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

2019 ◽  
Vol 99 (2) ◽  
pp. 159-167 ◽  
Author(s):  
D. Kahharova ◽  
B.W. Brandt ◽  
M.J. Buijs ◽  
M. Peters ◽  
R. Jackson ◽  
...  
Keyword(s):  
Dental Plaque ◽  
Illumina Miseq ◽  
Assessment System ◽  
Oral Microbiome ◽  
Caries Detection ◽  
Oral Microbiota ◽  
Healthy Children ◽  
Microbial Composition ◽  
Time Points ◽  
Over Time

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.

DNA extraction from concrete v2

2021 ◽  
Author(s):  
Anders Kiledal ◽  
Julia A Maresca
Keyword(s):  
Dna Extraction ◽  
Dental Plaque ◽  
Illumina Miseq ◽  
Amplicon Sequencing ◽  
Metagenomic Sequencing ◽  
Sample Analysis ◽  
Larger Sample ◽  
Laboratory Contamination ◽  
Biomass Sample ◽  
Over Time

This is a protocol for extracting DNA from concrete, based on the protocol developed by L. S. Weyrich, et al. for extraction of DNA from ancient calcified dental plaque. We have scaled it up for larger sample sizes and made some additional modifications for the chemistry of concrete. DNA extracted using this method is suitable for metagenomic sequencing by Illumina MiSeq and NextSeq, as well as amplicon sequencing. This protocol should yield 10 ng to 5 μg DNA per 10 g of concrete, depending on the age and integrity of the sample. Reference: L. S. Weyrich et al., Laboratory contamination over time during low-biomass sample analysis. Mol. Ecol. Resour. 19, 982–996 (2019).

scholarly journals Comparing dental plaque microbiome diversity of extrinsic black stain in the primary dentition using Illumina MiSeq sequencing technique

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Lulu Chen ◽  
Qiong Zhang ◽  
Yan Wang ◽  
Keke Zhang ◽  
Jing Zou
Keyword(s):  
Relative Abundance ◽  
Dental Plaque ◽  
Illumina Miseq ◽  
Primary Dentition ◽  
Tooth Surface ◽  
Oral Microbiota ◽  
Illumina Miseq Sequencing ◽  
Miseq Sequencing ◽  
Cross Sectional ◽  
Sequencing Technique

Abstract Background Extrinsic black stain (EBS) is characterized by discrete dark dots or lines on the tooth surface. The relationship between EBS and oral microbiota in children remains elusive. The aim of this study was to compare dental plaque microbiome in EBS children with that in EBS-free children in the primary dentition. Methods The Illumina MiSeq sequencing technique was utilized in the cross-sectional pilot study to investigate the diversity and composition of the supragingival plaque microbiota from 10 EBS-positive and 10 EBS-free children. The results were analysed with nonparametric Mann-Whitney U test, Pearson Chi-Square test, Fisher’s Exact test and one-way ANOVA tests. Results We identified 13 different phyla, 22 classes, 33 orders, 54 families, 105 genera, and 227 species from a total of 52,646 high-quality sequences. Between two groups, no statistical differences were observed in the estimators of community richness and diversity at 97% similarity, as well as in the Unweighted Unifrac principal co-ordinates analysis (PCoA). At the species level, higher level of relative abundance of Actinomyces naeslundii and lower level of relative abundance of a species belonging to Candidate_division_TM7 was observed in dental plaque of EBS-positive subjects, compared to dental plaque of EBS-free subjects (P < 0.05). This indicated that some species might be involved in the EBS process. Conclusion Changes in dental plaque microbiota is possibly relevant to the process of EBS in the primary dentition.

scholarly journals Dysbiosis of Oral Microbiota During Oral Squamous Cell Carcinoma Development

2021 ◽  
Vol 11 ◽  
Author(s):  
Purandar Sarkar ◽  
Samaresh Malik ◽  
Sayantan Laha ◽  
Shantanab Das ◽  
Soumya Bunk ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Oral Cancer ◽  
Oral Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Indian Subcontinent ◽  
Critical Role ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Microbial Composition

