Fretibacterium sp. human oral taxon 360 is a novel biomarker for periodontitis screening in the Japanese population

Exploring oral bacterial compositional network in two oral disease groups using a convergent approach of NGS-molecular diagnostics

BACKGROUND

Since most of the commonly known oral diseases are explained in link with balance of microbial community, an accurate bacterial taxonomy profiling for determining bacterial compositional network is essential. However, compared to intestinal microbiome, research data pool related to oral microbiome is small, and general 16S rRNA screening method has a taxonomy misclassification issue in confirming complex bacterial composition at the species level.

OBJECTIVE

Present study aimed to explore bacterial compositional networks at the species level within saliva of 39 oral disease patients (Dental Caries group: n = 26 and Periodontitis group: n = 13) through comparison with public Korean-specific healthy oral microbiome data.

METHODS

Here, we applied comprehensive molecular diagnostics based on qRT-PCR and Sanger sequencing methods to complement the technical limitations of NGS-based 16S V3-V4 amplicon sequencing technology.

RESULTS

As a result of microbiome profiling at the genus level, relative frequencies of many nitrate-reducing bacteria within each oral disease group were found to be significantly low compared to the healthy group. In addition, the molecular diagnostics-based bacterial identification method allowed the determination of the correct taxonomy of screened primary colonizers (Streptococcus and Actinomyces unclassification clusters) for each oral disease. Finally, as with the results of microbiome profiling at the genus level, many core-species classified within the saliva of each oral disease group were also related to nitrate-reduction, and it was estimated that various pathogens associated with each disease formed a bacterial network with the core-species.

CONCLUSION

Our study introduced a novel approach that can compensate for the difficulty of identifying an accurate bacterial compositional network at the species level due to unclear taxonomy classification by using the convergent approach of NGS-molecular diagnostics. Ultimately, we suggest that our experimental approach and results could be potential reference materials for researchers who intend to prevent oral disease by determining the correlation between oral health and bacterial compositional network according to the changes in the relative frequency for nitrate-reducing species.

Characterization of the Hoof Bacterial Communities of Active Digital Dermatitis Lesions in Feedlot Cattle

Digital dermatitis (DD) is a costly hoof infection, causing lameness and pain in feedlot cattle. DD lesions can develop nonlinearly through a series of clinical stages, which can be classified by Dopfer's M-stage scoring system. This widely adopted lesion scoring system recognizes five DD stages, where M1 (early lesion), M2 (acute ulcerative lesion), and M4.1 (chronic proliferative lesion with new developing lesion) are considered active but separate stages of the disease. This study assessed the skin surface microbiota of the active DD lesions of feedlot cattle. The DD lesions from three commercial feedlots were swabbed and then scored according to Dopfer's M-stage scoring system. Swab samples were collected from 12 M2- and 15 M4.1-stage lesions. A total of 21 control swab samples from healthy contralateral feet (DD control) were classified as stage M0. An additional six skin swabs (M0) were collected from completely healthy (CH control) cattle with no lesions. The bacterial communities of active DD lesions (M2 and M4.1) and healthy skin (M0) were profiled using 16S amplicon sequencing. Diversity analyses showed that the hoof bacterial communities of M2 and M4.1 lesions were each distinct from those of M0 skin. However, the bacterial communities between the two active lesion stages were not different from each other. A significant increase in the relative abundance of Spirochaetota and Fusobacteriota and an overall decrease in bacterial diversity contributed to the altered bacterial communities in M2 and M4.1 lesions compared to those of healthy skin (M0). Although stages M2 and M4.1 are considered clinically different stages, the lesion-associated bacterial community is similar between the two active stages.

