Nonsporing, anaerobic, gram-positive rods in saliva and the gingival crevice of humans

Unraveling the impact of primary immunodeficiency disorders on the microbiota of dental caries in children through 16S rRNA gene-based metagenomic analysis

Background/aim

Dental caries is a frequently occurring and multifactorial chronic disease in children resulting from the interaction of cariogenic bacteria and host susceptibility. The aim of this study was to elucidate the impacts of primary immunodeficiency disorders (PIDs) on microbiota of dental caries in children by 16S rRNA gene-based metagenomic analysis.

Materials and methods

Enrolled in this study were 15 children with primary PID with caries (PID group) and 15 healthy children with caries as a control (CG). The DMFT index, saliva flow rate, and buffering capacity of each participant were assessed before the metagenomic analyses were conducted. For taxonomic profiling, the reads were obtained by high-throughput sequencing of the V3-V4 hypervariable region of 16S rRNA.

Results

The DMFT score, saliva flow rate, and buffering capacity of the groups were similar. The flow rate and buffering capacity had no correlation with the number of species with 95% confidence. The metagenomic analysis resulted in the identification of 2440 bacterial species in all of the samples. Among the 50 most prevalent species present at ≥1% relative abundance, Prevotella melaninogenica and Prevotella salivae were differentially more abundant in the PID group. The PID group and CG showed similar species richness and evenness, but 4 of the 5 samples with the highest Shannon-Weiner and Inverse Simpson indices belonged to the PID group. The Spearman test results for correlation of the species in the PID subgroups showed that Prevotella oris had a positively correlated relationship with both Scardovia wiggsiae and Saccharibacteria genera incertae sedis.

Conclusion

This study provided insight into the caries microbiota of children with immunodeficiency diseases. Differentially abundant species, novel bacterial associations, and unique bacterial species were disclosed in the PID samples, indicating the role of the immune system in altering the caries microbiota. The prominent bacterial species and associations in the PID group should be suspected in regard to their link with present or future diseases.

The metabolic profile of Bifidobacterium dentium reflects its status as a human gut commensal

BACKGROUND

Bifidobacteria are commensal microbes of the mammalian gastrointestinal tract. In this study, we aimed to identify the intestinal colonization mechanisms and key metabolic pathways implemented by Bifidobacterium dentium.

RESULTS

B. dentium displayed acid resistance, with high viability over a pH range from 4 to 7; findings that correlated to the expression of Na+/H+ antiporters within the B. dentium genome. B. dentium was found to adhere to human MUC2+ mucus and harbor mucin-binding proteins. Using microbial phenotyping microarrays and fully-defined media, we demonstrated that in the absence of glucose, B. dentium could metabolize a variety of nutrient sources. Many of these nutrient sources were plant-based, suggesting that B. dentium can consume dietary substances. In contrast to other bifidobacteria, B. dentium was largely unable to grow on compounds found in human mucus; a finding that was supported by its glycosyl hydrolase (GH) profile. Of the proteins identified in B. dentium by proteomic analysis, a large cohort of proteins were associated with diverse metabolic pathways, indicating metabolic plasticity which supports colonization of the dynamic gastrointestinal environment.

CONCLUSIONS

Taken together, we conclude that B. dentium is well adapted for commensalism in the gastrointestinal tract.

Bifidobacterium dentium Fortifies the Intestinal Mucus Layer via Autophagy and Calcium Signaling Pathways

