Metagenomic analysis of oral microbiome in young children aged 6-8 years living in a rural isolated Chinese province

Influence of maternal oral microbiome on newborn oral microbiome in healthy pregnancies

BACKGROUND

Periodontal disease and its bacteria can be responsible for pregnancy complications and transmission of periodontal bacteria from mother to newborn.

METHODS

A salivary swab to 60 healthy, full-term newborns and their mothers was taken immediately after birth. The test was performed with Real Time PCR method to evaluate the expression of the gene through DNA amplification. The species considered were: Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia and Fusobacterium nucleatum ssp.

RESULTS

The newborn oral microbiome was composed primarily by saprophytes (98.38 + 4.88%), just like the mothers (98.8 + 3.69%). There was a statistically significant difference of the total microbiological density in newborns and mothers (p = 0.0001). Maternal and neonatal oral microbiome had a correlated total microbiological density only in 33.3% (N = 20/60) of cases. The analysis of the oral microbiome showed a pathological composition only in 12/60 babies (20%). The most frequent detected specie in newborns was Fusobacterium nucleatum (9/12 babies, 75%), as well as for the mothers (53.3%). However, the pathogen was present both in baby and his mother only in 3 dyads. Porphyromonas gingivalis showed the highest association mother-baby (4/12 dyads, 33%). Porphyromonas gingivalis was the pathogen with the highest bacterial load in the 12 mothers. We found a statistically significant difference in the total load of Porphyromonas gingivalis in mothers and babies (p = 0.02).

CONCLUSIONS

There was a statistically significant difference in the richness of the microbiome from newborns and mothers. Even comparing the microbiological density in the oral cavity of the individual mother-child pairs, we did not find a significant concordance. These results seem to suggest a low influence of maternal oral microbiome on the richness of the oral neonatal one. We didn't find mother-child concordance (p = 0.0001) in the presence of pathogenic periodontal micro-organisms. Fusobacterium nucleatum was the most frequent specie detected. Porphyromonas gingivalis instead was the bacteria with the higher possibility of transmission. In conclusion in our study maternal oral health doesn't affect healthy, full-term newborns' oral microbiome. Further studies are needed to understand the maternal influence on newborn's oral microbiome and its effects on babies long-term health.

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.

Untargeted metabolomics of saliva in caries-active and caries-free children in the mixed dentition

Objective

To compare the differences in salivary metabolites between caries-active and caries-free children in the mixed dentition, and explore their correlation with caries status.

Methods

The study involved 20 children (aged 8–9 years) in the mixed dentition, including 10 caries-active (aged 8.6 ± 0.49years) and 10 caries-free children(aged 8.5 ± 0.5years), with a male/female ratio of 1:1. The saliva samples were collected from all children. Metabolite extraction, LC-MS/MS-based untargeted metabolomics, qualitative and semi-quantitative analysis and bioinformatics analysis were performed to identify differential metabolites between the two sample groups. The differential metabolites identified were further analyzed in an attempt to find their correlations with caries status.

Results

In the positive ion mode, a total of 1606 molecular features were detected in the samples of the two groups, 189 of which were differential metabolites when comparing the caries-active group with the caries-free group, including 104 up-regulated and 85 down-regulated metabolites. In the negative ion mode, a total of 532 molecular features were detected in the samples of two groups, 70 of which were differential metabolites when comparing the caries-active group with the caries-free group, including 37 up-regulated and 33 down-regulated metabolites. In the positive ion mode, two of the top 5 up-regulated differential metabolites were found in and annotated to specific metabolic pathways, whereas in the negative ion mode, only one of the top 5 up-regulated differential metabolites was found in and annotated to specific metabolic pathways. In both the positive and negative ion modes, the top 5 down-regulated differential metabolites were both annotated to the metabolic pathways. KEGG pathway enrichment analysis of differential metabolites showed that histamine and arachidonic acid identified in the positive ion mode, as well as succinate and L-histidine identified in the negative ion mode were enriched in the top 3 significantly altered pathways.

Conclusion

The enriched differential metabolites including histamine, L-histidine and succinate were correlated with the presence of dental caries, but their role in the caries process needs to be further investigated.

