scholarly journals Assessing the variation within the oral microbiome of healthy adults

2020 ◽  
Author(s):  
Jacob T. Nearing ◽  
Vanessa DeClercq ◽  
Johan Van Limbergen ◽  
Morgan G.I. Langille
Keyword(s):  
Microbial Community ◽  
Oral Cavity ◽  
Oral Microbiome ◽  
Biological Factor ◽  
Validation Dataset ◽  
Sequence Variants ◽  
Confounding Factors ◽  
Microbiome Composition ◽  
Human Oral Cavity ◽  
Systemic Health

AbstractOver 1000 different species of microbes have been found to live within the human oral cavity where they play important roles in maintaining both oral and systemic health. Several studies have identified the core members of this microbial community, however, the factors that determine oral microbiome composition are not well understood. In this study we exam the salivary oral microbiome of 1049 Atlantic Canadians using 16S rRNA gene sequencing in order to determine which dietary, lifestyle, and anthropometric features play a role in shaping microbial community composition. Features that were identified as being significantly associated with overall composition were then additionally examined for genera and amplicon sequence variants that were associated with these features. Several associations were replicated in an additional secondary validation dataset. Overall, we found that several anthropometric measurements including waist hip ratio, height, and fat free mass, as well as age and sex, were associated with oral microbiome composition in both our exploratory and validation cohorts. We were unable to validate dietary impacts on the oral microbiome but did find evidence to suggest potential contributions from factors such as the number of vegetable and refined grain servings an individual consumes. Interestingly, each one of these factors on their own were associated with only minor shifts in the oral microbiome suggesting that future biomarker identification for several diseases associated with the oral microbiome may be undertaken without the worry of confounding factors obscuring biological signal.ImportanceThe human oral cavity is inhabited by a diverse community of microbes known as the human oral microbiome. These microbes play a role in maintaining both oral and systemic health and as such have been proposed to be useful biomarkers of disease. However, to identify these biomarkers, we first need to determine the composition and variation of the healthy oral microbiome. Within this report we investigate the oral microbiome of 1049 healthy individuals to determine which genera and amplicon sequence variants are commonly found between individual oral microbiomes. We then further investigate how lifestyle, anthropometric, and dietary choices impact overall microbiome composition. Interestingly, the results from this investigation showed that while many features were significantly associated with oral microbiome composition no single biological factor explained a variation larger than 2%. These results indicate that future work on biomarker detection may be encourage by the lack of strong confounding factors.

scholarly journals Assessing the Variation within the Oral Microbiome of Healthy Adults

mSphere ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Jacob T. Nearing ◽  
Vanessa DeClercq ◽  
Johan Van Limbergen ◽  
Morgan G. I. Langille
Keyword(s):  
Microbial Community ◽  
Oral Cavity ◽  
Oral Microbiome ◽  
Biological Factor ◽  
Sequence Variants ◽  
Confounding Factors ◽  
Validation Data ◽  
Microbiome Composition ◽  
Human Oral Cavity ◽  
Systemic Health

ABSTRACT More than 1,000 different species of microbes have been found to live within the human oral cavity, where they play important roles in maintaining both oral and systemic health. Several studies have identified the core members of this microbial community; however, the factors that determine oral microbiome composition are not well understood. In this study, we exam the salivary oral microbiome of 1,049 Atlantic Canadians using 16S rRNA gene sequencing to determine which dietary, lifestyle, and anthropometric features play a role in shaping microbial community composition. Features that were identified as being significantly associated with overall composition then were additionally examined for genera, amplicon sequence variants, and predicted pathway abundances that were associated with these features. Several associations were replicated in an additional secondary validation data set. Overall, we found that several anthropometric measurements, including waist-hip ratio (WHR), height, and fat-free mass, as well as age and sex, were associated with overall oral microbiome structure in both our exploratory and validation data sets. We were unable to validate any dietary impacts on overall taxonomic oral microbiome composition but did find evidence to suggest potential contributions from factors such as the number of vegetable and refined grain servings an individual consumes. Interestingly, each one of these factors on its own was associated with only minor shifts in the overall taxonomic composition of the oral microbiome, suggesting that future biomarker identification for several diseases associated with the oral microbiome can be undertaken without the worry of confounding factors obscuring biological signals. IMPORTANCE The human oral cavity is inhabited by a diverse community of microbes, known as the human oral microbiome. These microbes play a role in maintaining both oral and systemic health and, as such, have been proposed to be useful biomarkers of disease. However, to identify these biomarkers, we first need to determine the composition and variation of the healthy oral microbiome. In this report, we investigate the oral microbiome of 1,049 healthy individuals to determine which genera and amplicon sequence variants are commonly found between individual oral microbiomes. We then further investigate how lifestyle, anthropometric, and dietary choices impact overall microbiome composition. Interestingly, the results from this investigation showed that while many features were significantly associated with oral microbiome composition, no single biological factor explained a variation larger than 2%. These results indicate that future work on biomarker detection may be encouraged by the lack of strong confounding factors.

