scholarly journals Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Alon Shaiber ◽  
Amy D. Willis ◽  
Tom O. Delmont ◽  
Simon Roux ◽  
Lin-Xing Chen ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Dental Plaque ◽  
Niche Partitioning ◽  
Dispersal Limitation ◽  
Oral Microbiome ◽  
Microbial Life ◽  
Host Health ◽  
Phylogenomic Analyses ◽  
Candidate Phyla Radiation ◽  
Environmental Microbes

Abstract Introduction Microbial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and intriguing patterns of site specificity amidst the lack of dispersal limitation. However, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among taxa that belong to recently discovered branches of microbial life. Results Here, we assemble metagenomes from tongue and dental plaque samples from multiple individuals and reconstruct 790 non-redundant genomes, 43 of which resolve to TM7, a member of the Candidate Phyla Radiation, forming six monophyletic clades that distinctly associate with either plaque or tongue. Both pangenomic and phylogenomic analyses group tongue-specific clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 group with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and mobilome of cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of microbes. Additionally, we report that prophages are widespread among oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment. Conclusions Our data illuminate niche partitioning of enigmatic members of the oral cavity, including TM7, SR1, and GN02, and provide genomes for poorly characterized yet prevalent members of this biome, such as uncultivated Flavobacteriaceae.

scholarly journals Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome

2020 ◽  
Author(s):  
Alon Shaiber ◽  
Amy D. Willis ◽  
Tom O. Delmont ◽  
Simon Roux ◽  
Lin-Xing Chen ◽  
...  
Keyword(s):  
Dental Plaque ◽  
Niche Partitioning ◽  
Dispersal Limitation ◽  
Oral Microbiome ◽  
Site Specificity ◽  
Major Focus ◽  
Microbial Life ◽  
Host Health ◽  
Phylogenomic Analyses ◽  
Environmental Microbes

AbstractMicrobial residents of the human oral cavity have long been a major focus of microbiology due to their influence on host health and their intriguing patterns of site specificity amidst the lack of dispersal limitation. Yet, the determinants of niche partitioning in this habitat are yet to be fully understood, especially among the taxa that belong to recently discovered branches of microbial life. Here we assembled metagenomes from daily tongue and dental plaque samples from multiple individuals and reconstructed 790 non-redundant genomes, 43 of which resolved to TM7 that formed six monophyletic clades distinctly associated either with plaque or with tongue. Both pangenomic and phylogenomic analyses grouped tongue-specific TM7 clades with other host-associated TM7 genomes. In contrast, plaque-specific TM7 grouped together with environmental TM7 genomes. Besides offering deeper insights into the ecology, evolution, and the mobilome of the cryptic members of the oral microbiome, our study reveals an intriguing resemblance between dental plaque and non-host environments indicated by the TM7 evolution, suggesting that plaque may have served as a stepping stone for environmental microbes to adapt to host environments for some clades of human associated microbes. Additionally, we report that prophages are widespread amongst oral-associated TM7, while absent from environmental TM7, suggesting that prophages may have played a role in adaptation of TM7 to the host environment.

scholarly journals Cariogenic and Pro Health Taxa in the Oral Cavity Among Children and Adults A Scoping Review

2021 ◽  
Author(s):  
Deesha Bhaumik ◽  
Divya Manikandan ◽  
Betsy Foxman
Keyword(s):  
Dental Caries ◽  
Oral Cavity ◽  
Scoping Review ◽  
Dental Plaque ◽  
Multiple Testing ◽  
Oral Microbiome ◽  
Sample Type ◽  
Healthy Children ◽  
Sample Collection ◽  
Single Organism