Role of mutans streptococci, acid tolerant bacteria and oral Candida species in predicting the onset of early childhood caries

Aim

Early childhood caries is the most common chronic infectious disease in children in the United States. This study, which is part of a larger, longitudinal study exploring oral microbiological components of caries development in children, reports on the impact of total mutans streptococci (MS), total acid tolerant bacteria and Candida species on the development of dental caries in a subset of these children. Of particular interest was the relationship between caries development and co-colonization of mutans streptococci and Candida species.

Methods

Children between the ages of 12 and 47 months displaying no evidence of dental caries were recruited for a longitudinal study (n = 130). Twelve age- and gender-matched pairs were selected. In each pair, one child developed caries during the study, and one did not. Whole mouth plaque samples were collected by swab at baseline and every 6 months thereafter for a duration of 18 months and spiral plated for microbial counts (CFU/ml). Cut-offs based on percent of total cultivable flora were designated for all microbial measures. A scoring system designated the Plaque Microbial Index (PMI) was developed for use in statistical analyses to assess potential predictive factors for caries risk assessment.

Results

Children who developed caries were significantly more likely to harbor higher percentages of acid tolerant bacteria (p = 0.003), MS (p < 0.001) and have Candida species present (p < 0.001) at ≥1 visit leading up to caries onset. Mean PMI scores derived from the aforementioned microbial measures, were higher for caries active children than caries free children (p = 0.000147). Co-colonization of MS and Candida species was significantly associated with caries development (p < 0.001) and detection of both at the same visit had a 100% positive predictive value and 60% negative predictive value for caries development.

Conclusion

In children who developed caries, there was a statistically significant association with the percent of total flora that was acid tolerant, the percent of MS, the presence of Candida and co-colonization of MS and Candida species. Combining these microbial measures into PMI scores further delineated children who developed caries from those who remained caries-free. These microbiological measures show potential as predictive factors and risk assessment tools for caries development.

Salivary microbiome and metabolome analysis of severe early childhood caries

BACKGROUND

Severe early childhood caries (SECC) is an inflammatory disease with complex pathology. Although changes in the oral microbiota and metabolic profile of patients with SECC have been identified, the salivary metabolites and the relationship between oral bacteria and biochemical metabolism remains unclear. We aimed to analyse alterations in the salivary microbiome and metabolome of children with SECC as well as their correlations. Accordingly, we aimed to explore potential salivary biomarkers in order to gain further insight into the pathophysiology of dental caries.

METHODS

We collected 120 saliva samples from 30 children with SECC and 30 children without caries. The microbial community was identified through 16S ribosomal RNA (rRNA) gene high-throughput sequencing. Additionally, we conducted non-targeted metabolomic analysis through ultra-high-performance liquid chromatography combined with quadrupole time-of-flight mass spectrometry to determine the relative metabolite levels and their correlation with the clinical caries status.

RESULTS

There was a significant between-group difference in 8 phyla and 32 genera in the microbiome. Further, metabolomic and enrichment analyses revealed significantly altered 32 salivary metabolites in children with dental caries, which involved pathways such as amino acid metabolism, pyrimidine metabolism, purine metabolism, ATP-binding cassette transporters, and cyclic adenosine monophosphate signalling pathway. Moreover, four in vivo differential metabolites (2-benzylmalate, epinephrine, 2-formaminobenzoylacetate, and 3-Indoleacrylic acid) might be jointly applied as biomarkers (area under the curve = 0.734). Furthermore, the caries status was correlated with microorganisms and metabolites. Additionally, Spearman's correlation analysis of differential microorganisms and metabolites revealed that Veillonella, Staphylococcus, Neisseria, and Porphyromonas were closely associated with differential metabolites.

CONCLUSION

This study identified different microbial communities and metabolic profiles in saliva, which may be closely related to caries status. Our findings could inform future strategies for personalized caries prevention, detection, and treatment.