Infection with specific pathogens and alterations in tissue commensal microbial composition are intricately associated with the development of many human cancers. Likewise, dysbiosis of oral microbiome was also shown to play critical role in the initiation as well as progression of oral cancer. However, there are no reports portraying changes in oral microbial community in the patients of Indian subcontinent, which has the highest incidence of oral cancer per year, globally. To establish the association of bacterial dysbiosis and oral squamous cell carcinoma (OSCC) among the Indian population, malignant lesions and anatomically matched adjacent normal tissues were obtained from fifty well-differentiated OSCC patients and analyzed using 16S rRNA V3-V4 amplicon based sequencing on the MiSeq platform. Interestingly, in contrast to the previous studies, a significantly lower bacterial diversity was observed in the malignant samples as compared to the normal counterpart. Overall our study identified Prevotella, Corynebacterium, Pseudomonas, Deinococcus and Noviherbaspirillum as significantly enriched genera, whereas genera including Actinomyces, Sutterella, Stenotrophomonas, Anoxybacillus, and Serratia were notably decreased in the OSCC lesions. Moreover, we demonstrated HPV-16 but not HPV-18 was significantly associated with the OSCC development. In future, with additional validation, this panel could directly be applied into clinical diagnostic and prognostic workflows for OSCC in Indian scenario.

scholarly journals The Postmedieval Latvian Oral Microbiome in the Context of Modern Dental Calculus and Modern Dental Plaque Microbial Profiles

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 309
Author(s):  
Alisa Kazarina ◽  
Elina Petersone-Gordina ◽  
Janis Kimsis ◽  
Jevgenija Kuzmicka ◽  
Pawel Zayakin ◽  
...  
Keyword(s):  
Dental Plaque ◽  
Modern Human ◽  
Oral Microbiome ◽  
Dental Calculus ◽  
Microbial Composition ◽  
Metagenome Analysis ◽  
Microbiome Composition ◽  
Microbial Adaptation ◽  
Microbial Dna ◽  
Insight Into

Recent advantages in paleomicrobiology have provided an opportunity to investigate the composition of ancient microbial ecologies. Here, using metagenome analysis, we investigated the microbial profiles of historic dental calculus retrieved from archaeological human remains from postmedieval Latvia dated 16–17th century AD and examined the associations of oral taxa and microbial diversity with specific characteristics. We evaluated the preservation of human oral microbiome patterns in historic samples and compared the microbial composition of historic dental calculus, modern human dental plaque, modern human dental calculus samples and burial soil microbiota. Overall, the results showed that the majority of microbial DNA in historic dental calculus originated from the oral microbiome with little impact of the burial environment. Good preservation of ancient DNA in historical dental calculus samples has provided reliable insight into the composition of the oral microbiome of postmedieval Latvian individuals. The relative stability of the classifiable oral microbiome composition was observed. Significant differences between the microbiome profiles of dental calculus and dental plaque samples were identified, suggesting microbial adaptation to a specific human body environment.

scholarly journals Oral Microbiota Composition and Function Changes During Chronic Erythematous Candidiasis

2021 ◽  
Vol 11 ◽  
Author(s):  
Xin Lyu ◽  
Hui Zheng ◽  
Xu Wang ◽  
Heyu Zhang ◽  
Lu Gao ◽  
...  
Keyword(s):  
Healthy Subjects ◽  
Bacterial Species ◽  
Oral Bacteria ◽  
Oral Microbiome ◽  
Marker Genes ◽  
Oral Microbiota ◽  
Metagenomic Sequencing ◽  
Cytochrome Bc1 Complex ◽  
Microbial Composition ◽  
Treatment And Prevention

Oral microbiota is constantly changing with the host state, whereas the oral microbiome of chronic erythematous candidiasis remains poorly understood. The aim of this study was to compare oral microbial signatures and functional profiling between chronic erythematous candidiasis and healthy subjects. Using shotgun metagenomic sequencing, we analyzed the microbiome in 12 chronic erythematous candidiasis, 12 healthy subjects, and 2 chronic erythematous candidiasis cured by antifungal therapy. We found that the salivary microbiota of chronic erythematous candidiasis was significantly different from that of healthy subjects. Among them, Rothia mucilaginosa and Streptococcus mitis were the most abundant disease-enriched species (Mann-Whitney U-test, P &lt; 0.05). In addition, co-occurrence network analysis showed that C. albicans formed densely connected modules with oral bacterial species and was mainly positive connected to Streptococcus species. Furthermore, we investigated the functional potentials of the microbiome and identified a set of microbial marker genes associated with chronic erythematous candidiasis. Some of these genes enriching in chronic erythematous candidiasis are involved in eukaryotic ribosome, putative glutamine transport system, and cytochrome bc1 complex respiratory unit. Altogether, this study revealed the changes of oral microbial composition, the co-occurrence between C. albicans and oral bacteria, as well as the changes of microbial marker genes during chronic erythematous candidiasis, which provides evidence of oral microbiome as a target for the treatment and prevention of chronic erythematous candidiasis.

Human oral microbiome dysbiosis as a novel tool for detecting noninvasive biomarkers for colorectal cancer.