Abstract Introduction: Dental caries are not due to a single organism, but to complex interactions among multiple microbes found in the oral cavity. Microbiome studies have identified multiple organisms associated with dental caries in both the saliva and dental plaque, but taxa identified vary largely by study. Our scoping review aims to create a comprehensive list of cariogenic and prohealth taxa found in saliva and dental plaque among healthy children and adults that compare caries-active and caries-free populations. Methods: We searched published studies querying the PUBMED and EMBASE databases using the following keywords: (plaque OR saliva) AND caries AND (next generation sequencing OR checkerboard OR 16s rRNA or qPCR). Studies were limited to human studies published in English between January 1, 2010 and June 24, 2020.Results: Our search strategy identified 298 identified articles. After applying the exclusion criteria, 22 articles were included (Figure 1, Table 1 and 2). Taxa associated with caries or health varied widely among the studies reviewed, with notable differences by age and biologic sample type. While no single taxa was associated with caries in all studies, Streptococcus mutans was significantly associated with caries in 12/24 studies (50%) and Fusobacterium periodonticum was significantly associated with prohealth in 4/24 studies (16.7%). Conclusion: No taxa in plaque and salivary microbiomes were consistently associated with caries or prohealth across all studies. This may be due to the inconsistency of timing of sample collection during the caries process, differing sequencing methods, lack of correction for multiple testing or possibly indicate that there are multiple ways that the oral microbiome can be cariogenic or prohealth.

The role of probiotics in correction of microbiocenosis and cytokine balance of the oral cavity of patient with chronic inflammatory disease of periodont

2020 ◽  
Vol 25 (4) ◽  
pp. 323-330
Author(s):  
E. S. Ovcharenko ◽  
V. V. Erichev ◽  
S. I. Risovannij ◽  
T. V. Aksenova ◽  
S. V. Melekhov ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Periodontal Diseases ◽  
Treatment Protocol ◽  
Chronic Inflammatory Disease ◽  
Oral Microbiome ◽  
Comprehensive Treatment ◽  
Local Immunity ◽  
Treatment Techniques ◽  
Before And After

Relevance. A long-term inflammation in the oral cavity, unreasonable treatment of periodontal patients with antibiotics cause imbalance between certain types of fungal-bacterial associations accompanied by oral dysbiosis and change of local immune status. So, development and application of new comprehensive diagnosis and treatment techniques in periodontal patients, use of products for correction of microbiota and local immunity are a current and a long-term task. Purpose is to optimize the comprehensive treatment protocol of inflammatory periodontal diseases by introducing probiotics and evaluation of oral microbiome and cytokine profile.Materials and methods. 140 patients were examined. Of these 60 patients had chronic generalized plaque-induced gingivitis and 60 patients suffered from moderate chronic generalized periodontitis. Bacterial and fungal microbiome was assessed and the host immune response was evaluated in all patients before and after the treatment. Half of the patients were treated conventionally and the other half were treated according to a modified scheme: probiotic “Bifidumbacterin Forte” was added.Results. A large number of yeast-like fungi Candida and commensal bacteria were detected in periodontal pockets of patients with chronic generalized plaque-induced gingivitis and moderate chronic generalized periodontitis. That correlates with a significant increase of pro-inflammatory cytokines (TNF-α, IL—8), decrease of concentration of INF-γ and increase of antiinflammatory cytokine IL-4.Conclusion. Changes in clinical, microbiological and immunological values during a modified combination therapy with a probiotic and during a conventional treatment demonstrated that effectiveness of treatment of chronic gingivitis and chronic periodontitis increased by 40% and 37% respectively.

scholarly journals Bacteriocin-like activity of oral Fusobacterium nucleatum isolated from human and non-human primates

1999 ◽  
Vol 30 (4) ◽  
pp. 324-346 ◽  
Author(s):  
Elerson Gaetti-Jardim Júnior ◽  
Mario Julio Avila-Campos
Keyword(s):  
Oral Cavity ◽  
Microbial Ecology ◽  
Dental Plaque ◽  
Fusobacterium Nucleatum ◽  
Antagonistic Activity ◽  
Healthy Individuals ◽  
Bacterial Microbiota ◽  
Reference Strains

Fusobacterium nucleatum is indigenous of the human oral cavity and has been involved in different infectious processes. The production of bacteriocin-like substances may be important in regulation of bacterial microbiota in oral cavity. The ability to produce bacteriocin-like substances by 80 oral F. nucleatum isolates obtained from periodontal patients, healthy individuals and Cebus apella monkeys, was examinated. 17.5% of all tested isolates showed auto-antagonism and 78.8% iso- or hetero-antagonism. No isolate from monkey was capable to produce auto-inhibition. In this study, the antagonistic substances production was variable in all tested isolates. Most of the F. nucleatum showed antagonistic activity against tested reference strains. These data suggest a possible participation of these substances on the oral microbial ecology in humans and animals. However, the role of bacteriocins in regulating dental plaque microbiota in vivo is discussed.