Exploring Oral Microbiome in Healthy Infants and Children: A Systematic Review

Recent advances in the development of next-generation sequencing (NGS) technologies, such as the 16S rRNA gene sequencing, have enabled significant progress in characterizing the architecture of the oral microbiome. Understanding the taxonomic and functional components of the oral microbiome, especially during early childhood development, is becoming critical for identifying the interactions and adaptations of bacterial communities to dynamic conditions that may lead to the dysfunction of the host environment, thereby contributing to the onset and/or progression of a wide range of pathological conditions. We aimed to provide a comprehensive overview of the most recent evidence from studies of the oral microbiome of infants and young children, focusing on the development of oral microbiome in the window of birth to 18 years, focusing on infants. A systematic literature search was conducted in PubMed, Scopus, WOS, and the WHO clinical trial website for relevant articles published between 2006 to 2022 to identify studies that examined genome-wide transcriptome of the oral microbiome in birth, early childhood, and adolescence performed via 16s rRNA sequence analysis. In addition, the references of selected articles were screened for other relevant studies. This systematic review was performed in accordance PRISMA guidelines. Data extraction and quality assessment were independently conducted by two authors, and a third author resolved discrepancies. Overall, 34 studies were included in this systematic review. Due to a considerable heterogeneity in study population, design, and outcome measures, a formal meta-analysis was not carried out. The current evidence indicates that a core microbiome is present in newborns, and it is stable in species number. Disparity about delivery mode influence are found. Further investigations are needed.

Metabolic differences of the oral microbiome related to dental caries - A pilot study

OBJECTIVE

We aimed to investigate the composition and functions discrepancy of supragingival plaque associated with active deciduous teeth caries in mixed dentitions.

DESIGN

Thirty-three subjects with mixed dentition participated in this study. Children with deciduous teeth caries (dt ≥ 3) were recruited to the caries group, whereas children without deciduous teeth caries (dt = 0) were recruited to the caries-free group. Plaque were collected from deciduous teeth surface and permanent teeth surface respectively. A total of 66 samples of dental plaque were collected and conserved. Illumina 16S rRNA sequencing and diversity analysis were performed for microbiome. Untargeted liquid chromatograph-mass (LC-MS) and partial least squares discriminant analysis were performed for metabolome.

RESULTS

A dominant microbiome of 8 phyla and 22 genera were detected. The alpha diversity indices did not detect differences between the caries and caries-free groups (p > 0.05). Beta diversity analysis showed that the microbiota composition was similar between subgroups. Comparative analysis at genus level did not detect difference between caries and caries-free subgroups. The metabolomics analysis yielded 419 biochemical metabolites, 56 of which were related to caries status. Metabolites in glucose metabolism and byproducts of oxidative stress were identified as related to dental caries in mixed dentition. Dominant bacteria are positively correlated with metabolites, such as Streptococcus and organic acids.

CONCLUSIONS

The upgrade of glucose metabolism and oxidative stress was observed in caries status. Functions discrepancy of oral microbiome may be more pronounced than the composition of oral microbiome with active dental caries in mixed dentitions.

Maintaining oral health for a hundred years and more? - An analysis of microbial and salivary factors in a cohort of centenarians

Aim

To investigate associations between oral health-related conditions and the oral microbiome in a representative study sample of centenarians.

Materials and methods

Clinical and microbial parameters from 54 centenarians were assessed in the Heidelberg Dental Centenarian Study. Plaque and salivary samples were collected, and the microbiota was characterized by 16S rRNA gene sequencing.

Results

Diversity and structure of the oral microbiome were mainly influenced by the presence of natural teeth and the number of decayed, missing, and filled teeth (0.028 ≤ p ≤ 0.001 in plaque and salivary samples). Centenarians with less caries experience possessed a more diverse oral microbiome. Moreover, the number of dental visits also showed a significant influence on the microbial composition. Most centenarians presented with hyposalivation (mean stimulated flow rate = 0.84 ± 0.55 ml/min), a low buffering capacity, and an acidic pH. The latter was between 5.0 and 5.8 in 46.3% of cases, and we observed that an increased salivary pH correlated with higher alpha-diversity in both salivary and plaque samples.

Conclusion

The microbiome diversity correlated significantly with successful oral aging. In addition, regular dental visits were a beneficial factor. However, diversity can be negatively influenced by hyposalivation, associated with pH changes due to aging effects.

Meta-Analysis Using NGS Data: The Veillonella Species in Dental Caries

Objectives: In light of recent technological advances in Next-generation sequencing (NGS) and the accumulation of large, publicly available oral microbiome datasets, the need for meta-analysing data on caries microbiome is becoming feasible and essential. A consensus on the identification of enriched organisms in cariogenic dysbiotic biofilms would be reached. For example, members of the Veillonella genus have been detected in caries biofilms, and may have an underestimated contribution to the dysbiotic process. Hence, we aimed to determine the abundance of Veillonella species in dental caries in studies using NGS data.