scholarly journals Site-specificity of streptococci in the oral microbiome

2021 ◽  
Author(s):  
Anthony R. McLean ◽  
Julian Torres-Morales ◽  
Gary G. Borisy ◽  
Jessica L. Mark Welch
Keyword(s):  
Oral Cavity ◽  
Related Species ◽  
Oral Microbiome ◽  
Individual Species ◽  
Rrna Gene ◽  
Site Specificity ◽  
Oral Streptococci ◽  
Closely Related Species ◽  
Streptococcus Species ◽  
Human Oral Cavity

Patterns of microbial distribution are determined by as-yet poorly understood rules governing where microbes can grow and thrive. Therefore, a detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely-related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here we assess whether individual species within this genus are generalists using publicly available genomic sequence data that provides species-level resolution. We chose a set of high-quality representative genomes for Streptococcus species from the human oral microbiome. Onto these genomes, we mapped short-read metagenomic sequences from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every reliably detectable Streptococcus species in the human oral cavity was a site-specialist and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. These three species also share substantially the same species-specific core genes indicating that neither taxonomy nor gene content are clear predictors of site-specialization. Site-specificity may instead be influenced by subtle characteristics such as nucleotide-level divergences within conserved genes.

scholarly journals Veillonellae: Beyond Bridging Species in Oral Biofilm Ecology

2021 ◽  
Vol 2 ◽  
Author(s):  
Peng Zhou ◽  
Daniel Manoil ◽  
Georgios N. Belibasakis ◽  
Georgios A. Kotsakis
Keyword(s):  
Oral Cavity ◽  
Bacterial Species ◽  
Oral Microbiome ◽  
Future Research ◽  
Great Promise ◽  
Large Species ◽  
Oral Biofilm ◽  
Human Oral Cavity ◽  
Oral Biofilms ◽  
Polymicrobial Disease

The genus Veillonella comprises 16 characterized species, among which eight are commonly found in the human oral cavity. The high abundance of Veillonella species in the microbiome of both supra- and sub-gingival biofilms, and their interdependent relationship with a multitude of other bacterial species, suggest veillonellae to play an important role in oral biofilm ecology. Development of oral biofilms relies on an incremental coaggregation process between early, bridging and later bacterial colonizers, ultimately forming multispecies communities. As early colonizer and bridging species, veillonellae are critical in guiding the development of multispecies communities in the human oral microenvironment. Their ability to establish mutualistic relationships with other members of the oral microbiome has emerged as a crucial factor that may contribute to health equilibrium. Here, we review the general characteristics, taxonomy, physiology, genomic and genetics of veillonellae, as well as their bridging role in the development of oral biofilms. We further discuss the role of Veillonella spp. as potential “accessory pathogens” in the human oral cavity, capable of supporting colonization by other, more pathogenic species. The relationship between Veillonella spp. and dental caries, periodontitis, and peri-implantitis is also recapitulated in this review. We finally highlight areas of future research required to better understand the intergeneric signaling employed by veillonellae during their bridging activities and interspecies mutualism. With the recent discoveries of large species and strain-specific variation within the genus in biological and virulence characteristics, the study of Veillonella as an example of highly adaptive microorganisms that indirectly participates in dysbiosis holds great promise for broadening our understanding of polymicrobial disease pathogenesis.

scholarly journals Impact of sleep on the microbiome of oral biofilms

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0259850
Author(s):  
Maki Sotozono ◽  
Nanako Kuriki ◽  
Yoko Asahi ◽  
Yuichiro Noiri ◽  
Mikako Hayashi ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Oral Microbiome ◽  
Tooth Surface ◽  
Rrna Gene ◽  
Sample Collection ◽  
Microbiome Composition ◽  
Dental Biofilm ◽  
Gene Sequence Analysis ◽  
Oral Biofilms ◽  
Gingival Mucosa

Dysbiosis of the oral microbiome is associated with diseases such as periodontitis and dental caries. Because the bacterial counts in saliva increase markedly during sleep, it is broadly accepted that the mouth should be cleaned before sleep to help prevent these diseases. However, this practice does not consider oral biofilms, including the dental biofilm. This study aimed to investigate sleep-related changes in the microbiome of oral biofilms by using 16S rRNA gene sequence analysis. Two experimental schedules—post-sleep and pre-sleep biofilm collection—were applied to 10 healthy subjects. Subjects had their teeth and oral mucosa professionally cleaned 7 days and 24 h before sample collection. Samples were collected from several locations in the oral cavity: the buccal mucosa, hard palate, tongue dorsum, gingival mucosa, tooth surface, and saliva. Prevotella and Corynebacterium had higher relative abundance on awakening than before sleep in all locations of the oral cavity, whereas fluctuations in Rothia levels differed depending on location. The microbiome in different locations in the oral cavity is affected by sleep, and changes in the microbiome composition depend on characteristics of the surfaces on which oral biofilms form.

scholarly journals A Linear Plasmid-Like Prophage of Actinomyces odontolyticus Promotes Biofilm Assembly

