the human oral cavity, gastrointestinal tract, female genital tract and skin microbiota. Cervicofacial actinomycosis or "lumpy jaw syndrome" - the chronic, suppurative granulomatous disease caused by Actinomyces spp. And ALOs - is characterized by an initially slow and unspecific disease-presentation, which often mimics other pathologies, followed by the formation of painful abscesses and severe tissue destruction. Actinomycosis has been described as a rare disease, however, reliable epidemiological data are lacking. In addition, there is increasing awareness regarding the role of Actinomyces spp. in the development of osteoradionecrosis and medication-related osteonecrosis of the jaw. The aim of this narrative review is to succinctly summarize the current advances regarding the microbiological, clinical, diagnostic and therapeutic aspects of cervicofacial actinomycosis, in addition to the roles of Actinomyces species and ALOs as members of the oral microbiota and in dental biofilm, in other dental infections (caries, root canal infection, periapical infection, periodontitis) and osteonecrosis of the jaw, in the context of recent taxonomic changes affecting the genus. Our paper aims to be a blueprint for dentists, other physicians, microbiologists and researchers regarding the multifaceted field of cervicofacial actinomycosis.

Correlation between caries activity and salivary microbiota in preschool children

Early childhood caries (ECC) is the most common chronic infectious oral disease in preschool children worldwide. It is closely related to the caries activity (CA) of children. However, the distribution characteristics of oral saliva microbiomes in children with different CA are largely underexplored. The aim of this study was to investigate the microbial community in saliva of preschool children with different CA and caries status, and to analyze the difference of microbial community in saliva of children with different CA and its correlation with ECC. Subjects were divided into 3 groups based on the Cariostat caries activity test: Group H, high CA (n=30); Group M, medium CA (n = 30); Group L, low CA (n=30). Questionnaire survey was used to explore the related influencing factors of CA. According to the caries status (on the basis of decayed mising filled teeth), these subjects were divided into caries-free group (dmft=0, n=19), caries-low group (0 < dmft ≤ 4, n=27) and caries-high group (dmft > 4, n=44). Microbial profiles of oral saliva were analyzed using 16S rRNA gene sequencing. There were significant differences in the microbial structure (P < 0.05). Scardovia and Selenomonas were the biomarkers of both H group and high caries group. The genus Abiotrophia and Lautropia were the biomarkers of both the L group and the low caries group, while the Lactobacillus and Arthrospira spp. were significantly enriched in the M group. The area under the ROC curve of the combined application of dmft score, age, frequency of sugary beverage intake, and the genus Scardovia, Selenomonas, and Campylobacter in screening children with high CA was 0.842. Moreover, function prediction using the MetaCyc database showed that there were significant differences in 11 metabolic pathways of salivary microbiota among different CA groups. Certain bacteria genera in saliva such as Scardovia and Selenomonas may be helpful in screening children with high CA.

Detection of Streptococcus mutans and Streptococcus sobrinus and Their Association with Oral Microbiome Stressors in 6-18-month-old Infants

Aim

To determine the presence of Streptococcus mutans (S. mutans) and Streptococcus sobrinus (S. sobrinus) and their association with extrinsic and intrinsic variables in 6-18-month-old infants.

Methods

This was an analytical, cross-sectional study of 65 6-18-month-old infants who visited the Centers for Early Childhood in Buenos Aires City. Three groups were established according to the presence of teeth-group I (GI)-edentulous infants, group II (GII)-infants with 1-8 teeth, and group III (GIII)-infants with 9-16 teeth. Data on the variables, diet, use of artificial teats, and oral hygiene were gathered using a self-administered questionnaire. An oral examination was performed according to the International Caries Detection and Assessment System (ICDAS II) criterion. A saliva sample was taken by aspiration with a sterile plastic syringe. Cariogenic Streptococci (CS) were counted using the adherence test in modified gold broth (AT-MGB). Molecular detection and quantification were performed by quantitative polymerase chain reaction (qPCR) (gtfB, gtfT, and tuf).

Results

A total of 12% of infants received oral hygiene, 38% used bottles, 30% used pacifiers, and 55% had sugar intake. S. sobrinus and S. mutans were detected in 57.1 and 28.6% of the children with caries, respectively. Groups I, II, and III had CS counts of log 2, 3.4, and 3.7, respectively. S. sobrinus was detected in 26.7% of GI, 52.9% of GII, and 85.7% of GIII, while S. mutans was detected in 13.3%, 35.3%, and 57.7%, respectively.