Materials and Methods: Analysis was performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (registered at PROSPERO: CRD42020204150). Studies investigating microbial composition in saliva, dental biofilm, or carious dentin were included. Six databases and grey literature were searched. Two independent reviewers selected the papers and assessed the methodological quality.

Results: Searches retrieved 1,323 titles, from which 38 studies were included in a qualitative synthesis, comprising a total of 1,374 caries and 745 caries-free individuals. Most studies analysed 16S rRNA amplicons, and only 5 studies used shotgun metagenomics and metatranscriptomics. A geographical bias was observed. The methodological quality was downrated in 81.5% of the studies due to the lack of criteria for defining cases and standard criteria used for measurement of the condition in a reliable way. Six studies on early childhood caries (ECC) were meta-analysed, confirming a significant enrichment of Veillonella spp. in caries-associated biofilms (but not saliva) when compared to caries-free controls [mean difference: 2.22 (0.54–3.90); p = 0.01].

Conclusions:Veillonella spp. is more abundant in individuals suffering with ECC when compared to caries-free controls (very low evidence certainty), and should be considered for further studies to observe their metabolism in dental caries. There is an urgent need for a consensus in methodologies used to allow for more rigorous comparison between NGS studies, particularly including clinical data and details of caries diagnosis, as they are currently scarce. Inconsistent reporting on the NGS data affected the cross-study comparison and the biological connexions of the relative abundances on caries microbiome.

The Impact of Mouthwash on the Oropharyngeal Microbiota of Men Who Have Sex with Men: a Substudy of the OMEGA Trial

Mouthwash is a commonly used product and has been proposed as an alternative intervention to prevent gonorrhea transmission. However, the long-term effects of mouthwash on the oral microbiota are largely unknown. We investigated the impact of 12 weeks of daily mouthwash use on the oropharyngeal microbiota in a subset of men who have sex with men who participated in a randomized trial comparing the efficacy of two alcohol-free mouthwashes for the prevention of gonorrhea. We characterized the oropharyngeal microbiota using 16S rRNA gene sequencing of tonsillar fossae samples collected before and after 12 weeks of daily use of Listerine mouthwash or Biotène dry mouth oral rinse. Permutational multivariate analysis of variance (PERMANOVA) was used to assess differences in oropharyngeal microbiota composition following mouthwash use. Differential abundance testing was performed using ALDEx2, with false-discovery rate correction. A total of 306 samples from 153 men were analyzed (Listerine, n = 78 and Biotène, n = 75). There was no difference in the overall structure of the oropharyngeal microbiota following Listerine or Biotène use (PERMANOVA P = 0.413 and P = 0.331, respectively). Although no bacterial taxa were significantly differentially abundant following Listerine use, we observed a small but significant decrease in the abundance of both Streptococcus and Leptotrichia following Biotène use. Overall, our findings suggest that daily use of antiseptic mouthwash has minimal long-term effects on the composition of the oropharyngeal microbiota.

IMPORTANCE Given the role of the oral microbiota in human health, it is important to understand if and how external factors influence its composition. Mouthwash use is common in some populations, and the use of antiseptic mouthwash has been proposed as an alternative intervention to prevent gonorrhea transmission. However, the long-term effect of mouthwash use on the oral microbiota composition is largely unknown. We found that daily use of two different commercially available mouthwashes had limited long-term effects on the composition of the oropharyngeal microbiota over a 12-week period. The results from our study and prior studies highlight that different mouthwashes may differentially affect the oral microbiome composition and that further studies are needed to determine if mouthwash use induces short-term changes to the oral microbiota that may have detrimental effects.

Correlations between gastrointestinal and oral microbiota in children with cerebral palsy and epilepsy

