Impact of sleep on the microbiome of oral biofilms

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.

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Prevotella dentasini sp. nov., a black-pigmented species isolated from the oral cavity of donkeys

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.017020-0 ◽

2010 ◽

Vol 60 (7) ◽

pp. 1637-1639 ◽

Cited By ~ 10

Author(s):

Kazuko Takada ◽

Kazuhiko Hayashi ◽

Yutaka Sato ◽

Masatomo Hirasawa

Keyword(s):

16S Rrna ◽

Oral Cavity ◽

16S Rrna Gene ◽

Dna Hybridization ◽

Gene Sequence ◽

Sequence Similarity ◽

16S Rrna Gene Sequencing ◽

Rrna Gene ◽

Gene Sequence Analysis ◽

Rrna Gene Sequencing

Four strains (NUM 1903T, NUM 1904, NUM 1912 and NUM 1925) that were obligately anaerobic, pigmented, Gram-negative-staining rods were isolated from the oral cavity of donkeys. These strains were analysed using the Rapid ID 32A, API 20A and API ZYM systems, by DNA–DNA hybridization with other related species and by 16S rRNA gene sequencing. 16S rRNA gene sequence analysis showed that each of the new isolates was a member of the genus Prevotella and related to Prevotella multiformis PPPA21T, showing about 93 % sequence similarity. Based on phylogenetic and phenotypic evidence, it is proposed that the four strains are representatives of a novel species, for which the name Prevotella dentasini sp. nov. is proposed. The type strain is NUM 1903T (=JCM 15908T=DSM 22229T).

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Prevotella aurantiaca sp. nov., isolated from the human oral cavity

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.012831-0 ◽

2010 ◽

Vol 60 (3) ◽

pp. 500-503 ◽

Cited By ~ 21

Author(s):

Mitsuo Sakamoto ◽

Natsuko Suzuki ◽

Masaaki Okamoto

Keyword(s):

Sequence Analysis ◽

16S Rrna ◽

Oral Cavity ◽

16S Rrna Gene ◽

Gene Sequence ◽

Sequence Similarity ◽

16S Rrna Gene Sequence ◽

Rrna Gene ◽

Rrna Gene Sequence ◽

Gene Sequence Analysis

Two anaerobic, pigmented, non-spore-forming, Gram-stain-negative, rod-shaped strains isolated from the human oral cavity, OMA31T and OMA130, were characterized by determining their phenotypic and biochemical features, cellular fatty acid profiles and phylogenetic positions based on 16S rRNA gene sequence analysis. 16S rRNA gene sequence analysis showed that the new isolates belonged to a single species of the genus Prevotella. The two isolates showed 100 % 16S rRNA gene sequence similarity with each other and were most closely related to Prevotella intermedia ATCC 25611T with 96.4 % 16S rRNA gene sequence similarity; the next most closely related strains to the isolates were Prevotella pallens AHN 10371T (96.1 %) and Prevotella falsenii JCM 15124T (95.3 %). Phenotypic and biochemical characteristics of the isolates were the same as those of P. intermedia JCM 12248T, P. falsenii JCM 15124T and Prevotella nigrescens JCM 12250T. The isolates could be differentiated from P. pallens JCM 11140T by mannose fermentation and α-fucosidase activity. Conventional biochemical tests were unable to differentiate the new isolates from P. intermedia, P. falsenii and P. nigrescens. However, hsp60 gene sequence analysis suggested that strain OMA31T was not a representative of P. intermedia, P. pallens, P. falsenii or P. nigrescens. Based on these data, a novel species of the genus Prevotella, Prevotella aurantiaca sp. nov., is proposed, with OMA31T (=JCM 15754T=CCUG 57723T) as the type strain.

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Site-specificity of streptococci in the oral microbiome

10.1101/2021.11.29.470446 ◽

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.

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Veillonellae: Beyond Bridging Species in Oral Biofilm Ecology

Frontiers in Oral Health ◽

10.3389/froh.2021.774115 ◽

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.

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Assessing the variation within the oral microbiome of healthy adults

10.1101/2020.05.07.083634 ◽

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.