Influence of Gallic Acid-Containing Mouth Spray on Dental Health and Oral Microbiota of Healthy Dogs: A Pilot Study

The pilot study aimed to investigate the effects of GAMS on oral microbiota in healthy dog subjects. Thirty-eight dogs were recruited and randomly allocated to the placebo (n = 19) and treatment groups (n = 19). The dogs were treated with mouth spray once daily for 42 days. The changes in the gingival index (GI), plaque index (PI), and calculus index (CI) were measured at baseline (day 0) and end of the study (42nd day). The changes in the oral microbial composition of representative dogs (placebo, n = 7; and treatment, n = 7) were also evaluated at baseline and end of the study. Oral microbial composition was assessed by sequencing. The sequences were annotated using the QIIME 2.0^TM. The GI, PI, and CI indexes were reduced after the GAMS usage. The abundance of the commensal bacterial phylum Actinobacteria and Chloroflexi, genera Frederiksenia, and Bergeyella was improved after six weeks of GAMS usage. GAMS reduced the pathogenic bacterial species, including Neisseria sp., Desulfobulbus sp., Capnocytophaga canis, and Corynebacterium mustelae. Moreover, some pathogenic bacterial abundances were increased at the end of the study. All the microbial variations were observed within the group. The inter-group analysis revealed that the changes were unrelated to GAMS usage. Further studies need to be carried out using more experimental subjects to confirm the effectiveness of GAMS. More metagenomic data are required to evidence the GMAS impact on the oral microbiome of healthy dogs.

The Potential of a Saliva Test for Screening of Alveolar Bone Resorption

Oral health screening is important for maintaining and improving quality of life. The present study aimed to determine whether patients with a certain level of alveolar bone resorption could be screened by salivary bacterial test along with their background information. Saliva samples were collected from 977 Japanese patients, and the counts of each red-complex, that is, Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia, were measured using quantitative polymerase chain reaction analysis. Mean bone crest levels (BCLs) were measured using a full-mouth periapical radiograph. Multiple logistic regression analysis was used to determine associations between BCLs (1.5-4.0 mm in 0.5 mm increments) and explanatory variables, such as the number of each red-complex bacteria and the patients' age, sex, number of teeth, stimulated saliva volume, and smoking habits. When the cutoff BCL value was set at 3.0 mm, the area under the curve, sensitivity, and specificity values were optimal at 0.86, 0.82, and 0.76, respectively. In addition, all tested explanatory variables, except sex and T. denticola count, were significantly associated with BCLs according to a likelihood ratio test (p < 0.05). Additionally, the odds ratio (OR) was substantially increased when a patient was >40 years old and the bacterial count of P. gingivalis was >10⁷ cells/µL (OR: >6). Thus, P. gingivalis count and patients' background information were significantly associated with the presence of a certain amount of bone resorption, suggesting that it may be possible to screen bone resorption without the need for radiography or oral examination.

The making of the oral microbiome in Agta hunter-gatherers

Ecological and genetic factors have influenced the composition of the human microbiome during our evolutionary history. We analysed the oral microbiota of the Agta, a hunter-gatherer population where some members have adopted an agricultural diet. We show that age is the strongest factor modulating the microbiome, probably through immunosenescence since we identified an increase in the number of species classified as pathogens with age. We also characterised biological and cultural processes generating sexual dimorphism in the oral microbiome. A small subset of oral bacteria is influenced by the host genome, linking host collagen genes to bacterial biofilm formation. Our data also suggest that shifting from a fish/meat diet to a rice-rich diet transforms their microbiome, mirroring the Neolithic transition. All of these factors have implications in the epidemiology of oral diseases. Thus, the human oral microbiome is multifactorial and shaped by various ecological and social factors that modify the oral environment.

Analysis of subgingival micro-organisms based on multi-omics and Treg/Th17 balance in type 2 diabetes with/without periodontitis