We here studied the correlation between gut and oral microbiota in children with cerebral palsy and Epilepsy (CPE). We enrolled 27 children with this condition from the social welfare center of Longgang District, collected their oral plaque and stool samples, and analyzed their gut microbiota (GM) and oral microbiota (OM) through 16S rRNA gene sequencing. Taxonomical annotation revealed that the levels of Firmicutes and Bacteroides in the oral cavity were significantly lower in CPE children than in healthy children, whereas the abundance of Actinomycetes increased significantly in CPE children. In addition, Prevotella, Fusobacterium, and Neisseria were the top three abundant genera, representing 15.49%, 9.34%, and 7.68% of the OM and suggesting potential correlations with caries, periodontitis, and malnutrition. For the GM, Bifidobacterium, Bacteroides, and Prevotella were the top three abundant genera in CPE children and probably contributed to the development of chronic inflammation and malnutrition. Furthermore, the OM and GM correlated with each other closely, and the bacterial components of these microbiota in CPE children were remarkably different from those in healthy children, such as Bifidobacterium, Fusobacterium, Bacteroides, and Neisseria. Conclusively, dysbiotic OM can translocate to the intestinal tract and induce GM dysbiosis, suggesting the consistency between OM and GM variations. Altered oral and gut microbial structures have potential impacts on the occurrence of clinical diseases such as periodontitis, caries, and malnutrition.

Metagenomic Analysis Reveals Neisseria bacilliformis Variation in the Early Childhood Caries Plaque Microbiome

The progression of early childhood caries (ECC) is caused by microbial colonized in dental plaque. However, the association framework both from 16s genus down to high resolution metagenomic strain level and from composition to genome function analysis on caries lacks. 16S rRNA sequence revealed the composition of 3-6 years dental caries (ECC, n = 29), and severe dental caries (SECC, n = 36) children are significantly different from caries-free controls (CF, n = 31). Especially, genus Neisseria is enriched in caries (P < 0.05). Metagenomics sequence of 3 ECCs, 3 SECCs, and 3 CFs reveals Neisseria bacilliformis ATCC BAA-1200 in genus Neisseria is also significantly enriched in caries (P < 0.05). Then, we recovered high-quality metagenomic assembly genomes (MAG), named bin 86, which have 99% identity with Neisseria bacilliformis ATCC BAA-1200 genome. Function analysis of Neisseria bacilliformis ATCC BAA-1200 genome shows its metabolism power of sugar and adhesion, colonization, acid production, and acid tolerance ability, which suggested Neisseria bacilliformis ATCC BAA-1200 may serve as a biomarker for childhood caries.

Comparative Microbial Profiles of Caries and Black Extrinsic Tooth Stain in Primary Dentition

Extrinsic black tooth stain (BS) is a common oral disease associated with lower caries experience in preschool children, although the microbiotic features contributing to the low risk of caries in this group remain elusive. In this study, we aimed at identifying the dominant bacteria in dental plaque to indicate the incidence of caries in the primary dentition. Subjects were divided into 3 groups based on the clinical examination: group CF, children without pigment who had no caries lesions or restorations (n = 18); group CS, children who were diagnosed with severe early childhood caries (n = 17); and group BS, children with pigment (black extrinsic stain) without caries or restorations (n = 15). The total microbial genomic DNA was extracted and subjected to bacterial 16S ribosomal RNA gene sequencing using an Illumina HiSeq platform. The differential dominant bacteria were determined using Wilcoxon rank-sum testing and linear discriminant analysis effect size (LEfSe). Co-occurrence network analysis was performed using sparse correlations for compositional data, calculation and functional features were predicted using PICRUSt. Interestingly, our results showed that the relative abundance of Pseudopropionibacterium, Actinomyces, Rothia, and Cardiobacterium was from high to low and that of Porphyromonas was low to high in the BS, CF, and CS groups, consistent with the clinical incidence of caries in the 3 groups. Moreover, an increased level of Selenomonas_3, Fusobacterium, and Leptotrichia was associated with high caries prevalence. We found that the interactions among genera in the BS and CS plaque communities are less complex than those in the CF communities at the taxon level. Functional features, including cofactor and vitamin metabolism, glycan biosynthesis and metabolism, and translation, significantly increased in caries plaque samples. These bacterial competition- and commensalism-induced changes in microbiota would result in a change of their symbiotic function, finally affecting the balance of oral microflora.

The impact of caries status on supragingival plaque and salivary microbiome in children with mixed dentition: a cross-sectional survey

Background

Supragingival plaque and saliva are commonly used for microbiome analysis. Many epidemiological studies have identified deciduous teeth caries as a risk factor for caries development in first permanent molar (FPM); nevertheless, to the best of our knowledge, there are no reports on the effects of deciduous teeth caries on the microbiome of healthy FPM. Additionally, it remains unclear whether saliva can be used instead of supragingival plaque for caries microbial studies. Therefore, we aimed to elucidate this issue, and to characterize and compare the oral microbiome of healthy FPMs in children with different caries statuses and that from children with and without caries in a similar microhabitat, by PacBio sequencing. Currently, few studies have investigated the oral microbiome of children using this technique.

