Variations of Oral Microbiome in Chronic Insomnia Patients with Different Tongue Features

Chronic insomnia is a disease which brings intense mental pain and disturbing complications to patients worldwide. The oral microbiome exhibits a mechanistic influence on human health. Therefore, it is crucial to understand the oral microbial diversity in insomnia. Tongue diagnosis has been considered a critical basic procedure in insomnia therapeutic decision-making in Traditional Chinese Medicine (TCM). Hence, it is significant to elucidate the various oral microbiome differences in chronic insomnia patients with different tongue features. In this paper, we used 16S rRNA gene sequencing and bioinformatics analysis to investigate dynamic changes in oral bacterial profile and correlations between chronic insomnia patients and healthy individuals, as well as in patients with different tongue coatings. Moreover, the relationship between the severity of insomnia and oral microbiota was explored. Our findings showed that chronic insomnia patients harbored a significantly higher diversity of oral bacteria when compared to healthy controls. More importantly, the results revealed that the diversity and relative abundance of the bacterial community was significantly altered among different tongue coatings in patients but not in healthy individuals. Oral bacteria with a relative abundance [Formula: see text]1% and [Formula: see text] among different tongue groups were considered remarkable bacteria, which included three phyla Proteobacteria, Bacteroidetes, Gracilibacteria, and four genera, Streptococcus, Prevotella_7, Rothia, and Neisseria. Our findings indicate that changes in oral microbiome correlate with tongue coatings in patients with chronic insomnia. Thus, the remarkable microbiome may provide inspiration for further studies on the correlation between tongue diagnosis and oral microbiome in chronic insomnia patients.

Download Full-text

Oral Microbiota Identifies Patients in Early Onset Rheumatoid Arthritis

Microorganisms ◽

10.3390/microorganisms9081657 ◽

2021 ◽

Vol 9 (8) ◽

pp. 1657

Author(s):

Anders Esberg ◽

Linda Johansson ◽

Ingegerd Johansson ◽

Solbritt Rantapää Dahlqvist

Keyword(s):

Rheumatoid Arthritis ◽

Early Onset ◽

Amplicon Sequencing ◽

Oral Bacteria ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Disease Manifestation ◽

Periodontal Status ◽

Quality Register

Rheumatoid arthritis (RA) is the most common autoimmune inflammatory disease, and single periodontitis-associated bacteria have been suggested in disease manifestation. Here, the oral microbiota was characterized in relation to the early onset of RA (eRA) taking periodontal status into consideration. 16S rRNA gene amplicon sequencing of saliva bacterial DNA from 61 eRA patients without disease-modifying anti-rheumatic drugs and 59 matched controls was performed. Taxonomic classification at 98.5% was conducted against the Human Oral Microbiome Database, microbiota functions were predicted using PICRUSt, and periodontal status linked from the Swedish quality register for clinically assessed caries and periodontitis. The participants were classified into three distinct microbiota-based cluster groups with cluster allocation differences by eRA status. Independently of periodontal status, eRA patients had enriched levels of Prevotella pleuritidis, Treponema denticola, Porphyromonas endodontalis and Filifactor alocis species and in the Porphyromonas and Fusobacterium genera and functions linked to ornithine metabolism, glucosylceramidase, beta-lactamase resistance, biphenyl degradation, fatty acid metabolism and 17-beta-estradiol-17-dehydrogenase metabolism. The results support a deviating oral microbiota composition already in eRA patients compared with healthy controls and highlight a panel of oral bacteria that may be useful in eRA risk assessment in both periodontally healthy and diseased persons.

Download Full-text

OTUs clustering should be avoided for defining oral microbiome

10.1101/2021.08.09.455616 ◽

2021 ◽

Author(s):

Alba Regueira-Iglesias ◽

Lara Vazquez-Gonzalez ◽

Carlos Balsa-Castro ◽

Triana Blanco-Pintos ◽

Victor Manuel Arce ◽

...