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Prevotella saccharolytica sp. nov., isolated from the human oral cavity

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.014720-0 ◽

2010 ◽

Vol 60 (10) ◽

pp. 2458-2461 ◽

Cited By ~ 15

Author(s):

Julia Downes ◽

Anne C. R. Tanner ◽

Floyd E. Dewhirst ◽

William G. Wade

Keyword(s):

Oral Cavity ◽

Type Strain ◽

Gene Sequence ◽

Novel Species ◽

Rrna Gene ◽

Long Chain Fatty Acids ◽

The Novel ◽

Rrna Gene Sequence ◽

Human Oral Cavity ◽

Gene Sequence Analysis

Two strains of anaerobic, Gram-stain-negative bacilli isolated from the human oral cavity (D033B-12-2T and D080A-01) were subjected to a comprehensive range of phenotypic and genotypic tests and were found to be distinct from any previously described species. 16S rRNA gene sequence analysis revealed that the strains were related most closely to the type strain of Prevotella marshii (93.5 % sequence identity). The novel strains were saccharolytic and produced acetic acid and succinic acid as end products of fermentation. The principal cellular long-chain fatty acids were C16 : 0, iso-C14 : 0, C14 : 0, anteiso-C15 : 0, iso-C16 : 0 and C16 : 0 3-OH. The G+C content of the DNA of strain D033B-12-2T was 44 mol%. Strains D033B-12-2T and D080A-01 are considered to represent a single novel species of the genus Prevotella, for which the name Prevotella saccharolytica sp. nov. is proposed. The type strain is D033B-12-2T (=DSM 22473T =CCUG 57944T).

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Streptococcus sanguinis as an opportunistic bacteria in human oral cavity: Adherence, colonization, and invasion

Padjadjaran Journal of Dentistry ◽

10.24198/pjd.vol28no1.13515 ◽

2016 ◽

Vol 28 (1) ◽

Author(s):

Hening Tjaturina Pramesti

Keyword(s):

Cell Wall ◽

Oral Cavity ◽

Acid Synthesis ◽

Human Tooth ◽

Tooth Surface ◽

Interspecies Interactions ◽

Streptococcus Sanguinis ◽

Dental Biofilm ◽

Human Oral Cavity ◽

Opportunistic Bacteria

Streptococcus sanguinis (formerly S. sanguis) is a Gram-positive, facultative anaerobe, nonmotile , normal inhabitant of the human oral cavity, and a member of the viridans group of streptococci. Among the streptococcus, S. sanguinis is a primary colonizer in the human tooth surface or it is recognize as a ‘pioneer’ by forming dental plaque. The aim of this paper is to review the role of Streptococcus sanguinis in the adherence to and invasion of human tissues. S. sanguinis has been reported that it is associated with healthy tooth surfaces but not with caries. S. sanguinis tend to involved in an interspecies interactions with Streptococcus mutans, which is known as competition/coexistence within dental biofilm. In their colonization, this bacteria used enzyme sortase A (SrtA) to cleave LPXTG-containing proteins sequence and anchored the cell wall, while virulence factors in infective endocarditis involved housekeeping functions such as cell wall synthesis, amino acid and nucleic acid synthesis, and the ability to survive under anaerobic conditions.

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Oral Microbiome Signatures in Hematological Cancers Reveal Predominance of Actinomyces and Rothia Species

Journal of Clinical Medicine ◽

10.3390/jcm9124068 ◽

2020 ◽

Vol 9 (12) ◽

pp. 4068

Author(s):

Jean-Luc C. Mougeot ◽

Micaela F. Beckman ◽

Holden C. Langdon ◽

Michael T. Brennan ◽

Farah Bahrani Mougeot

Keyword(s):