2018 ◽  
Vol 84 (17) ◽  
Author(s):  
Mengyu Shen ◽  
Yuhui Yang ◽  
Wei Shen ◽  
Lujia Cen ◽  
Jeffrey S. McLean ◽  
...  
Keyword(s):  
Oral Cavity ◽  
Human Microbiome ◽  
Genomic Analysis ◽  
Electron Microscopic Examination ◽  
Oral Microbiome ◽  
Extracellular Dna ◽  
Linear Plasmid ◽  
Electron Microscopic ◽  
Content Type ◽  
Human Oral Cavity

ABSTRACT The human oral cavity is home to a large number of bacteria and bacteriophages (phages). However, the biology of oral phages as members of the human microbiome is not well understood. Recently, we isolated Actinomyces odontolyticus subsp. actinosynbacter strain XH001 from the human oral cavity, and genomic analysis revealed the presence of an intact prophage named xhp1. Here, we demonstrated that xhp1 is a linear plasmid-like prophage, which is a newly identified phage of A. odontolyticus. The prophage xhp1 genome is a 35-kb linear double-stranded DNA with 10-bp single-stranded, 3’ cohesive ends. xhp1 exists extrachromosomally, with an estimated copy number of 5. Annotation of xhp1 revealed 54 open reading frames, while phylogenetic analysis suggests that it has limited similarity with other phages. xhp1 phage particles can be induced by mitomycin C and belong to the Siphoviridae family, according to transmission electron microscopic examination. The released xhp1 particles can reinfect the xhp1-cured XH001 strain and result in tiny blurry plaques. Moreover, xhp1 promotes XH001 biofilm formation through spontaneous induction and the release of host extracellular DNA (eDNA). In conclusion, we identified a linear plasmid-like prophage of A. odontolyticus, which enhances bacterial host biofilm assembly and could be beneficial to the host for its persistence in the oral cavity. IMPORTANCE The biology of phages as members of the human oral microbiome is understudied. Here, we report the characterization of xhp1, a novel linear plasmid-like prophage identified from a human oral isolate, Actinomyces odontolyticus subsp. actinosynbacter strain XH001. xhp1 can be induced and reinfect xhp1-cured XH001. The spontaneous induction of xhp1 leads to the lysis of a subpopulation of bacterial hosts and the release of eDNA that promotes biofilm assembly, thus potentially contributing to the persistence of A. odontolyticus within the oral cavity.

scholarly journals Mycoplasma salivarium detected in a microbial community with Candida glabrata in the biofilm of an occluded biliary stent

2010 ◽  
Vol 59 (2) ◽  
pp. 239-241 ◽  
Author(s):  
Birgit Henrich ◽  
Marcus Schmitt ◽  
Nora Bergmann ◽  
Klaus Zanger ◽  
Ralf Kubitz ◽  
...  
Keyword(s):  
Microbial Community ◽  
Oral Cavity ◽  
Candida Glabrata ◽  
Biliary Stent ◽  
Human Oral Cavity ◽  
First Time

Mycoplasma salivarium, preferentially an inhabitant of the human oral cavity, has rarely been found in other locations associated with disease. We describe here, for what is believed to be the first time, the detection of M. salivarium, together with Candida glabrata, in an occluded biliary stent of an icteric, cholestatic patient.

scholarly journals UTILITY OF HERBS WITH ITS PHYSICOCHEMICAL PARAMETER IN ORAL HEALTH: A REVIEW

2021 ◽  
Vol 9 (7) ◽  
pp. 1507-1510
Author(s):  
Gupta N. D ◽  
Jain S. S.
Keyword(s):  
Oral Cavity ◽  
Oral Hygiene ◽  
Periodontal Diseases ◽  
Oral Microbiome ◽  
Physicochemical Parameter ◽  
Oral Diseases ◽  
Oral Microflora ◽  
Oral Pain ◽  
Systemic Health ◽  
Micro Organisms

Oral hygiene is the key to one's healthy life. Maintaining oral hygiene is directly related to the body's first line of defence mechanism. It maintains both oral as well as systemic health. Oral microflora plays a very important role in oral hygiene. It is a complex ecosystem of several species of micro-organisms such as streptococci, Neisseria, Veillonella, Actinomyces and other obligate anaerobes. This microbiome is mainly affected by an acidic diet and the acidic environment of the oral cavity. Poor oral hygiene decreases the rate of survival of the oral microbiome and causes dental caries, periodontal diseases, halitosis oral pain & discomfort. Hence, it becomes very essential to maintain the environment of oral cavity friendly to oral microflora. Ayurveda is the science of preserving one’s health has described various herbs to maintain oral hygiene such as Khadira (Catechu tree), Sunthi (Ginger), Da- ruharidra (Indian Berbery), Tankana (Borax), etc. But, to attain its global acceptability physicochemical parameter is used to describe their action. Based on physicochemical parameters herbs seem to be effective in the maintenance of oral hygiene and can reduce the chances of oral diseases. Keywords: Oral hygiene, Oral microflora, physicochemical parameter, pH, etc.

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.

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