Prevalence of microorganisms associated with feline gingivostomatitis

2018 ◽  
Vol 21 (2) ◽  
pp. 103-108 ◽  
Author(s):  
Hitoshi Nakanishi ◽  
Masaru Furuya ◽  
Takehisa Soma ◽  
Yoshiki Hayashiuchi ◽  
Ryusaku Yoshiuchi ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Pasteurella Multocida ◽  
Age Distribution ◽  
Anaerobic Bacteria ◽  
Chronic Inflammatory Disease ◽  
Oral Microbiome ◽  
Pcr Assay ◽  
Significant Difference ◽  
Feline Herpesvirus ◽  
Positive Rate

Objectives Feline gingivostomatitis (FGS) is a painful chronic inflammatory disease of the oral cavity. The purpose of this study was to examine the frequency of detection of certain common feline bacteria and viruses to determine any potential associations with FGS. Methods A multicentre case-control study design was conducted. In total, 72 control cats and 32 cats with FGS were included in the study. Oral swabs were cultured for bacterial identification and a PCR assay was carried out to examine the infection of feline calicivirus (FCV), feline herpesvirus-1 (FHV-1), Chlamydia felis, Mycoplasma felis and Bordetella bronchiseptica. Results There was a significant difference in age distribution between the control and the FGS group. Based on a PCR assay, the positive rate of FCV was significantly higher in FGS cats than control animals. For other infectious pathogens, including FHV-1, C felis and M felis, there was no significant difference. Bacterial culture of oral swabs revealed that Pasteurella multocida was most frequently detected, but the detection rate was significantly lower in FGS cats. In FGS cats, the incidence of Enterococcus faecalis and anaerobic bacteria were more frequently isolated than in control cats. Conclusions and relevance This study indicates that the positive rate of FCV was significantly higher in cats with FGS, and the microflora of the oral cavity of cats with FGS might be disrupted, although additional studies are required to compare the oral microbiome in cats of a variety of ages.

scholarly journals Role of Oral Microbiome Signatures in Diagnosis and Prognosis of Oral Cancer

2019 ◽  
Vol 18 ◽  
pp. 153303381986735 ◽  
Author(s):  
Indranil Chattopadhyay ◽  
Mukesh Verma ◽  
Madhusmita Panda
Keyword(s):  
Oral Cancer ◽  
Epithelial Cells ◽  
Oral Cavity ◽  
Bacterial Species ◽  
Treatment Strategies ◽  
Genetic Alterations ◽  
Oral Microbiome ◽  
Oral Carcinogenesis ◽  
Early Diagnostic

Despite advancement in cancer treatment, oral cancer has a poor prognosis and is often detected at late stage. To overcome these challenges, investigators should search for early diagnostic and prognostic biomarkers. More than 700 bacterial species reside in the oral cavity. The oral microbiome population varies by saliva and different habitats of oral cavity. Tobacco, alcohol, and betel nut, which are causative factors of oral cancer, may alter the oral microbiome composition. Both pathogenic and commensal strains of bacteria have significantly contributed to oral cancer. Numerous bacterial species in the oral cavity are involved in chronic inflammation that lead to development of oral carcinogenesis. Bacterial products and its metabolic by-products may induce permanent genetic alterations in epithelial cells of the host that drive proliferation and/or survival of epithelial cells. Porphyromonas gingivalis and Fusobacterium nucleatum induce production of inflammatory cytokines, cell proliferation, and inhibition of apoptosis, cellular invasion, and migration thorough host cell genomic alterations. Recent advancement in metagenomic technologies may be useful in identifying oral cancer–related microbiome, their genomes, virulence properties, and their interaction with host immunity. It is very important to address which bacterial species is responsible for driving oral carcinogenesis. Alteration in the oral commensal microbial communities have potential application as a diagnostic tool to predict oral squamous cell carcinoma. Clinicians should be aware that the protective properties of the resident microflora are beneficial to define treatment strategies. To develop highly precise and effective therapeutic approaches, identification of specific oral microbiomes may be required. In this review, we narrate the role of microbiome in the progression of oral cancer and its role as an early diagnostic and prognostic biomarker for oral cancer.