Type 2 diabetes mellitus (T2DM) and periodontitis are common and interrelated diseases, resulting in altered host response microbiota. The subgingival micro-organisms play a key role in periodontitis pathogenesis. To assess the shift of subgingival microbiome and metabolome in T2DM, we performed an analysis of the subgingival microbiome in patients with T2DM (n = 20) compared with non-diabetes (ND) subjects (n = 21). Furthermore, patients were subdivided into 10 T2DM with periodontitis (DP), 10 T2DM without periodontitis (DNP), 10 periodontitis (P), and 11 healthy control (H) groups. 16SrRNA gene sequencing combined with ultra high-performance liquid chromatography-mass spectrometry (UHPLC-MS) based metabolomics was performed in all participants. T lymphocyte immunity was analyzed by flow cytometry. Furthermore, the network relationship among subgingival micro-organisms, metabolites, blood glucose level, and T lymphocyte immunity were analyzed. The results showed that the difference of the subgingival microbiome from healthy to periodontitis status was less prominent in T2DM compared with ND, though the clinical signs of disease were similar. The bacteria Eubacterium nodatum group, Filifactor, Fretibacterium, Peptostreptococcus, and Desulfovibrio, amongst others, may be important in the pathopoiesia of periodontitis in the T2DM state. In addition, some dominant bacteria showed network relationships. The Treg/Th17 ratio was lower in the DP and DNP groups than in the P and H groups-though that of P was lower than for H. The percentage of CD4+/CD8+ PD1 and CD8+ PDL1 was higher in the DP and DNP groups than in the H group; the percentage of CD8+ PDL1 was higher in the DP than P groups. Subgingival micro-organisms in periodontitis had a significant metabolic shift in terms of their signature metabolites. Butyrate metabolism and phenylalanine metabolism may play a role in the pathogenesis of periodontitis with/without T2DM. Specifically, biphenyl degradation, tryptophan metabolism, and the two-component system may play important roles in periodontitis with T2DM. Lastly, the network relationship among subgingival micro-organisms, metabolites, blood glucose level, and T lymphocyte immunity were unbalanced. This study identified the changes in the subgingival microbiome associated with periodontitis in T2DM, as well as the associated network between bacterial flora, metabolism dysbiosis, and immune regulation.

Characterization of the oral and fecal microbiota associated with atopic dermatitis in dogs selected from a purebred Shiba Inu colony

Atopic dermatitis (AD) is a chronic and relapsing multifactorial inflammatory skin disease that also affects dogs. The oral and gut microbiota are associated with many disorders, including allergy. Few studies have addressed the oral and gut microbiota in dogs, although the skin microbiota has been studied relatively well in these animals. Here, we studied the AD-associated oral and gut microbiota in 16 healthy and nine AD dogs from a purebred Shiba Inu colony. We found that the diversity of the oral microbiota was significantly different among the dogs, whereas no significant difference was observed in the gut microbiota. Moreover, a differential abundance analysis detected the Family_XIII_AD3011_group (Anaerovoracaceae) in the gut microbiota of AD dogs; however, no bacterial taxa were detected in the oral microbiota. Third, the comparison of the microbial co-occurrence patterns between AD and healthy dogs identified differential networks in which the bacteria in the oral microbiota that were most strongly associated with AD were related with human periodontitis, whereas those in the gut microbiota were related with dysbiosis and gut inflammation. These results suggest that AD can alter the oral and gut microbiota in dogs.

Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease

Candidate phyla radiation (CPR) is an emerging division of the bacterial domain within the human microbiota. Still poorly known, these microorganisms were first described in the environment in 1981 as "ultramicrobacteria" with a cell volume under 0.1 μm³ and were first associated with the human oral microbiota in 2007. The evolution of technology has been paramount for the study of CPR within the human microbiota. In fact, since these ultramicrobacteria have yet to be axenically cultured despite ongoing efforts, progress in imaging technology has allowed their observation and morphological description. Although their genomic abilities and taxonomy are still being studied, great strides have been made regarding their taxonomic classification, as well as their lifestyle. In addition, advancements in next-generation sequencing and the continued development of bioinformatics tools have allowed their detection as commensals in different human habitats, including the oral cavity and gastrointestinal and genital tracts, thus highlighting CPR as a nonnegligible part of the human microbiota with an impact on physiological settings. Conversely, several pathologies present dysbiosis affecting CPR levels, including inflammatory, mucosal, and infectious diseases. In this exhaustive review of the literature, we provide a historical perspective on the study of CPR, an overview of the methods available to study these organisms and a description of their taxonomy and lifestyle. In addition, their distribution in the human microbiome is presented in both homeostatic and dysbiotic settings. Future efforts should focus on developing cocultures and, if possible, axenic cultures to obtain isolates and therefore genomes that would provide a better understanding of these ultramicrobacteria, the importance of which in the human microbiome is undeniable.