Keyword(s):

Microbial Diversity ◽

Operational Taxonomic Unit ◽

Oral Bacteria ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

High Coverage ◽

Archaeal Species ◽

Health And Disease ◽

Similarity Relationships

This in silico investigation aimed to: 1) evaluate a set of primer pairs with high coverage, including those most commonly used in the literature, to find the different oral species with 16S rRNA gene amplicon similarity/identity (ASI) values ≥97%; and 2) identify oral species that may be erroneously clustered in the same operational taxonomic unit (OTU) and ascertain whether they belong to distinct genera or other higher taxonomic ranks. Thirty-nine primer pairs were employed to obtain amplicon sequence variants (ASVs) from the complete genomes of 186 bacterial and 135 archaeal species. For each primer, ASVs without mismatches were aligned using BLASTN and their similarity values were obtained. Finally, we selected ASVs from different species with an ASI value ≥97% that were covered 100% by the query sequences. For each primer, the percentage of species-level coverage with no ASI≥97% (SC-NASI≥97%) was calculated. Based on the SC-NASI≥97% values, the best primer pairs were OP_F053-KP_R020 for bacteria (65.05%), KP_F018-KP_R002 for archaea (51.11%), and OP_F114-KP_R031 for bacteria and archaea together (52.02%). Eighty percent of the oral-bacteria and oral-archaea species shared an ASI≥97% with at least one other taxa, including Campylobacter, Rothia, Streptococcus, and Tannerella, which played conflicting roles in the oral microbiota. Moreover, around a quarter and a third of these two-by-two similarity relationships were between species from different bacteria and archaea genera, respectively. Furthermore, even taxa from distinct families, orders, and classes could be grouped in the same cluster. Consequently, irrespective of the primer pair used, OTUs constructed with a 97% similarity provide an inaccurate description of oral-bacterial and oral-archaeal species, greatly affecting microbial diversity parameters. As a result, clustering by OTUs impacts the credibility of the associations between some oral species and certain health and disease conditions. This limits significantly the comparability of the microbial diversity findings reported in oral microbiome literature.

Download Full-text

Impact of Oropharyngeal Administration of Colostrum in Preterm Newborns’ Oral Microbiome

Nutrients ◽

10.3390/nu13124224 ◽

2021 ◽

Vol 13 (12) ◽

pp. 4224

Author(s):

Ramon V. Cortez ◽

Andrea Fernandes ◽

Luiz Gustavo Sparvoli ◽

Marina Padilha ◽

Rubens Feferbaum ◽

...

Keyword(s):

Preterm Infants ◽

16S Rrna Gene Sequencing ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Alpha And Beta Diversity ◽

Longitudinal Observational Study ◽

Key Factor ◽

Rrna Gene Sequencing ◽

Preterm Newborns

The initial colonization of the human microbiota is of paramount importance. In this context, the oropharyngeal administration of colostrum is a safe, viable, and well-tolerated practice even by the smallest preterm infants. Therefore, this study evaluated the effects of oropharyngeal administration of colostrum on the establishment of preterm infants’ oral microbiota. A longitudinal observational study was carried out with 20 premature neonates, divided into two groups: one receiving the protocol (Oropharyngeal Administration of Colostrum; OAC) and the other one receiving Standard Caare (SC). Saliva samples were collected from the newborns weekly during the study period (from the day of birth until the 21st day of life) for analysis of oral microbiota through 16S rRNA gene sequencing. We observed that the colonization of the oral microbiota of preterm newborns preseanted a higher relative abundance of Staphylococcus on the 7th day of life, mainly in the OAC group. Additionally, an increased abundance of Bifidobacterium and Bacteroides was observed in the OAC group at the first week of life. Regarding alpha and beta diversity, time was a key factor in the oral modulation of both groups, showing how dynamic this environment is in early life.

Download Full-text

Analysis of the Effects of Dietary Pattern on the Oral Microbiome of Elite Endurance Athletes

Nutrients ◽

10.3390/nu11030614 ◽

2019 ◽

Vol 11 (3) ◽

pp. 614 ◽

Cited By ~ 17

Author(s):

Nida Murtaza ◽

Louise Burke ◽

Nicole Vlahovich ◽

Bronwen Charlesson ◽

Hayley O’Neill ◽

...

Keyword(s):

Discriminant Analysis ◽

Relative Abundance ◽

Distance Measure ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Unifrac Distance ◽