Conclusion

The prevalence of S. sobrinus was higher than S. mutans in all groups. The presence of CS was significantly associated with sugar intake. No association was found between S. mutans and S. sobrinus and the presence of caries, hygiene habits, or use of artificial teats.

Clinical Significance

This study supports the role of diet in developing a cariogenic biofilm in children under 2 years of age.

How to cite this article

Cornejo CF, Soken LJ, Salgado PA, et al. Detection of Streptococcus mutans and Streptococcus sobrinus and Their Association with Oral Microbiome Stressors in 6-18-month-old Infants. Int J Clin Pediatr Dent 2023;16(1):68-73.

Salivary microbiome in children with Down syndrome: a case-control study

BACKGROUND

Down syndrome (DS), a most frequently occurring genetic disorder, is associated with oral morphological abnormalities and higher incidence rates of oral diseases. Recent studies have analyzed the oral microbiome to elucidate their relationships with oral diseases and general health; however, reports on the oral microbiome in individuals with DS are scarce. This study aimed to characterize the oral microbiome in children with DS.

METHODS

A total of 54 children aged 1-13 years were enrolled in this case-control study. Of these children, 27 had DS (Case: DS group) and 27 were age-matched healthy children (Control: ND group). Saliva in the oral cavity was collected with a swab, cultured, and tested for cariogenic and periodontopathic bacteria by quantitative polymerase chain reaction (qPCR) detection, and the salivary microbiome was analyzed using next-generation sequencing. The student's t-test, Fisher's exact test, Mann-Whitney U test, and permutational multivariate analysis of variance were used for statistical analysis.

RESULTS

Results of culture and qPCR detection tests for cariogenic and periodontopathic bacteria showed no significant differences in the detected bacteria between the DS and ND groups, with the exception of a significantly higher detection rate of Candida albicans in children with DS with mixed dentition. A comparison of the salivary microbiomes by 16S sequencing showed no significant difference in α diversity; however, it showed a significant difference in β diversity. Children with DS had a higher relative abundance of Corynebacterium and Cardiobacterium, and lower relative abundance of TM7.

CONCLUSIONS

This study provided basic data on the salivary microbiome of children with DS and showed the microbiological markers peculiar to children with DS. However, further research to identify the relationship with oral diseases is warranted.

A Study on Bacteria in Saliva of Autistic Children at Early Life

Background: Studies have shown that oral bacteria are involved in the occurrence of some neurological diseases. Autism spectrum disorder (ASD), a neurodevelopmental disorder occurring in early life, is closely related to intestinal bacteria. At present, the role of the oral microbiota in ASD rarely remains unexplored. Objectives: This study aimed to explore the differences of bacteria in saliva between autistic and healthy children in early childhood and investigate whether there are any specific salivary bacteria serving as biomarkers of ASD. Methods: A total of 10 autistic children aged 2 - 6 years and 10 healthy children matched in age, gender, and region in China were involved in this study. 16S ribosomal ribonucleic acid sequencing was employed to detect the disparities of bacteria in saliva between autistic children and healthy children. Moreover, the relationship between salivary differential bacteria and intestinal bacteria in autistic children was analyzed to screen out salivary differential bacteria that were unrelated to intestinal bacteria. Results: There were 14 bacteria in the saliva of children with autism, which were different from those of the control group (P < 0.05). Correlation analysis showed that the salivary Bacteroides fragilis had no apparent relationship with intestinal bacteria (P > 0.05); nevertheless, the rest of the differential bacteria in saliva were significantly related to intestinal bacteria. Conclusions: There were differential bacteria in the saliva of children with ASD and healthy controls, indicating that salivary bacteria might play a role in ASD. Nevertheless, further studies are needed to identify the pathogenesis of ASD.

Study of oral microbiota diversity among groups of families originally from different countries

The diversity of oral microbiota is affected by diets habits, gender, age, ethnic group, and environment. The acquisition of oral microbiota and the role of family on oral microbiota development is poorly understood. This study aims to characterize and compare the oral bacterial microbiota among families using 16S rRNA gene sequencing. This work was conducted in Jeddah city from 2020 to 2021, in which four families composed of 20 members of different ethnicity and lifestyle were recruited. After the collection of saliva samples, the DNA was extracted and processed for 16S rRNA gene metagenomics sequencing. Among 378 OUTs generated, 39 (10.3%) were unique in group A, 13 (3.4%) unique in group B, and 11 (2.9%) were unique in groups C and D. We observed a significant variation at the level of top abundance phylum (14), families (23), genera (24), and species (22) of bacteria among family members. Within family groups, different bacterial species were reported to be more dominant among certain family members than the other; Prevotella melaninogenica, Prevotella histicola and Haemophilus parainfluenzae, Veillonella atypica, Porphyromonas pasteri and Haemophilus pittmaniae were more dominant in parents of some families than the other family member. In summary, this study highlights the precise and perceptible association of oral microbial between family members. Our findings documented the clustering of certain bacterial species in family groups, supporting the role of community in the development of oral microbiota.