Analysis of subgingival microbiota in monozygotic twins with different severity and progression risk of periodontitis

The study aims to reveal the composition of subgingival bacteria in monozygotic twins with discordant in severity and progression risk of periodontitis. Microbiome analysis indicated that most bacteria were heritable but differed in their abundance and immune response. The dysbiotic bacteria can be considered as risk markers for periodontitis progression.

The bacteriome of the oral cavity in healthy dogs and dogs with periodontal disease

OBJECTIVE

To compare the bacteriome of the oral cavity in healthy dogs and dogs with various stages of periodontal disease.

ANIMALS

Dogs without periodontal disease (n = 12) or with mild (10), moderate (19), or severe (10) periodontal disease.

PROCEDURES

The maxillary arcade of each dog was sampled with a sterile swab, and swabs were submitted for next-generation DNA sequencing targeting the V1-V3 region of the 16S rRNA gene.

RESULTS

714 bacterial species from 177 families were identified. The 3 most frequently found bacterial species were Actinomyces sp (48/51 samples), Porphyromonas cangingivalis (47/51 samples), and a Campylobacter sp (48/51 samples). The most abundant species were P cangingivalis, Porphyromonas gulae, and an undefined Porphyromonas sp. Porphyromonas cangingivalis and Campylobacter sp were part of the core microbiome shared among the 4 groups, and P gulae, which was significantly enriched in dogs with severe periodontal disease, was part of the core microbiome shared between all groups except dogs without periodontal disease. Christensenellaceae sp, Bacteroidales sp, Family XIII sp, Methanobrevibacter oralis, Peptostreptococcus canis, and Tannerella sp formed a unique core microbiome in dogs with severe periodontal disease.

CONCLUSIONS AND CLINICAL RELEVANCE

Results highlighted that in dogs, potential pathogens can be common members of the oral cavity bacteriome in the absence of disease, and changes in the relative abundance of certain members of the bacteriome can be associated with severity of periodontal disease. Future studies may aim to determine whether these changes are the cause or result of periodontal disease or the host immune response.

Rumen Fermentation-Microbiota-Host Gene Expression Interactions to Reveal the Adaptability of Tibetan Sheep in Different Periods

Simple Summary

The Qinghai-Tibet Plateau has a unique ecological environment, involving high altitude, low oxygen levels, strong ultraviolet rays, and severe imbalances in seasonal forage supply, which poses a serious threat to the livestock that feeds on natural pastures to maintain their survival. We have carried out a long-term follow-up study on rumen fermentation characteristics, the microbiota, and rumen epithelial gene expression of local Tibetan sheep. Correlation analysis showed that there were interactions among rumen fermentation characteristics, the microbiota, and host gene expression, mainly by adjusting the amino acid metabolism pathway and energy metabolism pathway to improve energy utilization. At the same time, we adjusted the balance of the rumen “core microbiota”, which was regulated to promote the development of rumen and maintain the homeostasis of rumen environment (which relies Tibetan sheep can better adapt to the harsh environment in different periods of the Qinghai-Tibet Plateau). This provides a theoretical basis for the breeding and management of Tibetan sheep on the Qinghai-Tibet Plateau.

Abstract

As an important ruminant on the Qinghai-Tibet Plateau, Tibetan sheep can maintain their population reproduction rate in the harsh high-altitude environment of low temperature and low oxygen, which relies on their special plateau adaptations mechanism that they have formed for a long time. Microbiomes (known as “second genomes”) are closely related to the nutrient absorption, adaptability, and health of the host. In this study, rumen fermentation characteristics, the microbiota, and rumen epithelial gene expression of Tibetan sheep in various months were analyzed. The results show that the rumen fermentation characteristics of Tibetan sheep differed in different months. The total SCFAs (short-chain fatty acids), acetate, propionate, and butyrate concentrations were highest in October and lowest in June. The CL (cellulase) activity was highest in February, while the ACX (acid xylanase) activity was highest in April. In addition, the diversity and abundance of rumen microbes differed in different months. Bacteroidetes (53.4%) and Firmicutes (27.4%) were the dominant phyla. Prevotella_1 and Rikenellaceae_RC9_gut_group were the dominant genera. The abundance of Prevotella_1 was highest in June (27.8%) and lowest in December (17.8%). In addition, the expression of CLAUDIN4 (Claudin-4) and ZO1 (Zonula occludens 1) was significantly higher in April than in August and December, while the expression of SGLT1 (Sodium glucose linked transporter 1) was highest in August. Correlation analysis showed that there were interactions among rumen fermentation characteristics, the microbiota, and host gene expression, mainly by adjusting the amino acid metabolism pathway and energy metabolism pathway to improve energy utilization. At the same time, we adjusted the balance of the rumen “core microbiota” to promote the development of rumen and maintain the homeostasis of rumen environment, which makes Tibetan sheep better able to adapt to the harsh environment in different periods of the Qinghai-Tibet Plateau.