Much remains unknown about how the intestinal microbiome interfaces with the protective intestinal mucus layer. Bifidobacterium species colonize the intestinal mucus layer and can modulate mucus production by goblet cells. However, select Bifidobacterium strains can also degrade protective glycans on mucin proteins. We hypothesized that the human-derived species Bifidobacterium dentium would increase intestinal mucus synthesis and expulsion, without extensive degradation of mucin glycans. In silico data revealed that B. dentium lacked the enzymes necessary to extensively degrade mucin glycans. This finding was confirmed by demonstrating that B. dentium could not use naive mucin glycans as primary carbon sources in vitro To examine B. dentium mucus modulation in vivo, Swiss Webster germfree mice were monoassociated with live or heat-killed B. dentium Live B. dentium-monoassociated mice exhibited increased colonic expression of goblet cell markers Krüppel-like factor 4 (Klf4), Trefoil factor 3 (Tff3), Relm-β, Muc2, and several glycosyltransferases compared to both heat-killed B. dentium and germfree counterparts. Likewise, live B. dentium-monoassociated colon had increased acidic mucin-filled goblet cells, as denoted by Periodic Acid-Schiff-Alcian Blue (PAS-AB) staining and MUC2 immunostaining. In vitro, B. dentium-secreted products, including acetate, were able to increase MUC2 levels in T84 cells. We also identified that B. dentium-secreted products, such as γ-aminobutyric acid (GABA), stimulated autophagy-mediated calcium signaling and MUC2 release. This work illustrates that B. dentium is capable of enhancing the intestinal mucus layer and goblet cell function via upregulation of gene expression and autophagy signaling pathways, with a net increase in mucin production.IMPORTANCE Microbe-host interactions in the intestine occur along the mucus-covered epithelium. In the gastrointestinal tract, mucus is composed of glycan-covered proteins, or mucins, which are secreted by goblet cells to form a protective gel-like structure above the epithelium. Low levels of mucin or alterations in mucin glycans are associated with inflammation and colitis in mice and humans. Although current literature links microbes to the modulation of goblet cells and mucins, the molecular pathways involved are not yet fully understood. Using a combination of gnotobiotic mice and mucus-secreting cell lines, we have identified a human-derived microbe, Bifidobacterium dentium, which adheres to intestinal mucus and secretes metabolites that upregulate the major mucin MUC2 and modulate goblet cell function. Unlike other Bifidobacterium species, B. dentium does not extensively degrade mucin glycans and cannot grow on mucin alone. This work points to the potential of using B. dentium and similar mucin-friendly microbes as therapeutic agents for intestinal disorders with disruptions in the mucus barrier.

A Comparative Evaluation of Bifidobacteria Levels in Early Childhood Caries and Severe Early Childhood Caries

Background:

Bifidobacteria levels in saliva were found to be significantly correlated in adults with dental caries but less information available in the literature regarding its role in children.

Aim:

The aim is to compare the salivary levels of Bifidobacteria in children who are caries free with that of early childhood caries (ECC) and severe ECC (S-ECC).

Materials and Methods:

Saliva was collected using the tongue-loop method from a total of 60 children between the age group of 3–5 years and they were further divided into 3 groups. In addition, the age and gender of the children, sugar amount in diet, sugar frequency in diet, were recorded.

Results:

Bifidobacteria was isolated from all the three groups, but more were from S-ECC, followed by ECC and very few cases of caries-free children and was found to statistically significant (P < 0.001). Salivary levels of Bifidobacteria were significantly correlated with amount of sugar in the diet and frequency of sugar consumption.

Conclusions:

Salivary levels of Bifidobacteria were significantly associated with S-ECC and ECC, followed by caries free group. In future, it can be used as a salivary marker for caries risk assesment.

Salivary levels of Bifidobacteria in caries-free and caries-active children

BACKGROUND

Salivary levels of Bifidobacteria have been shown to be significantly correlated with caries experience in adults but not as yet in children.

HYPOTHESIS

Salivary levels of Bifidobacteria are positively associated with caries experience in children.

AIM

To compare the salivary concentrations of Bifidobacteria of caries-free and caries-active children.

DESIGN

Saliva was collected using the tongue-loop method from 38 caries-active children and from 22 clinically caries-free children, and the numbers of Bifidobacteria, mutans streptococci, lactobacilli and yeasts were determined. Additionally, the age and gender of the children, a plaque index, sugar amount in diet, sugar frequency in diet, hygiene practice and fluoride toothpaste usage were recorded.

RESULTS

Bifidobacteria were isolated from 95% of the caries-active children and from only 9% of the caries-free children (P < 0.001). Salivary levels of Bifidobacteria were significantly correlated with amount of sugar in the diet, frequency of sugar consumption and oral hygiene practice. The significant variables that discriminated between the caries-free and caries-active subjects were salivary levels of Bifidobacteria, salivary levels of mutans streptococci and oral hygiene practice (χ(2) = 72.57, P < 0.001) and overall 90.0% of cases were correctly classified.