scholarly journals Helicobacter pylori colonization and oral health in children

2017 ◽  
Vol 12 (2) ◽  
pp. 41-44
Author(s):  
Vasile Valeriu LUPU ◽  
◽  
Gabriela PĂDURARU ◽  
Anca ADAM ◽  
Ana-Maria DĂBULEANU ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Oral Health ◽  
Gastric Mucosa ◽  
Oral Cavity ◽  
Gold Standard ◽  
Dental Plaque ◽  
Negative Bacterium ◽  
Gram Negative ◽  
Standard Triple Therapy ◽  
H Pylori

Helicobacter pylori (H. pylori) is a microaerophilic gram-negative bacterium infecting approximately one half of the world’s population. The oral cavity and dental plaque may be a reservoir for H. pylori infection. Diagnosis of H. pylori infection in children differs from that of adults. Although H. pylori has long been known to be detected in the oral cavity, the significance of such findings are controversial. Oral H. pylori may play an important role in re-infection of the gastric mucosa. The gold standard for eradicating H. pylori infection is standard triple therapy. The studies have shown promising results in the management of both oral and gastric H. pylori.

scholarly journals The dental calculus metabolome in modern and historic samples

2017 ◽  
Author(s):  
Irina M. Velsko ◽  
Katherine A. Overmyer ◽  
Camilla Speller ◽  
Matthew Collins ◽  
Louise Loe ◽  
...  
Keyword(s):  
Dental Plaque ◽  
Ultra Performance Liquid Chromatography ◽  
Oral Microbiome ◽  
Chemical Degradation ◽  
Dental Calculus ◽  
Metabolite Profiles ◽  
Free Nucleotides ◽  
Liquid Chromatography Tandem Mass ◽  
Long Time

AbstractIntroductionDental calculus is a mineralized microbial dental plaque biofilm that forms throughout life by precipitation of salivary calcium salts. Successive cycles of dental plaque growth and calcification make it an unusually well-preserved, long-term record of host-microbial interaction in the archaeological record. Recent studies have confirmed the survival of authentic ancient DNA and proteins within historic and prehistoric dental calculus, making it a promising substrate for investigating oral microbiome evolution via direct measurement and comparison of modern and ancient specimens.ObjectiveWe present the first comprehensive characterization of the human dental calculus metabolome using a multi-platform approach.MethodsUltra performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) quantified 285 metabolites in modern and historic (200 years old) dental calculus, including metabolites of drug and dietary origin. A subset of historic samples was additionally analyzed by high-resolution gas chromatography-MS (GC-MS) and UPLC- MS/MS for further characterization of polar metabolites and lipids, respectively. Metabolite profiles of modern and historic calculus were compared to identify patterns of persistence and loss.ResultsDipeptides, free amino acids, free nucleotides, and carbohydrates substantially decrease in abundance and ubiquity in archaeological samples, with some exceptions. Lipids generally persist, and saturated and mono-unsaturated medium and long chain fatty acids appear to be well-preserved, while metabolic derivatives related to oxidation and chemical degradation are found at higher levels in archaeological dental calculus than fresh samples.ConclusionsThe results of this study indicate that certain metabolite classes have higher potential for recovery over long time scales and may serve as appropriate targets for oral microbiome evolutionary studies.