Study of microbiocenosis of canine dental biofilms

Dental biofilm is a complex microbial community influenced by many exogenous and endogenous factors. Despite long-term studies, its bacterial composition is still not clearly understood. While most of the research on dental biofilms was conducted in humans, much less information is available from companion animals. In this study, we analyzed the composition of canine dental biofilms using both standard cultivation on solid media and amplicon sequencing, and compared the two approaches. The 16S rRNA gene sequences were used to define the bacterial community of canine dental biofilm with both, culture-dependent and culture-independent methods. After DNA extraction from each sample, the V3-V4 region of the 16S rRNA gene was amplified and sequenced via Illumina MiSeq platform. Isolated bacteria were identified using universal primers and Sanger sequencing. Representatives of 18 bacterial genera belonging to 5 phyla were isolated from solid media. Amplicon sequencing largely expanded this information identifying in total 284 operational taxonomic units belonging to 10 bacterial phyla. Amplicon sequencing revealed much higher diversity of bacteria in the canine dental biofilms, when compared to standard cultivation approach. In contrast, cultured representatives of several bacterial families were not identified by amplicon sequencing.

The prevalence of novel periodontal pathogens and bacterial complexes in Stage II generalized periodontitis based on 16S rRNA next generation sequencing

Objective:

To define the subgingival microbial profile associated with Stage II generalized periodontitis using next-generation sequencing and to determine the relative abundance of novel periodontal pathogens and bacterial complexes.

Methodology:

Subgingival biofilm samples were collected from 80 subjects diagnosed with Stage II generalized periodontitis. Bacterial DNA was extracted, and 16S rRNA-based bacterial profiling via next-generation sequencing was carried out. The bacterial composition and diversity of microbial communities based on the age and sex of the patients were analyzed. The bacterial species were organized into groups: bacterial complexes (red, orange, purple, yellow, and green), novel periodontal pathogens, periodontal health-related species, and unclassified periodontal species. The results were analyzed and statistically evaluated.

Results:

The highest number of bacteria belonged to the phylum Bacteroidetes and Firmicutes. In terms of relative abundance, the orange complex represented 18.99%, novel bacterial species (Fretibacterium spp. and Saccharibacteria spp.) comprised 17.34%, periodontal health-related species accounted for 16.75% and unclassified periodontal species represented (Leptotrichia spp. and Selenomonas spp.) 15.61%. Novel periodontal pathogens had outweighed the periodontal disease-related red complex (5.3%). The one-sample z-test performed was statistically significant at p<0.05. The Beta diversity based on the unweighted UniFrac distance at the species level demonstrated a total variance of 15.77% based on age and 39.19% on sex, which was not statistically significant.

Conclusion:

The bacterial species corresponding to the disease-related orange complex and novel periodontal pathogens are predominant in Stage II generalized periodontitis.

Comparative analysis of oral microbiome from Zang and Han populations living at different altitudes

OBJECTIVES

The aim of this study was to obtain greater insight into the environmental and genetic factors affecting the oral microbiome.

DESIGN

To this end, we investigated the oral microbiome composition in Han and Zang populations living at different altitudes. The saliva microbiome in 115 individuals from Zang and Han populations living at different altitudes was analyzed using the 16 s rRNA gene sequencing method on the Illumina MiSeq platform. The dominant species in the oral microbiome were verified by quantitative real-time polymerase chain reaction (qPCR) analysis.