Methods

Thirty children (aged 7–9 years) with mixed dentition were enrolled; 15 had dental caries, and 15 did not. Supragingival plaques of deciduous molars and maxillary FPMs, and non-stimulating saliva samples were collected. DNA was extracted and the v1–v9 regions of 16S rRNA were amplified. Subsequently, PacBio sequencing and bioinformatic analyses were performed for microbiome identification.

Results

The microbial alpha diversity of the saliva samples was lower than that of the supragingival plaque (p < 0.05); however, no differences were detected between deciduous teeth and FPMs (p > 0.05). In addition, the alpha and beta diversity of children with and without caries was also similar (p > 0.05). Nonmetric multidimensional scaling and Adonis analyses indicated that the microbial structure of salivary and supragingival plaque samples differ (p < 0.05). Further analysis of deciduous teeth plaque showed that Streptococcus mutans, Propionibacterium acidifaciens, and Veillonella dispar were more abundant in children with caries than in those without (p < 0.05); while in FPMs plaque, Selenomonas noxia was more abundant in healthy children (p < 0.05). No differences in microorganisms abundance were found in the saliva subgroups (p > 0.05).

Conclusion

We have determined that supragingival plaque was the best candidate for studying carious microbiome. Furthermore, S. mutans, V. dispar, and P. acidifaciens were highly associated with deciduous teeth caries. S. noxia may be associated with the abiding health of FPM; however, this requires additional studies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12903-021-01683-0.

Geographic Variation Did Not Affect the Predictive Power of Salivary Microbiota for Caries in Children With Mixed Dentition

Dental caries is one of the most prevalent chronic oral diseases, affecting approximately half of children worldwide. The microbial composition of dental caries may depend on age, oral health, diet, and geography, yet the effect of geography on these microbiomes is largely underexplored. Here, we profiled and compared saliva microbiota from 130 individuals aged 6 to 8 years old, representing both healthy children (H group) and children with caries-affected (C group) from two geographical regions of China: a northern city (Qingdao group) and a southern city (Guangzhou group). First, the saliva microbiota exhibited profound differences in diversity and composition between the C and H groups. The caries microbiota featured a lower alpha diversity and more variable community structure than the healthy microbiota. Furthermore, the relative abundance of several genera (e.g., Lactobacillus, Gemella, Cryptobacterium and Mitsuokella) was significantly higher in the C group than in the H group (p<0.05). Next, geography dominated over disease status in shaping salivary microbiota, and a wide array of salivary bacteria was highly predictive of the individuals’ city of origin. Finally, we built a universal diagnostic model based on 14 bacterial species, which can diagnose caries with 87% (AUC=86.00%) and 85% (AUC=91.02%) accuracy within each city and 83% accuracy across cities (AUC=92.17%). Although the detection rate of Streptococcus mutans in populations is not very high, it could be regarded as a single biomarker to diagnose caries with decent accuracy. These findings demonstrated that despite the large effect size of geography, a universal model based on salivary microbiota has the potential to diagnose caries across the Chinese child population.

Oral Microbiota of Children Is Conserved across Han, Tibetan and Hui Groups and Is Correlated with Diet and Gut Microbiota

The oral microbiota can be affected by several factors; however, little is known about the relationship between diet, ethnicity and commensal oral microbiota among school children living in close geographic proximity. In addition, the relationship between the oral and gut microbiota remains unclear. We collected saliva from 60 school children from the Tibetan, Han and Hui ethnicities for a 16S rRNA gene sequencing analysis and comparison with previously collected fecal samples. The study revealed that Bacteroidetes and Proteobacteria were the dominant phyla in the oral microbiota. The Shannon diversity was lowest in the Tibetan group. A PCA showed a substantial overlap in the distribution of the taxa, indicating a high degree of conservation among the oral microbiota across ethnic groups while the enrichment of a few specific taxa was observed across different ethnic groups. The consumption of seafood, poultry, sweets and vegetables was significantly correlated with multiple oral microbiotas. Furthermore, 123 oral genera were significantly associated with 191 gut genera. A principal coordinate analysis revealed that the oral microbiota clustered separately from the gut microbiota. This work extends the findings of previous studies comparing microbiota from human populations and provides a basis for the exploration of the interactions governing the tri-partite relationship between diet, oral microbiota and gut microbiota.