CONCLUSIONS

Salivary levels of Bifidobacteria are significantly associated with caries experience in children. The salivary levels of this genus may be a useful marker of caries risk.

Oral Bifidobacteria

Bifidobacteria are aciduric bacteria that might play a role in the caries process. To test the hypothesis that Bifidobacteria behave as caries-associated organisms, as predicted by the ecological plaque hypothesis, we determined salivary levels of Bifidobacteria and caries-associated organisms for 156 older adults. Salivary levels of Bifidobacteria, mutans streptococci, lactobacilli, and yeasts were correlated with each other (p < 0.001), negatively correlated with salivary flow rate (p < 0.001), and positively correlated with plaque index (p < 0.05). Salivary Bifidobacteria levels were positively associated with the number of filled (p < 0.001) and decayed (p = 0.036) tooth surfaces and negatively associated with number of teeth (p < 0.001) and salivary flow rate (p = 0.049). In regression analyses, caries experience was significantly associated with only salivary Bifidobacteria (p < 0.001) and yeast (p < 0.001) levels and the individual’s age (p = 0.021). Bifidobacteria should be regarded as caries-associated organisms whose role in the caries process and as markers of caries risk requires further investigation.

Intra-individual diversity and similarity of salivary and faecal microbiota

In the present study, polyphasic analysis [cultivation, combined with the fingerprinting of individual isolates, and denaturing gradient gel electrophoresis (DGGE)] was applied to study whether similar features concerning the diversity and temporal stability of selected bacterial groups could be detected intra-individually in two different niches - the oral cavity and the colon - from ten adult volunteers consuming probiotics. The predominant bacterial microbiota, Clostridium coccoides-Eubacterium rectale group and bifidobacterial populations, were generally stable in salivary and faecal samples, with the greater diversity seen in faeces. Furthermore, different species predominated at the two different sites. Lactobacillus group DGGE profiles were unstable, yet the intra-individual profiles from faecal and salivary samples collected at the same time resembled each other. The ingested probiotic product did not affect the stability of the bacterial groups studied. The culture-based analysis showed that most subjects harboured identical indigenous Lactobacillus genotypes in saliva and faeces (Lactobacillus rhamnosus, Lactobacillus gasseri, Lactobacillus paracasei and Lactobacillus plantarum group). Thus, identical indigenous lactobacilli were able to inhabit both ends of the orogastrointestinal tract, whereas the composition of the other bacterial groups studied varied between the two sites.

Isolation and identification of bifidobacteriaceae from human saliva

Bifidobacteriaceae were isolated from saliva and infected dentine by using a mupirocin-based selective medium. Of the saliva samples, 94% harbored bifids. The mean concentration (+/- the standard error) was 4.46 (+/-0.12) log(10)(CFU per ml + 1), and the predominant isolates were Bifidobacterium dentium, B. longum, Scardovia inopinata, Parascardovia denticolens, and Alloscardovia omnicolens.

Oral adhesion and survival of probiotic and other lactobacilli and bifidobacteria in vitro

INTRODUCTION

Most probiotic products are consumed orally and hence it is feasible that the bacteria in these products may also attach to oral surfaces; however, the effects of these bacteria on the oral ecosystem are mostly unknown. Our aim was to evaluate the oral colonization potential of different probiotic, dairy, and fecal Lactobacillus and Bifidobacterium strains in vitro.

METHODS

The binding of 17 Lactobacillus and seven Bifidobacterium strains to hydroxyapatite and microtitre wells coated with human saliva was tested. Binding of selected strains to human buccal epithelial cells and co-adherence with Fusobacterium nucleatum were also investigated. In addition, the survival in sterilized human whole saliva was examined.

RESULTS

There was a large variation in binding to saliva-coated surfaces and buccal epithelial cells but all strains survived in saliva. The binding pattern of the probiotics did not differ from the binding of the fecal strains. F. nucleatum altered the binding of both the low-binding bifidobacteria and the high-binding lactobacilli.