Bacterial Species ◽

Alpha Diversity ◽

In Silico Analysis ◽

Oral Microbiome ◽

Rrna Gene ◽

Host Immune System ◽

Linear Discriminant ◽

Microbiome Composition ◽

Hematological Cancers ◽

Healthy Control

The endogenous microbiome of healthy individuals in oral cavities is diverse, representing over 700 bacterial species. Imbalance in oral and gut microbiome composition and associated gene expression has been linked to different forms of hematological (blood) cancers. Our objective is to compare oral microbiome profiles of patients with blood cancers (BC group: N = 39 patients, n = 124 oral samples) to those of healthy control subjects (HC group: N = 27 subjects, n = 100 oral samples). Saliva samples and swabs of buccal mucosa, supragingival plaque, and tongue were collected from blood cancer patients and healthy controls. Next-generation sequencing (16S-rRNA gene V3–V4 region) was used to determine the relative abundance of bacterial taxa present at the genus and species levels. Differences in oral microbiome beta-diversity were determined using multivariate permutational analysis of variance (PERMANOVA). Linear discriminant analysis (LDA) effect size (LEfSe) analysis was performed to identify differentiating bacterial taxa in pairwise comparisons. The PATRICv3.6.7 online tool was used to determine the predominance of potential pathogenicity in the BC group. The oral microbiome beta-diversities of the BC and HC groups differed and corresponded to a reduced alpha-diversity in the BC group. LEfSe analysis showed significant LDA scores for Actinomyces and Rothia spp., differentiating the BC group from the HC group. In silico analysis using PATRICv3.6.7 demonstrated that the groups of bacteria possessing traits of “antibiotic resistance”, “oral pathogen”, and “virulence” was enriched in the BC group. Although 56% of the BC patients received antibiotics within two weeks of the oral bacterial sampling, Actinomyces genus remained the top differentiating feature in the BC group regardless of the administration of antibiotics, while Rothia dentocariosa was detected as the top differentiating feature in the BC patients who did not receive antibiotics, but not in those who received antibiotics. Further investigation is needed to better understand the interactions of certain oral species with the host immune system to better characterize clinically relevant associations with hematological cancers.

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Prevotella marshii sp. nov. and Prevotella baroniae sp. nov., isolated from the human oral cavity

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.63634-0 ◽

2005 ◽

Vol 55 (4) ◽

pp. 1551-1555 ◽

Cited By ~ 52

Author(s):

Julia Downes ◽

Iain Sutcliffe ◽

Anne C. R. Tanner ◽

William G. Wade

Keyword(s):

Oral Cavity ◽

Dna Hybridization ◽

Type Strain ◽

Gene Sequence ◽

Novel Species ◽

Rrna Gene ◽

Homogeneous Groups ◽

Human Oral Cavity ◽

Gene Sequence Analysis ◽

Phenotypic Tests

Eleven strains of anaerobic Gram-negative bacilli isolated from the human oral cavity were subjected to a comprehensive range of phenotypic and genotypic tests and were found to comprise two homogeneous groups, designated E2 and E4. 16S rRNA gene sequence analysis revealed that members of both groups belonged to the genus Prevotella but were distinct from any species with validly published names. This distinction was confirmed by DNA–DNA hybridization and phenotypic tests. Two novel species are therefore proposed: Prevotella marshii sp. nov. (group E2) and Prevotella baroniae (group E4). Both species are saccharolytic; the end-products of fermentation for P. marshii are acetic, propionic and succinic acids, while P. baroniae produces acetic and succinic acids with minor amounts of isovaleric and isobutyric acids. The G+C content of the DNA of the type strain of Prevotella marshii is 51 mol% and that of Prevotella baroniae is 52 mol%. The type strain for P. marshii is E9.34T (=DSM 16973T=CCUG 50419T) and that for P. baroniae is E9.33T (=DSM 16972T=CCUG 50418T).

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Impacts of sleep on the characteristics of dental biofilm

Scientific Reports ◽

10.1038/s41598-020-80541-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Maki Sotozono ◽

Nanako Kuriki ◽

Yoko Asahi ◽

Yuichiro Noiri ◽

Mikako Hayashi ◽

...

Keyword(s):

Quantitative Analysis ◽

Dental Caries ◽

Oral Cavity ◽

Periodontal Disease ◽

Oral Care ◽

Tooth Surface ◽

Oral Diseases ◽

Dental Biofilm

AbstractDental biofilm present on the tooth surface is associated with oral diseases, such as dental caries and periodontal disease. Because bacterial numbers rapidly increase in saliva during sleep, oral care before sleeping is recommended for the prevention of chronic oral diseases. However, temporal circadian changes in the quantity and quality of dental biofilms are poorly understood. This study aimed to investigate the impacts of sleeping on dental biofilm amounts and compositions by using an in situ model. The use of this in situ model enabled us to investigate dental biofilm formed in the oral cavity and to perform a quantitative analysis. Subjects began wearing oral splints in the morning or before sleeping, and biofilm samples were collected at 8, 16, and 24 h after the subjects began wearing oral splints; these samples were then used in various experiments. No significant changes in the numbers of biofilm-forming bacteria were caused by sleep. However, the relative abundances of genera related to periodontitis (i.e., Fusobacterium and Prevotella) increased after awakening. In conclusion, the numbers of biofilm-forming bacteria were not affected by sleep, and the abundances of obligate anaerobes increased after sleep. This research may aid in defining efficacious preventive oral care.

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