scholarly journals Prevalence ofHelicobacter pylori vacAGenotypes andcagAGene in Dental Plaque of Asymptomatic Mexican Children

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Alejandra Mendoza-Cantú ◽  
Víctor Hugo Urrutia-Baca ◽  
Cynthia Sofía Urbina-Ríos ◽  
Myriam Angélica De la Garza-Ramos ◽  
Martha Elena García-Martínez ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Oral Cavity ◽  
Dental Plaque ◽  
Gastrointestinal Disease ◽  
Oral Infection ◽  
Rrna Gene ◽  
Mexican Children ◽  
Asymptomatic Children ◽  
Dyspeptic Symptoms ◽  
H Pylori

The variability inHelicobacter pylori vacAandcagAgenes has been related to the progression of the gastrointestinal disease; also the presence ofH. pyloriin the oral cavity has been associated with periodontal disease in adults, but, in children without dyspeptic symptoms, little is known about this. We evaluated the prevalence ofH. pyloriand the presence ofvacA/cagAgenotypes in the oral cavity of Mexican children without dyspeptic symptoms. The gingival status was measured, and dental plaque samples (n=100) were taken. 38% of children were positive forH. pylori16S rRNA gene by qPCR. A significant association betweenH. pylorioral infection and gingival status was observed (P<0.001). In 34.6% (9/26) of mild gingivitis cases,s1m2genotype was found, whiles1m1was typed in 50% (3/6) of moderate gingivitis. ThecagAprevalence amongH. pylori-positive children was 80.8% (21/26), 83.3% (5/6), and 16.7% (1/6) of cases of mild gingivitis, moderate gingivitis, and nongingivitis, respectively (P<0.001). Thes1m1/cagA+ combinational genotype was the most detected in children with gingivitis. Our results suggest that the prevalence ofH. pyloriand detection ofvacA/cagAgenotypes-associated gastrointestinal disease in the oral cavity could be related to the progression of gingivitis in asymptomatic children.

Multifunctional artificial saliva preparation – challenges and needs

2021 ◽  
Vol 8 ◽  
pp. 37-46
Author(s):  
Katarzyna Niemirowicz-Laskowska ◽  
Joanna Mystkowska ◽  
Dawid Łysik ◽  
Sylwia Chmielewska ◽  
Łukasz Suprewicz ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Artificial Saliva ◽  
Salivary Secretion ◽  
Biological Properties ◽  
Pharmacological Therapy ◽  
Oral Microbiome ◽  
Dry Mouth ◽  
Rheological Parameters ◽  
Saliva Substitutes

Saliva plays a crucial role in maintaining homeostasis not only within the oral cavity but also in further sections of the gastrointestinal tract. Pleiotropic properties of saliva include participation in the digestion of carbohydrates, cleansing and moisturizing the oral cavity, and maintaining the composition of the oral microbiome. The result of impaired function of the salivary gland is reduced salivation – hyposalivation, leading to dry mouth – xerostomia. It is established that numerous physiological factors (age, sex, weight change) and pathological factors (polytherapy, head and neck cancer, coexisting diseases such as diabetes, depression, cardiovascular diseases) lead to the reduction in saliva secretion, and in effect, causing a dry mouth. Treatment of salivary secretion disorders involves pharmacological therapy (including hormone therapy) or replacement therapy which based on the use of saliva substitutes. In the case of disturbances in the secretion of natural saliva, the application of the artificial saliva preparations should support the chewing processes, moisturize the oral cavity, and fulfill the biological functions of saliva. However, to date, on the pharmaceutical market, there are no saliva substitutes that meet the biological criteria and maintaining favorable physicochemical properties and rheological parameters. Taking into account the problems of the patients which are burden by impaired salivary secretion, the aim of our research was to attempt to develop an artificial saliva preparation that reflecting as much as possible the properties of natural saliva, both in terms of mechanical and biological properties. As part of the research, the chemical composition was developed and a detailed study of the physicochemical and rheological parameters of artificial saliva preparations containing mucins as well as their microbiological and biocompatibility assessment, at in vitro level were carried out.

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