Bacterial association and comparison between lung and intestine in rats

The association between lung and intestine has already been reported, but the differences in community structures or functions between lung and intestine bacteria yet need to explore. To explore the differences in community structures or functions, the lung tissues and fecal contents in rats were collected and analyzed through 16S rRNA sequencing. It was found that intestine bacteria was more abundant and diverse than lung bacteria. In intestine bacteria, Firmicutes and Bacteroides were identified as major phyla while Lactobacillus was among the most abundant genus. However, in lung the major identified phylum was Proteobacteria and genus Pseudomonas was most prominent genus. On the other hand, in contrast the lung bacteria was more concentrated in cytoskeleton and function in energy production and conversion. While, intestine bacteria were enriched in RNA processing, modification chromatin structure, dynamics and amino acid metabolism. The study provides the basis for understanding the relationships between lung and intestine bacteria.

Salivary Oral Microbiome of Children With Juvenile Idiopathic Arthritis: A Norwegian Cross-Sectional Study

Background

The oral microbiota has been connected to the pathogenesis of rheumatoid arthritis through activation of mucosal immunity. The objective of this study was to characterize the salivary oral microbiome associated with juvenile idiopathic arthritis (JIA), and correlate it with the disease activity including gingival inflammation.

Methods

Fifty-nine patients with JIA (mean age, 12.6 ± 2.7 years) and 34 healthy controls (HC; mean age 12.3 ± 3.0 years) were consecutively recruited in this Norwegian cross-sectional study. Information about demographics, disease activity, medication history, frequency of tooth brushing and a modified version of the gingival bleeding index (GBI) and the simplified oral hygiene index (OHI-S) was obtained. Microbiome profiling of saliva samples was performed by sequencing of the V1-V3 region of the 16S rRNA gene, coupled with a species-level taxonomy assignment algorithm; QIIME, LEfSe and R-package for Spearman correlation matrix were used for downstream analysis.

Results

There were no significant differences between JIA and HC in alpha- and beta-diversity. However, differential abundance analysis revealed several taxa to be associated with JIA: TM7-G1, Solobacterium and Mogibacterium at the genus level; and Leptotrichia oral taxon 417, TM7-G1 oral taxon 352 and Capnocytophaga oral taxon 864 among others, at the species level. Haemophilus species, Leptotrichia oral taxon 223, and Bacillus subtilis, were associated with healthy controls. Gemella morbillorum, Leptotrichia sp. oral taxon 498 and Alloprevotella oral taxon 914 correlated positively with the composite juvenile arthritis 10-joint disease activity score (JADAS10), while Campylobacter oral taxon 44 among others, correlated with the number of active joints. Of all microbial markers identified, only Bacillus subtilis and Campylobacter oral taxon 44 maintained false discovery rate (FDR) < 0.1.

Conclusions

In this exploratory study of salivary oral microbiome we found similar alpha- and beta-diversity among children with JIA and healthy. Several taxa associated with chronic inflammation were found to be associated with JIA and disease activity, which warrants further investigation.

The oral microbiome and salivary proteins influence caries in children aged 6 to 8 years

BACKGROUND

Oral microbiome and salivary proteins play a critical role in the occurrence and development of caries. In this study, we used metagenomic and metaproteomic analyses to explore the microbiological and proteinic biomarkers and investigate the etiology of caries in 6-8 years old children. Our study aims to offer a better comprehension of these factors and the relationship with caries, and these findings might facilitate caries risk assessment and provide a basis for future prevention strategies.

METHODS

Children 6 to 8 years old living in rural isolated areas including 40 caries-active subjects and 40 caries-free subjects were recruited. Supragingival plaque and unstimulated saliva were collected for 16S rDNA pyrosequencing and isobaric tags for relative and absolute quantitation (iTRAQ) technique coupled with quantitative nano-flow liquid chromatography-tandem mass spectrometry (LC-MS/MS), respectively.