Maturation of the oral microbiota during primary teeth eruption: a longitudinal, preliminary study

Introduction

Oral microbiota that established in the early years of life may influence the child’s oral health in the long term. Until now, no consensus is reached about whether the development of the oral microbiota is more related with age increase or more with teeth eruption.

Objective

To analyze the microbiota development of both saliva and supragingival plaque during the gradual eruption of primary teeth in caries-free infants and toddlers.

Methods

Saliva and plaque samples were collected at five and four dentition states, respectively, and were identified by bacterial 16S rRNA gene sequencing.

Results

During the longitudinal observation, the saliva ecosystem seemed more complex and dynamic than the plaque, with larger bacteria quantity and more significantly varied species over time. About 70% of the initial colonized OTUs in plaque persisted until the completion of the primary dentition. Transient bacteria were mostly detected in the early saliva and plaque microbiota, which came from the environment and other sites of the human body. Microbial diversity in both saliva and plaque varied greatly from pre-dentition to full eruption of eight anterior teeth, but not during the eruption of primary molars.

Conclusion

Oral bacterial development follows an ordered sequence during the primary teeth eruption. ‘Fully eruption of all primary anterior teeth’ is a critical stage in this process.

Periodontitis and diabetes mellitus co-morbidity: A molecular dialogue

BACKGROUND

Type 2 diabetes mellitus (T2DM) and periodontitis are two biologically linked diseases that often coexist in complex interaction. While periodontitis may lead to insulin receptor desensitization, diabetes may increase the expression of inflammatory cytokines, such as Tumor Necrosis Factor-α (TNF-α) and Interleukin 6 (IL-6), in the gingival crevicular fluid and activate osteoclasts via Receptor activator of nuclear factor kappa-Β ligand (RANK-L) production, leading to bone resorption. However, the association between the two diseases processes, where one may exacerbate the progression of the other, is unclear. In addition, both diseases have similar mechanistic themes, such as chronic inflammation and oxidative stress. This review aimed to investigate the pathophysiological and molecular mechanisms underlying T2DM and periodontitis.

HIGHLIGHT

Uncontrolled diabetes is often associated with severe periodontitis, measured by clinical attachment loss. Alteration in the oral microbiome composition, which may activate the host inflammatory response and lead to irreversible oxidative stress, is a common finding in both diseases. An understanding of the molecular crosstalk between the two disease processes is crucial for developing therapeutic targets that inhibit bone resorption and halt the progression of periodontitis in patients with diabetes.

CONCLUSION

The Oral microbiome composition in T2DM and periodontitis shifts toward dysbiosis, favoring bacterial pathogens, such as Fusobacteria and Porphyromonas species. Both conditions are marked by pro-inflammatory immune activity via the activation of Interleukin 17 (IL-17), Interleukin 1 (IL-1), TNF-α, and Nuclear Factor Kappa Beta (NF-κB). Common molecular crosstalk signaling appears to involve advanced glycation end products (AGEs) and oxidative stress. Thus, future drug targets are multifactorial, ranging from modulatory of host inflammatory response to preventing the accumulation of AGEs and oxidative free radicals.

The Clinical Potential of Oral Microbiota as a Screening Tool for Oral Squamous Cell Carcinomas

Introduction

The oral squamous cell carcinoma (OSCC) is detrimental to patients’ physical and mental health. The prognosis of OSCC depends on the early diagnosis of OSCC in large populations.

Objectives

Here, the present study aimed to develop an early diagnostic model based on the relationship between OSCC and oral microbiota.

Methods

Overall, 164 samples were collected from 47 OSCC patients and 48 healthy individuals as controls, including saliva, subgingival plaque, the tumor surface, the control side (healthy mucosa), and tumor tissue. Based on 16S rDNA sequencing, data from all the five sites, and salivary samples only, two machine learning models were developed to diagnose OSCC.

Results

The average diagnostic accuracy rates of five sites and saliva were 98.17% and 95.70%, respectively. Cross-validations showed estimated external prediction accuracies of 96.67% and 93.58%, respectively. The false-negative rate was 0%. Besides, it was shown that OSCC could be diagnosed on any one of the five sites. In this model, Actinobacteria, Fusobacterium, Moraxella, Bacillus, and Veillonella species exhibited strong correlations with OSCC.