CONCLUSION

The differences in binding in vitro may indicate that there are also differences in the persistence of the different probiotic strains in the oral cavity in vivo.

Occurrence of the family bifidobacteriaceae in human dental caries and plaque

Despite the constant presence of members of Bifidobacteriaceae in the human oral cavity, few studies of their occurrence in this habitat have been made. The presence and the distribution in human plaque and dental caries of Bifidobacterium dentium, Scardovia inopinata and Parascardovia denticolens, all belonging to the family Bifidobacteriaceae, were studied. The identification to species level was based on morphological and growth type features, fermentation tests, polyacrylamide gel electrophoresis of the soluble proteins and DNA-DNA homology. The three species, isolated on propionic acid trypticase phytone yeast extract medium, were present in 13 out of 19 and in 11 out of 15 subjects examined for dental caries and plaque, respectively. S. inopinata was the species most frequently isolated in dental caries, whereas B. dentium was more numerous in dental plaque. The prevalence of P. denticolens was similar in the two habitats. In conclusion, the prevalence of bifidobacteria species (B. dentium, P. denticolens, S. inopinata) in relation to non-bifidobacteria isolates was significantly different in caries versus plaque samples (p<0.0001; chi2 test).

Identification of oral Actinomyces species using DNA probes

Oral Actinomyces comprise a major segment of both the supra- and subgingival microbiota; however, little is known about the distribution of individual species in different sites or clinical conditions. The purpose of the present investigation was to develop DNA probes for suggested species and genotypes of oral Actinomyces. Whole genomic DNA probes to 12 human oral species and/or serotypes were labeled with digoxigenin and used to seek cross-reactions among the taxa using the checkerboard DNA-DNA hybridization assay. The Actinomyces formed three distinct groups: 1) Actinomyces georgiae, Actinomyces meyeri and Actinomyces odontolyticus serotypes I and II; 2) Actinomyces viscosus and Actinomyces naeslundii serotypes I, II, III and WVA 963; and 3) Actinomyces gerencseriae and Actinomyces israelii. Cross-reactions among taxa were detected and minimized by increasing the temperature of the post-hybridization high-stringency wash to 80 degrees C. Despite the elevation in high stringency wash temperature, cross-reactions among strains of the A. naeslundii/A. viscosus group persisted. Probes for two of the three currently recognized genospecies in this group were prepared by removing the DNA in common between cross-reacting species using subtraction hybridization and polymerase chain reaction. Nine species and genospecies could be clearly separated by a combination of whole genomic and subtraction hybridization probes and by increasing the high-stringency wash temperature. A total of 195 fresh isolates of Actinomyces were grouped in a blind study using DNA probes and separately by SDS-PAGE protein profiles. Concordance between the two methods was 97.3%. The probes and hybridization conditions were tested for their ability to detect the Actinomyces species and genospecies in samples of supragingival and subgingival plaque from periodontitis subjects using checkerboard DNA-DNA hybridization. The probes detected the species in samples of supragingival and subgingival plaque. We concluded that whole genomic and subtraction hybridization DNA probes facilitate the detection and enumeration of species and genospecies of Actinomyces in plaque samples.

Characterization of Actinomyces with genomic DNA fingerprints and rRNA gene probes

Cellular DNA from 25 Actinomyces naeslundii and Actinomyces viscosus strains belonging to the 7 taxonomic clusters of Fillery et al. (1978) and several unclustered strains was obtained by enzymatic and N-lauroylsarcosine/guanidine isothiocyanate treatment of whole cells, followed by extraction of the nucleic acid. The DNA samples were digested with restriction endonucleases BamHI or PvuII, and agarose gel electrophoresis was used to obtain DNA fingerprints. The DNA fragments were subjected to Southern blot hybridization with a digoxigenin-labeled cDNA probe transcribed from Escherichia coli 16S and 23S rRNA. The patterns of bands from genomic (DNA fingerprints) and rDNA fingerprints (ribotypes) were used for comparison between the taxonomic cluster strains and strains within clusters. Representative strains from each taxonomic cluster provided different BamHI DNA fingerprints and ribotype patterns with 3 to 9 distinct bands. Some strains within a cluster showed identical ribotype patterns with both endonucleases (A. naeslundii B120 and A. naeslundii B102 from cluster 3), while others showed the same pattern with BamHI but a different pattern with PvuII (A. naeslundii ATCC 12104 and 398A from cluster 5). A viscosus ATCC 15987 (cluster 7) and its parent strain T6 yielded identical fingerprint and ribotype patterns. The genomic diversity revealed by DNA fingerprinting and ribotyping demonstrates that these techniques, which do not require phenotypic expression, are suited for study of the oral ecology of the Actinomyces, and for epidemiological tracking of specific Actinomyces strains associated with caries lesions and sites of periodontal destruction.