RESULTS

We found 6 phyla and 13 genera predominant in all the samples, and differences in relative abundances can be observed. The Alpha diversity analysis demonstrated that the richness and diversity of the bacterial communities were similar between children with caries-free and caries-active groups; LEfSe detected differences in the bacterial community including Dialister, Selenomonas, Actinomyces, and Mogibacterium in the caries-active group (P < 0.05) and Capnocytophaga, Fusobacterium, Desulfuromonadales, Haemophilus, and Porphyromonas in the caries-free group(P < 0.05). The core microbiome was defined as 18 predominant genera in children with caries. The results of the salivary proteome identified 9135 unique peptides and 1662 proteins group from 20 salivary samples. Two hundred fifty-eight proteins were differentially expressed between the caries-free and caries-active groups.

CONCLUSIONS

The diversity of the microbial community has little effect on caries but some bacteria with different relative abundance between the caries-active and caries-free group could be considered as potential biomarkers for children with caries. In addition, as a critical host factor of caries, the salivary proteins are different in caries-free and caries-active groups.

Ethnic variation of oral microbiota in children

Despite widely used preventive measures such as sealant programs to control caries prevalence, disparities are seen among ethnic groups. Supragingival plaque harbors hundreds of bacterial species, playing a significant role in oral health and disease. It is unknown whether the ethnic variation influences the supragingival microbiota in children. In our study, variations in microbiota of the supragingival plaque was investigated from 96 children between 6 and 11 years old in four ethnic groups (African American, Burmese, Caucasian, and Hispanic) from the same geographic location by 16S rRNA gene sequencing. We found that the microbial alpha and beta diversity of supragingival microbiota significantly differed between ethnic groups. The supragingival plaque microbiota had the most complex microbial community in Burmese children. Within-group microbiota similarity in Burmese or Caucasian children was significantly higher than between-groups similarity. We identified seven ethnic group-specific bacterial taxa after adjusting for dental plaque index, decayed missing filled teeth (DMFT) and the frequency of brushing. Children with high plaque index and high DMFT values were more similar to each other in the overall microbial community, compared to low plaque index or low DMFT groups in which inter-subject variation is high. Several bacterial taxa associated with high plaque index or high DMFT were ethnic group-specific. These results demonstrated that supragingival microbiota differed among ethnicity groups in children.

Oral Microbiome in Four Female Centenarians

The oral microbiome of healthy older adults has valuable information about a healthy microbiome. In this study, we collected and analyzed the oral microbiome of denture plaque and tongue coating samples from four female centenarians. After DNA extraction and purification, pyrosequencing of the V3–V4 hypervariable regions of the 16S rRNA was carried out. The bacterial taxonomy for each lead was assigned based on a search of the EzBioCloud 16S database. We obtained a total of 199,723 valid, quality-controlled reads for denture plaque and 210,750 reads for tongue coating. The reads were assigned 407 operational taxonomic units with a 97% identity cutoff. Twenty-nine species were detected in both denture plaque and tongue coatings from all subjects. Firmicutes was the most abundant phylum; the Streptococcus salivarius group was the most abundant species in both the denture plaque and tongue coatings; and the Fusobacterium nucleatum group was detected in all subjects. In the bacterial profile, species formed clusters composed of bacteria with a wide range of prevalence and abundance, not dependent on phyla; each cluster may have specific species that could be candidates for a core microbiome. Firmicutes and Veillonella were abundant phyla on both plaque and tongue coatings of centenarians.

Oral Microbiome of Children Living in an Isolated Area in Myanmar

Several studies have shown that the oral microbiome is related to systemic health, and a co-relation with several specific diseases has been suggested. The oral microbiome depends on environmental- and community-level factors. In this observational study, the oral microbiomes of children of isolated mountain people were analyzed with respect to the core oral microbiome and etiology of dental caries. We collected samples of supragingival plaque from children (age 9–13) living in the Chin state of Myanmar. After DNA extraction and purification, next-generation sequencing of the V3–V4 hypervariable regions of the 16S rRNA was conducted. From thirteen subjects, 263,458 valid reads and 640 operational taxonomic units were generated at a 97% identity cut-off value. At the phylum level, Proteobacteria was the most abundant, followed by Firmicutes and Bacteroides. Forty-four bacteria were detected in total from all the subjects. For children without dental caries, Proteobacteria was abundant. In contrast, in children with dental caries, Firmicutes and Bacteroides were abundant. The oral microbiome of children living in an isolated area may be affected by environmental- and community-level factors. Additionally, the composition of the oral microbiome may affect the risk of dental caries.

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.