Linear Discriminant ◽

Principal Coordinates ◽

Low Carbohydrate

Although the oral microbiota is known to play a crucial role in human health, there are few studies of diet x oral microbiota interactions, and none in elite athletes who may manipulate their intakes of macronutrients to achieve different metabolic adaptations in pursuit of optimal endurance performance. The aim of this study was to investigate the shifts in the oral microbiome of elite male endurance race walkers from Europe, Asia, the Americas and Australia, in response to one of three dietary patterns often used by athletes during a period of intensified training: a High Carbohydrate (HCHO; n = 9; with 60% energy intake from carbohydrates; ~8.5 g kg−1 day−1 carbohydrate, ~2.1 g kg−1 day−1 protein, 1.2 g kg−1 day−1 fat) diet, a Periodised Carbohydrate (PCHO; n = 10; same macronutrient composition as HCHO, but the intake of carbohydrates is different across the day and throughout the week to support training sessions with high or low carbohydrate availability) diet or a ketogenic Low Carbohydrate High Fat (LCHF; n = 10; 0.5 g kg−1 day−1 carbohydrate; 78% energy as fat; 2.1 g kg−1 day−1 protein) diet. Saliva samples were collected both before (Baseline; BL) and after the three-week period (Post treatment; PT) and the oral microbiota profiles for each athlete were produced by 16S rRNA gene amplicon sequencing. Principal coordinates analysis of the oral microbiota profiles based on the weighted UniFrac distance measure did not reveal any specific clustering with respect to diet or athlete ethnic origin, either at baseline (BL) or following the diet-training period. However, discriminant analyses of the oral microbiota profiles by Linear Discriminant Analysis (LDA) Effect Size (LEfSe) and sparse Partial Least Squares Discriminant Analysis (sPLS-DA) did reveal changes in the relative abundance of specific bacterial taxa, and, particularly, when comparing the microbiota profiles following consumption of the carbohydrate-based diets with the LCHF diet. These analyses showed that following consumption of the LCHF diet the relative abundances of Haemophilus, Neisseria and Prevotella spp. were decreased, and the relative abundance of Streptococcus spp. was increased. Such findings suggest that diet, and, in particular, the LCHF diet can induce changes in the oral microbiota of elite endurance walkers.

Download Full-text

Oral Microbiota Development in Early Childhood

Scientific Reports ◽

10.1038/s41598-019-54702-0 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 7

Author(s):

Beatrice Kennedy ◽

Sari Peura ◽

Ulf Hammar ◽

Silvia Vicenzi ◽

Anna Hedman ◽

...

Keyword(s):

Early Childhood ◽

Relative Abundance ◽

Early Life ◽

Alpha Diversity ◽

Antibiotic Use ◽

Population Based ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Microbiota Composition

AbstractEarly life determinants of the oral microbiota have not been thoroughly elucidated. We studied the association of birth and early childhood characteristics with oral microbiota composition using 16 S ribosomal RNA (rRNA) gene sequencing in a population-based Swedish cohort of 59 children sampled at 6, 12 and 24 months of age. Repeated-measurement regression models adjusted for potential confounders confirmed and expanded previous knowledge about the profound shift of oral microbiota composition in early life. These alterations included increased alpha diversity, decreased beta diversity and alteration of bacterial composition with changes in relative abundance of 14 of the 20 most common operational taxonomic units (OTUs). We also found that birth characteristics, breastfeeding and antibiotic use were associated with overall phyla distribution and/or with the relative abundance of specific OTUs. Further, we detected a novel link between morning salivary cortisol level, a physiological marker of neuroendocrine activity and stress, and overall phyla distribution as well as with decreased abundance of the most common OTU mapped to the Streptococcaceae family. In conclusion, a major part of the maturation of the oral microbiome occurs during the first two years of life, and this development may be influenced by early life circumstances.

Download Full-text

Dynamic Alterations of Oral Microbiota Related to Halitosis in Preschool Children

Frontiers in Cellular and Infection Microbiology ◽

10.3389/fcimb.2021.599467 ◽

2021 ◽

Vol 11 ◽

Author(s):

Yu Zhang ◽

Ce Zhu ◽

Guizhi Cao ◽

Jingyu Zhan ◽

Xiping Feng ◽

...

Keyword(s):

Preschool Children ◽

Prediction Model ◽

Relative Abundance ◽

Clinical Manifestations ◽

Oral Microbiome ◽

Control Group ◽

Rrna Gene ◽

Oral Microbiota ◽

Tongue Coating

ObjectiveThis longitudinal study was aimed to evaluate the dynamic shift in oral microbiota during the process of halitosis progression among preschool children.MethodsThe oral examinations, questionnaires and tongue coating specimens were collected at the baseline and 12-month follow-up. All children were oral healthy at the enrollment. At the 12-month follow-up, children who developed halitosis were included to the halitosis group (n = 10). While children who matched the age, gender, kindergarten and without halitosis were included to the control group (n = 10). 16S rRNA gene sequencing was used to reveal the shift of the tongue coating microbiome in these children during the 12- month period with the Human Oral Microbiome Database.ResultsA remarkable shift in relative abundance of specific bacteria was observed prior to halitosis development. The principal coordinates and alpha diversity analyses revealed different shifting patterns of halitosis and the healthy participants’ microbiome structures and bacterial diversity over the 12-month follow-up. Both groups showed variable microbiota community structures before the onset of halitosis. Halitosis-enriched species Prevotella melaninogenica, Actinomyces sp._HMT_180 and Saccharibacteria TM7_G-1_bacterium_HMT_352 were finally selected as biomarkers in the halitosis-onset prediction model after screening, with a prediction accuracy of 91.7%.ConclusionsThe microbiome composition and relative abundance of the tongue coatings in the halitosis and control groups remarkably differed, even prior to the onset of the clinical manifestations of halitosis. The halitosis prediction model constructed on the basis of tongue coating microbiome biomarkers indicated the microbial shifts before the halitosis onset. Therefore, this can be considered for the timely detection and intervention of halitosis in children.