Immunoglobulins in milk from cows immunized with oral strains of Actinomyces, Prevotella, Porphyromonas, and Fusobacterium

Immunization of pregnant cows with bacteria leads to the presence of high concentrations of specific antibodies in colostrum and milk. A total of 14 cows was immunized with single strains of heat-killed oral bacteria or pools of strains of Actinomyces, Porphyromonas, Prevotella, and Fusobacterium. Two cows were treated with adjuvant alone. The mean percentages of IgG1, IgG2, IgM, and IgA in all of the milks were 83.8, 3.8, 9.3, and 3.1, respectively. ELISA and whole cell agglutination assays demonstrated high titers in the milks from the cows immunized with either individual strains or the bacterial pools. The highest titers determined by ELISA belonged to the IgG1 isotype and in several milks were 64-fold greater than titers in milk from cows treated with adjuvant alone. The concentrations of all antibodies and the titers determined by ELISA and whole cell agglutination assays markedly decreased from the first to the sixth milkings. The functional specificity of the antibodies was demonstrated by agglutination tests against a wide range of bacteria including members of Actinomyces, Fusobacterium, Porphyromonas, Prevotella, Streptococcus, Eubacterium, Propionibacterium, Peptostreptococcus, Bacteroides, Actinobacillus, Haemophilus, Capnocytophaga, and Wolinella. Minimal cross-reactions with bacteria in other genera were observed with all of the milks. High-titer milk preparations have been obtained from immunized cows, and the capacity of the bovine antibodies to agglutinate target bacteria indicates their potential usefulness in oral passive immunization studies.

Distribution of antigenic determinants between Actinomyces viscosus and Actinomyces naeslundii

A total of 18 monoclonal antibodies was raised against whole cells of Actinomyces viscosus and Actinomyces naeslundii. The monoclonal antibodies were used to determine the cross-reacting patterns among 26 strains of these species. Eleven different antigenic determinants were found. The specificity profiles of the antibodies indicated that the antigenic determinants of A. viscosus and A. naeslundii were arranged in a complicated mosaic. Extensive cross-reactions occurred between A. viscosus strains and strains of "typical" and "atypical" A. naeslundii. However, cross-reactions were rare between the two groups of A. naeslundii. A. viscosus appears to occupy a "middle position" between the two A. naeslundii groups. In addition to their value in seroclassification, some of the monoclonal antibodies were found to be useful in the identification of these species. One monoclonal antibody appeared to be selective for the "typical" A. naeslundii group. A. viscosus and "atypical" A. naeslundii-specific antibodies were also found, though they did not label every strain in their respective clusters. A. viscosus detection might be improved if mixtures of monoclonal antibodies were used.

Artificial caries produced by different oral bacterial cultures incubated with bovine dental enamel

Early caries-like lesions were formed in enamel incubated in glucose broths inoculated with different cultures of oral bacteria. Analysis of the broths by gas chromatography revealed, after appropriate incubation, the presence of lactic, succinic, formic, acetic, propionic, isobutyric, n-butyric, isovaleric or n-caproic or mixtures of these acid catabolites. Subsurface lesions formed with all acids and mixtures providing that the terminal pH dropped less than or equal to 5.6. However, the processes conformed in part only with the idealized simple diffusion phenomenon for caries formation, indicating the presence of other factors which could affect the production of lesions in biological systems.