2021 ◽  
Vol 39 (3_suppl) ◽  
pp. 23-23
Author(s):  
Cheng Kong
Keyword(s):  
Colorectal Cancer ◽  
Colorectal Tumor ◽  
Oral Microbiome ◽  
Colorectal Carcinogenesis ◽  
Oral Microbiota ◽  
Healthy Controls ◽  
Microbial Composition ◽  
Potential Association ◽  
Tumor Association ◽  
Noninvasive Biomarkers

23 Background: The oral microbiome may play an important role in colorectal carcinogenesis. However, few studies have investigated the association between oral microbiome and the development of colorectal cancer (CRC). We aimed to investigate whether oral health–colorectal tumor association has an underlying microbial basis, in the quest for novel non-invasive biomarkers for CRC. Methods: We collected oral swab samples from 161 patients with CRC, 34 patients with colorectal adenoma (CRA), and 58 healthy volunteers. The oral microbiota was assessed using 16S rRNA sequencing. The oral microbiome was characterized, microbial markers were identified, and colorectal tumor (CRA and CRC) classifiers were constructed and validated. Results: Oral microbial composition and diversity were significantly different among the three groups; the CRA group had the highest diversity. Analysis of the functional potential of oral microbiota demonstrated that the pathway involving cell motility was overrepresented in the CRA and CRC groups relative to that in the healthy controls. Moreover, a random forest model was constructed based on oral microbial markers, which could distinguish the colorectal tumor groups from the healthy controls and achieve a powerful classification potential in the discovery and validation cohorts. Conclusions: This study suggests a potential association between oral microbiome dysbiosis and colorectal cancer. Oral microbiota-based biomarkers may be helpful in predicting the risk of developing CRA and CRC.

scholarly journals Nitric Oxide Donor Modulates a Multispecies Oral Bacterial Community—An In Vitro Study

2019 ◽  
Vol 7 (9) ◽  
pp. 353 ◽  
Author(s):  
Takayuki Nambu ◽  
Dan Wang ◽  
Chiho Mashimo ◽  
Hugo Maruyama ◽  
Kosuke Kashiwagi ◽  
...  
Keyword(s):  
Nitric Oxide ◽  
Dental Plaque ◽  
Oral Microbiome ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Nitric Oxide Donor ◽  
Tetrazolium Salt ◽  
Oral Microbiota ◽  
Continuous Change ◽  
Α Diversity

The deterioration of human oral microbiota is known to not only cause oral diseases but also to affect systemic health. Various environmental factors are thought to influence the disruption and restoration of the oral ecosystem. In this study, we focused on the effect of nitric oxide (NO) produced by denitrification and NO synthase enzymes on dental plaque microbiota. Interdental plaques collected from 10 subjects were exposed to NO donor sodium nitroprusside (SNP) and then cultured in a specialized growth medium. Depending on the concentration of exposed SNP, a decrease in α-diversity and a continuous change in β-diversity in the dental plaque community were shown by sequencing bacterial 16S rRNA genes. We also identified eight operational taxonomic units that were significantly altered by NO exposure. Among them, the exposure of NO donors to Fusobacterium nucleatum cells showed a decrease in survival rate consistent with the results of microbiota analysis. Meanwhile, in addition to NO tolerance, an increase in the tetrazolium salt-reducing activity of Campylobacter concisus cells was confirmed by exposure to SNP. This study provides an overview of how oral plaque microbiota shifts with exposure to NO and may contribute to the development of a method for adjusting the balance of the oral microbiome.

scholarly journals Site- and Taxa-Specific Disease-Associated Oral Microbial Structures Distinguish Inflammatory Bowel Diseases

2021 ◽  
Author(s):  
Hari K Somineni ◽  
Jordan H Weitzner ◽  
Suresh Venkateswaran ◽  
Anne Dodd ◽  
Jarod Prince ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Oral Microbiome ◽  
Spatial And Temporal Variation ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Microbial Composition ◽  
Healthy Control ◽  
Inflammatory Bowel ◽  
A Site

Abstract Background The gut and oral microbiome have independently been shown to be associated with inflammatory bowel disease (IBD). However, it is not known to what extent gut and oral microbial disease markers converge in terms of their composition in IBD. Further, the spatial and temporal variation within the oral microenvironments of IBD remain to be elucidated. Patients and Methods We used a prospectively recruited cohort of patients with IBD (n = 47) and unrelated healthy control patients (n = 18) to examine the spatial and temporal distribution of microbiota within the various oral microenvironments, represented by saliva, tongue, buccal mucosa, and plaque, and compared them with stool. Microbiome characterization was performed using 16S rRNA gene sequencing. Results The oral microbiome displayed IBD-associated dysbiosis, in a site- and taxa-specific manner. Plaque samples depicted a relatively severe degree of dysbiosis, and the disease-associated dysbiotic bacterial groups were predominantly the members of the phylum Firmicutes. Our 16S rRNA gene analyses show that oral microbiota can distinguish patients with IBD from healthy control patients, with salivary microbiota performing the best, closely matched by stool and other oral sites. Longitudinal profiles of microbial composition suggest that some taxa are more consistently perturbed than others, preferentially in a site-dependent fashion. Conclusions Collectively, these data indicate the potential of using oral microbial profiles in screening and monitoring patients with IBD. Furthermore, these results support the importance of spatial and longitudinal microbiome sampling to interpret disease-associated dysbiotic states and eventually to gain insights into disease pathogenesis.