RESULTS

The Han population, living at an altitude of 500 m, had higher microbiome diversity than the Zang population living at altitudes of 3000-4000 m. People living at 3000 m had a higher relative abundance of Leptothrix genus, but people living at 500 m had a higher relative abundance of Capnocytophaga genus according to Lefse difference analysis (P < 0.05). Compared to the Zang population, the Han population had higher relative abundances of Porphyromonas and Treponema genus organisms, especially Porphyromonas (P < 0.001). qPCR analysis confirmed that people living at high altitudes had the highest relative abundance of Porphyromonas gingivalis (P < 0.01).

CONCLUSIONS

This study showed that both genetics and the environment had significant influences on the oral microbiome composition. The study proposed a meaningful research direction to explore the relationship between different ethnic and altitude groups and oral diseases, such as periodontal diseases.

Unculturable and culturable periodontal-related bacteria are associated with periodontal inflammation during pregnancy and with preterm low birth weight delivery

Recent studies revealed culturable periodontal keystone pathogens are associated with preterm low birth weight (PLBW). However, the oral microbiome is also comprised of hundreds of 'culture-difficult' or 'not-yet-culturable' bacterial species. To explore the potential role of unculturable and culturable periodontitis-related bacteria in preterm low birth weight (PLBW) delivery, we recruited 90 pregnant women in this prospective study. Periodontal parameters, including pocket probing depth, bleeding on probing, and clinical attachment level were recorded during the second trimester and following interviews on oral hygiene and lifestyle habits. Saliva and serum samples were also collected. After delivery, birth results were recorded. Real-time PCR analyses were performed to quantify the levels of periodontitis-related unculturable bacteria (Eubacterium saphenum, Fretibacterium sp. human oral taxon(HOT) 360, TM7 sp. HOT 356, and Rothia dentocariosa), and cultivable bacteria (Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum and Prevotella intermedia) in saliva samples. In addition, ELISA analyses were used to determine the IgG titres against periodontal pathogens in serum samples. Subjects were categorized into a Healthy group (H, n = 20) and periodontitis/gingivitis group (PG, n = 70) according to their periodontal status. The brushing duration was significantly lower in the PG group compared to the H group. Twenty-two of 90 subjects delivered PLBW infants. There was no significant difference in periodontal parameters and serum IgG levels for periodontal pathogens between PLBW and healthy delivery (HD) groups. However, ordinal logistic regression analysis revealed that a higher abundance of Treponema denticola, Prevotella intermedia, Fretibacterium sp. HOT360 and lower levels of Rothia dentocariosa were significantly associated with the presence of periodontal disease during pregnancy. Moreover, the amount of Eubacterium saphenum in saliva and serum IgG against Aggregatibacter actinomycetemcomitans were negatively correlated with PLBW. Taken together, unculturable periodontitis-associated bacteria may play an important role both in the presence of periodontal inflammation during pregnancy and subsequent PLBW.

Significant Short-Term Shifts in the Microbiomes of Smokers With Periodontitis After Periodontal Therapy With Amoxicillin & Metronidazole as Revealed by 16S rDNA Amplicon Next Generation Sequencing

The aim of this follow-up study was, to compare the effects of mechanical periodontal therapy with or without adjunctive amoxicillin and metronidazole on the subgingival microbiome of smokers with periodontitis using 16S rDNA amplicon next generation sequencing. Fifty-four periodontitis patients that smoke received either non-surgical periodontal therapy with adjunctive amoxicillin and metronidazole (n = 27) or with placebos (n = 27). Subgingival plaque samples were taken before and two months after therapy. Bacterial genomic DNA was isolated and the V4 hypervariable region of the bacterial 16S rRNA genes was amplified. Up to 96 libraries were normalized and pooled for Illumina MiSeq paired-end sequencing with almost fully overlapping 250 base pairs reads. Exact ribosomal sequence variants (RSVs) were inferred with DADA2. Microbial diversity and changes on the genus and RSV level were analyzed with non-parametric tests and a negative binomial regression model, respectively. Before therapy, the demographic, clinical, and microbial parameters were not significantly different between the placebo and antibiotic groups. Two months after the therapy, clinical parameters improved and there was a significantly increased dissimilarity of microbiomes between the two groups. In the antibiotic group, there was a significant reduction of genera classified as Porphyromonas, Tannerella, and Treponema, and 22 other genera also decreased significantly, while Selenomonas, Capnocytophaga, Actinomycetes, and five other genera significantly increased. In the placebo group, however, there was not a significant decrease in periodontal pathogens after therapy and only five other genera decreased, while Veillonella and nine other genera increased. We conclude that in periodontitis patients who smoke, microbial shifts occurred two months after periodontal therapy with either antibiotics or placebo, but genera including periodontal pathogens decreased significantly only with adjunctive antibiotics.