Conclusion

This study provided a noninvasive and inexpensive way to diagnose malignancy based on oral microbiota without radiation. Applying machine learning methods in microbiota data to diagnose OSCC constitutes an example of a microbial assistant diagnostic model for other malignancies.

Dynamic Observation of the Effect of Maternal Caries on the Oral Microbiota of Infants Aged 12-24 Months

Aim

To provide a dynamic description of the oral microbial composition in mothers with and without dental caries and their children aging 12-24 months.

Methodology

A total of 20 pairs of mothers and their children aged 12 months were included and followed up at 18 and 24 months of age. Ten mothers with dental caries(MEG) and their children(CEG) were in the exposure group, and ten caries-free mothers(MCG) and their children(CCG)in control group. Supragingival plaque biofilm samples were collected and DNA was extracted for bacterial 16S rRNA gene sequencing.

Results

A total of 18 pairs completed follow-ups. At a 3% divergence level, the number of common operational taxonomic units found between the mothers and children increased as the children aged. Proteobacteria, Bacteroidetes, Firmicutes, Fusobacteria, and Actinobacteria accounted for more than 80% phyla of each group. A microbial community structure analysis showed that the differences between mothers and children were significant in all groups except for the MEG24 and CEG24 groups.

Conclusions

Oral microbiota of children was more like their mothers' with increasing age, regardless of whether the mothers had dental caries. Mothers with dental caries may have a greater influence on the oral microbiota of children's than those without dental caries as children age.

Microbial population shift and metabolic characterization of silver diamine fluoride treatment failure on dental caries

The objective of this pilot study was to describe the microbial profiles present in the plaque and saliva of children who continued to develop new carious lesions following treatment with silver diamine fluoride ("nonresponders") compared to caries active, caries-free, and children immediately receiving SDF treatment for untreated caries in order to identify potential microbial differences that may relate to a re-incidence of caries. Saliva and plaque samples from infected and contralateral sites were obtained from twenty children who were either caries free, had active carious lesions, were caries active and received SDF treatment immediately before sampling, or had previously received SDF treatment and developed new caries. In total, 8,057,899 Illumina-generated sequence reads from 60 samples were obtained. Reads were processed using the Quantitative Insights Into Microbial Ecology pipeline. Group differences were assessed using Analysis of Variance Models and Tukey Honest Significant Differences. To identify significant taxa between treatment groups, Linear discriminant analysis Effect Size (LefSe) and Analysis of Differential Abundance Taking Sample Variation Into Account were used. Differential abundant analysis indicated that members of the Lachnospiraceae family were significantly enriched in non-responders and the genus Tannerella and species Granulicatella adiances were also highly abundant in this group. LefSe analysis between non-responders and SDF-treated groups revealed that genera Leptotrichia and Granulicatella were enriched in non-responders. We observed the highest abundance of phosphotransferase system and lowest abundance of lipopolysaccharide synthesis in non-responders. The microbiome in dental biofilms is responsible for initiation and progression of dental caries. SDF has been shown to be effective in arresting the progression carious lesions, in part due to its antimicrobial properties. Findings suggest that the differential abundance of select microbiota and specific pathway functioning in individuals that present with recurrent decay after SDF treatment may contribute to a potential failure of silver diamine fluoride to arrest dental caries. However, the short duration of sample collection following SDF application and the small sample size emphasize the need for further data and additional analysis.

Comparison of oral microbiome profiles in 18-month-old infants and their parents

The onset and progress of dental caries and periodontal disease is associated with the oral microbiome. Therefore, it is important to understand the factors that influence oral microbiome formation. One of the factors that influence oral microbiome formation is the transmission of oral bacteria from parents. However, it remains unclear when the transmission begins, and the difference in contributions of father and mother. Here, we focused on the oral microbiome of 18-month-old infants, at which age deciduous dentition is formed and the oral microbiome is likely to become stable, with that of their parents. We collected saliva from forty 18-month-old infants and their parents and compared the diversity and composition of the microbiome using next-generation sequencing of 16S rRNA genes. The results showed that microbial diversity in infants was significantly lower than that in parents and composition of microbiome were significantly different between infants and parents. Meanwhile, the microbiome of the infants was more similar to that of their mothers than unrelated adults. The bacteria highly shared between infants and parents included not only commensal bacteria but also disease related bacteria. These results suggested that the oral microbiome of the parents influences that of their children aged < 18 months.