scholarly journals Rapid and Sensitive PCR-Dipstick DNA Chromatography for Multiplex Analysis of the Oral Microbiota

2014 ◽  
Vol 2014 ◽  
pp. 1-10 ◽  
Author(s):  
Lingyang Tian ◽  
Takuichi Sato ◽  
Kousuke Niwa ◽  
Mitsuo Kawase ◽  
Anne C. R. Tanner ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dental Plaque ◽  
Bacterial Species ◽  
Oral Microbiota ◽  
Streptococcus Sobrinus ◽  
Microbial Composition ◽  
Test Species ◽  
Multiplex Analysis ◽  
Latex Beads ◽  
Target Dna

A complex of species has been associated with dental caries under the ecological hypothesis. This study aimed to develop a rapid, sensitive PCR-dipstick DNA chromatography assay that could be read by eye for multiplex and semiquantitative analysis of plaque bacteria. Parallel oligonucleotides were immobilized on a dipstick strip for multiplex analysis of target DNA sequences of the caries-associated bacteria,Streptococcus mutans,Streptococcus sobrinus,Scardovia wiggsiae,Actinomycesspecies, andVeillonella parvula. Streptavidin-coated blue-colored latex microspheres were to generate signal. Target DNA amplicons with an oligonucleotide-tagged terminus and a biotinylated terminus were coupled with latex beads through a streptavidin-biotin interaction and then hybridized with complementary oligonucleotides on the strip. The accumulation of captured latex beads on the test and control lines produced blue bands, enabling visual detection with the naked eye. The PCR-dipstick DNA chromatography detected quantities as low as 100 pg of DNA amplicons and demonstrated 10- to 1000-fold higher sensitivity than PCR-agarose gel electrophoresis, depending on the target bacterial species. Semiquantification of bacteria was performed by obtaining a series of chromatograms using serial 10-fold dilution of PCR-amplified DNA extracted from dental plaque samples. The assay time was less than 3 h. The semiquantification procedure revealed the relative amounts of each test species in dental plaque samples, indicating that this disposable device has great potential in analysis of microbial composition in the oral cavity and intestinal tract, as well as in point-of-care diagnosis of microbiota-associated diseases.

scholarly journals Gender Variations in the Oral Microbiomes of Elderly Patients with Initial Periodontitis

2021 ◽  
Vol 2021 ◽  
pp. 1-16
Author(s):  
Jie Zhao ◽  
Ying-Hui Zhou ◽  
Ya-Qiong Zhao ◽  
Yao Feng ◽  
Fei Yan ◽  
...  
Keyword(s):  
Immune System ◽  
Elderly Patients ◽  
16S Rrna Gene Sequencing ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Microbial Composition ◽  
Linear Discriminant ◽  
Immune System Diseases ◽  
Analytical Approaches

Periodontitis is a globally prevalent disease that imposes a functional and aesthetic burden on patients. The oral microbiome influences human health. The aim of this study was at assessing gender variation in the subgingival bacterial microbiome of elderly patients with initial periodontitis and to determine the causes of this variation. Twelve males and twenty females (range 50–68 years old) with initial periodontitis provided subgingival plaque samples. 16S rRNA gene sequencing, QIIME-based data processing, and statistical analyses were carried out using several different analytical approaches to detect differences in the oral microbiome between the two groups. Males had higher Chao1 index, observed species, and phylogenetic diversity whole tree values than females. Analysis of β-diversity indicated that the samples were reasonably divided by the gender. The linear discriminant analysis effect size showed that the most representative biomarkers were the genus Haemophilus in males, whereas the dominant bacteria in females were Campylobacter. Kyoto Encyclopedia of Genes and Genomes analysis showed that predicting changes in the female oral microbiota may be related to the immune system and immune system diseases are the main factor in males. These data suggest that gender may be a differentiating factor in the microbial composition of subgingival plaques in elderly patients with initial periodontitis. These results could deepen our understanding of the role of gender in the oral microbiota present during initial periodontitis.

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