The periodontopathic bacteria in placenta, saliva and subgingival plaque of threatened preterm labor and preterm low birth weight cases: a longitudinal study in Japanese pregnant women

OBJECTIVES

This study determined the quantity of periodontopathic bacteria in saliva, subgingival plaque, and placenta on the threatened preterm labor (TPL) and preterm low birth weight (PLBW) subjects in order to identify specific periodontal pathogens with high association to adverse pregnancy outcomes.

METHODS

We used real-time PCR with TaqMan probe and ELISA to detect the amount of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum, and Prevotella intermedia in subgingival plaque, saliva, and placenta tissue, in addition to serum IgG titers against these bacteria in 28 patients with TPL and 36 healthy pregnant women.

RESULTS

Thirteen of 64 births delivered PLBW infants. All 6 periodontopathic bacteria were detected in the placenta samples. The amount of F. nucleatum and detection frequency of T. denticola in placental samples was significantly higher in the TPL group than in the healthy group. Meanwhile, the age, anti-P. gingival IgG in serum, amount of P. gingivalis and T. forsythia in plaque samples, detection frequency of P. intermedia in saliva, and percentage of pocket probing depth ≥ 5 mm were higher in TPL-PLBW births than those in TPL-Healthy delivery (HD) group and/or in H-HD group. Ordinal logistic regression analysis revealed that the presence of F. nucleatum in placental tissues was significantly associated with TPL, while the maternal age was significantly associated with PLBW in TPL.

CONCLUSION

Our findings suggested all 6 bacteria may access the placenta. The increased presence of F. nucleatum in placenta might be related to TPL, while advanced maternal age might be associated with PLBW in TPL.

CLINICAL RELEVANCE

Periodontal therapy should be applied to reduce the deep periodontal pocket sites and the colonization of periodontal pathogens in high-risk population.

Profiling the Salivary microbiome of the Qatari population

BACKGROUND

The role of the human microbiome in human health and disease has been studied in various body sites. However, compared to the gut microbiome, where most of the research focus is, the salivary microbiome still bears a vast amount of information that needs to be revealed. This study aims to characterize the salivary microbiome composition in the Qatari population, and to explore specific microbial signatures that can be associated with various lifestyles and different oral conditions.

MATERIALS AND METHODS

We characterized the salivary microbiome of 997 Qatari adults using high-throughput sequencing of the V1-V3 region of the 16S rRNA gene.

RESULTS

In this study, we have characterized the salivary microbiome of 997 Qatari participants. Our data show that Bacteroidetes, Firmicutes, Actinobacteria and Proteobacteria are the common phyla isolated from the saliva samples, with Bacteroidetes being the most predominant phylum. Bacteroidetes was also more predominant in males versus females in the study cohort, although differences in the microbial diversity were not statistically significant. We also show that, a lower diversity of the salivary microbiome is observed in the elderly participants, with Prevotella and Treponema being the most significant genera. In participants with oral conditions such as mouth ulcers, bleeding or painful gum, our data show that Prevotella and Capnocytophaga are the most dominant genera as compared to the controls. Similar patterns were observed in participants with various smoking habits as compared to the non-smoking participants. Our data show that Streptococcus and Neisseria are more dominant among denture users, as compared to the non-denture users. Our data also show that, abnormal oral conditions are associated with a reduced microbial diversity and microbial richness. Moreover, in this study we show that frequent coffee drinkers have higher microbial diversity compared to the non-drinkers, indicating that coffee may cause changes to the salivary microbiome. Furthermore, tea drinkers show higher microbial richness as compared to the non-tea drinkers.