Acquisition, Divergence, and Personalization of the Female Perineal Microbiomes Are Driven by Developmental Milestones and Disrupted by Urinary Tract Infection: A Pilot Study

Introduction: The pediatric perineal microbiomes inhabit a dynamic environment with changes related to diet, toileting habits, and hormonal development. We hypothesized that next-generation sequencing would reveal different perineal bacterial signatures associated with developmental milestones in premenstrual females. Furthermore, we predicted that these microbial changes would be disrupted in premenstrual females with a history of urinary tract infection (UTI). Study Design: Healthy females were recruited at well-child visits. Subjects were divided into 4 developmental groups: (1) 0-3 month old newborns; (2) 4-10 month old infants transitioning to solid foods; (3) 2-6 year old toddlers peri-toilet training; and (4) 7-12 year old premenstrual girls. A separate group of females with a history of culture proven UTI and off antibiotics >1 month was also recruited. DNA was isolated from swabs of the perineum and subjected to 16S rRNA sequencing. The diversity and species changes between developmental cohorts and age matched children with history of UTI was determined. Results: A total of 75 subjects were recruited: 15 in each group. There was a clear evolution of the perineal microbiomes with development. There was a significant microbial disruption in girls with a history of UTI, irrespective of developmental milestone age group. The periurethral/perivaginal site displayed greater changes in microbiome structure than other sites in girls with a history of UTI. Discussion: This pilot study evaluates the normal microbiome of the premenstrual girl at specific developmental milestones. Although the number of children per cohort was limited to 15, we observed statistical significance corresponding with developmental milestones. This study provides the first, culture independent delineation of the development of the perineal microbiome in girls. Furthermore, the sites closest to the site of infection appear to be more sensitive to antibiotic remodeling than those more distant. The factors that remodel the perineal microbiomes and predispose females, particularly girls, to UTIs (e.g., increase in uropathogen presence, absence of protective organisms) are unclear. Identification of specific signatures that increase susceptibility to UTI and their sequelae will improve patient care and promote personalized medicine.

Maturation of the Oral Microbiome in Caries-Free Toddlers: A Longitudinal Study

Understanding the development of the oral microbiota in healthy children is of great importance to oral and general health. However, limited data exist on a healthy maturation of the oral microbial ecosystem in children. Moreover, the data are biased by mislabeling “caries-free” populations. Therefore, we aimed to characterize the healthy salivary and dental plaque microbiome in young children. Caries-free (ICDAS [International Caries Detection and Assessment System] score 0) children (n = 119) and their primary caregivers were followed from 1 until 4 y of child age. Salivary and dental plaque samples were collected from the children at 3 time points (T1, ~1 y old; T2, ~2.5 y old; and T3, ~4 y old). Only saliva samples were collected from the caregivers. Bacterial V4 16S ribosomal DNA amplicons were sequenced using Illumina MiSeq. The reads were denoised and mapped to the zero-radius operational taxonomic units (zOTUs). Taxonomy was assigned using HOMD. The microbial profiles of children showed significant differences (P = 0.0001) over time. Various taxa increased, including Fusobacterium, Actinomyces, and Corynebacterium, while others showed significant decreases (e.g., Alloprevotella and Capnocytophaga) in their relative abundances over time. Microbial diversity and child-caregiver similarity increased most between 1 and 2.5 y of age while still not reaching the complexity of the caregivers at 4 y of age. The microbiome at 1 y of age differed the most from those at later time points. A single zOTU (Streptococcus) was present in all samples (n = 925) of the study. A large variation in the proportion of shared zOTUs was observed within an individual child over time (2% to 42% of zOTUs in saliva; 2.5% to 38% in dental plaque). These findings indicate that the oral ecosystem of caries-free toddlers is highly heterogeneous and dynamic with substantial changes in microbial composition over time and only few taxa persisting across the 3 y of the study. The salivary microbiome of 4-y-old children is still distinct from that of their caregivers.

Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis

Microbial communities are complex and dynamic, composed of hundreds of taxa interacting across multiple spatial scales. Advances in sequencing and imaging technology have led to great strides in understanding both the composition and the spatial organization of these complex communities. In the human mouth, sequencing results indicate that distinct sites host microbial communities that not only are distinguishable but to a meaningful degree are composed of entirely different microbes. Imaging suggests that the spatial organization of these communities is also distinct. Together, the literature supports the idea that most oral microbes are site specialists. A clear understanding of microbiota structure at different sites in the mouth enables mechanistic studies, informs the generation of hypotheses, and strengthens the position of oral microbiology as a model system for microbial ecology in general.