CONCLUSION

This is the first study to assess the salivary microbiome in an Arab population, and one of the largest population-based studies aiming to the characterize the salivary microbiome composition and its association with age, oral health, denture use, smoking and coffee-tea consumption.

An optimised saliva collection method to produce high-yield, high-quality RNA for translational research

Saliva represents an ideal matrix for diagnostic biomarker development as it is readily available and requires no invasive collection procedures. However, salivary RNA is labile and rapidly degrades. Previous attempts to isolate RNA from saliva have yielded poor quality and low concentrations. Here we compare collection and processing methods and propose an approach for future studies. The effects of RNA stabilisers, storage temperatures, length of storage and fasting windows were investigated on pooled saliva samples from healthy volunteers. Isolated RNA was assessed for concentration and quality. Bacterial growth was investigated through RT-PCR using bacterial and human primers. Optimal conditions were implemented and quality controlled in a clinical setting. The addition of RNAlater increased mean RNA yield from 4912 ng/μl to 15,473 ng and RNA Integrity Number (RIN) from 4.5 to 7.0. No significant changes to RNA yield were observed for storage at room temperature beyond 1 day or at -80 °C. Bacterial growth did not occur in samples stored at ambient temperature for up to a week. There was a trend towards higher RNA concentration when saliva was collected after overnight fasting but no effect on RIN. In the clinic, RNA yields of 6307 ng and RINs of 3.9 were achieved, improving on previous reports. The method we describe here is a robust, clinically feasible saliva collection method using preservative that gives high concentrations and improved RINs compared to saliva collected without preservative.

The salivary microbiota in health and disease

The salivary microbiota (SM), comprising bacteria shed from oral surfaces, has been shown to be individualized, temporally stable and influenced by diet and lifestyle. SM reflects local bacterial alterations of the supragingival and subgingival microbiota, and periodontitis and dental-caries associated characteristics of SM have been reported. Also, data suggest an impact of systemic diseases on SM as demonstrated in patients with a wide variety of systemic diseases including diabetes, cancer, HIV and rheumatoid arthritis. The presence of systemic diseases seems to influence salivary levels of specific bacterial species, as well as α- and β-diversity of SM. The composition of SM might thereby potentially mirror oral and general health status. The contentious development of advanced molecular techniques such as metagenomics, metatranscriptomics and metabolomics has enabled the possibility to address bacterial functions rather than presence in microbial samples. However, at present only a few studies have employed such techniques on SM to reveal functional and metabolic characteristics in oral health and disease. Future studies are therefore warranted to illuminate the possible impact of metabolic functions of SM on oral and general health status. Ultimately, such an approach has the possibility to reveal novel and personalized therapeutic avenues in oral and general medicine.

Periodontal pathogens and clinical parameters in chronic periodontitis

The use of next generation sequencing and bioinformatics has revealed the complexity and richness of the human oral microbiota. While some species are well known for their periodontal pathogenicity, the molecular-based approaches for bacterial identification have raised awareness about new putative periodontal pathogens. Although they are found increased in case of periodontitis, there is currently a lack of data on their interrelationship with the periodontal measures. We processed the sequencing data of the subgingival microbiota of 75 patients with hemochromatosis and chronic periodontitis in order to characterize the well-described and newly identified subgingival periodontal pathogens. We used correlation tests and statistical models to assess the association between the periodontal pathogens and mean pocket depth, and to determine the most relevant bacterial biomarkers of periodontitis severity. Based on correlation test results, nine taxa were selected and included in the statistical models. The multiple linear regression models adjusted for systemic and periodontal clinical variables showed that mean pocket depth was negatively associated with Aggregatibacter and Rothia, and positively associated with Porphyromonas. Furthermore, a bacterial ratio that was previously described as a signature of dysbiosis in periodontitis (%Porphyromonas+%Treponema+%Tannerella)/(%Rothia+%Corynebacterium) was the most significant predictor. In this specific population, we found that the best model in predicting the mean pocket depth was microbial dysbiosis using the dysbiosis ratio taxa formula. While further studies are needed to assess the validity of these results on the general population, such a dysbiosis ratio could be used in the future to monitor the subgingival microbiota.