Download Full-text

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

Journal of Immunology Research ◽

10.1155/2021/7403042 ◽

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.

Download Full-text

Investigation of the impact of commonly used medications on the oral microbiome of individuals living without major chronic conditions

PLoS ONE ◽

10.1371/journal.pone.0261032 ◽

2021 ◽

Vol 16 (12) ◽

pp. e0261032

Author(s):

Vanessa DeClercq ◽

Jacob T. Nearing ◽

Morgan G. I. Langille

Keyword(s):

Thyroid Hormones ◽

Relative Abundance ◽

Beta Diversity ◽

Chronic Conditions ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Shannon Diversity ◽

Significant Difference ◽

The Impact

Background Commonly used medications produce changes in the gut microbiota, however, the impact of these medications on the composition of the oral microbiota is understudied. Methods Saliva samples were obtained from 846 females and 368 males aged 35–69 years from a Canadian population cohort, the Atlantic Partnership for Tomorrow’s Health (PATH). Samples were analyzed by 16S rRNA gene sequencing and differences in microbial community compositions between nonusers, single-, and multi-drug users as well as the 3 most commonly used medications (thyroid hormones, statins, and proton pump inhibitors (PPI)) were examined. Results Twenty-six percent of participants were taking 1 medication and 21% were reported taking 2 or more medications. Alpha diversity indices of Shannon diversity, Evenness, Richness, and Faith’s phylogenetic diversity were similar among groups, likewise beta diversity as measured by Bray-Curtis dissimilarity (R2 = 0.0029, P = 0.053) and weighted UniFrac distances (R2 = 0.0028, P = 0.161) were non-significant although close to our alpha value threshold (P = 0.05). After controlling for covariates (sex, age, BMI), six genera (Saprospiraceae uncultured, Bacillus, Johnsonella, Actinobacillus, Stenotrophomonas, and Mycoplasma) were significantly different from non-medication users. Thyroid hormones, HMG-CoA reductase inhibitors (statins) and PPI were the most reported medications. Shannon diversity differed significantly among those taking no medication and those taking only thyroid hormones, however, there were no significant difference in other measures of alpha- or beta diversity with single thyroid hormone, statin, or PPI use. Compared to participants taking no medications, the relative abundance of eight genera differed significantly in participants taking thyroid hormones, six genera differed in participants taking statins, and no significant differences were observed with participants taking PPI. Conclusion The results from this study show negligible effect of commonly used medications on microbial diversity and small differences in the relative abundance of specific taxa, suggesting a minimal influence of commonly used medication on the salivary microbiome of individuals living without major chronic conditions.

Download Full-text

Association of Bitter Taste Receptor T2R38 Polymorphisms, Oral Microbiota, and Rheumatoid Arthritis

Current Issues in Molecular Biology ◽

10.3390/cimb43030103 ◽

2021 ◽

Vol 43 (3) ◽

pp. 1460-1472

Author(s):

Vivianne Cruz de Jesus ◽

Manu Singh ◽

Robert J. Schroth ◽

Prashen Chelikani ◽

Carol A. Hitchon

Keyword(s):

Rheumatoid Arthritis ◽

Relative Abundance ◽

Bitter Taste ◽

Bacterial Species ◽

Taste Receptor ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Microbial Composition ◽

The Impact

The association of taste genetics and the oral microbiome in autoimmune diseases such as rheumatoid arthritis (RA) has not been reported. We explored a novel oral mucosal innate immune pathway involving the bitter taste G protein-coupled receptor T2R38. This case–control study aimed to evaluate whether T2R38 polymorphisms associate with the buccal microbial composition in RA. Genomic DNA was obtained from buccal swabs of 35 RA patients and 64 non-RA controls. TAS2R38 genotypes were determined by Sanger sequencing. The buccal microbiome was assessed by Illumina MiSeq sequencing of the V4-16S rRNA gene. Bacterial community differences were analyzed with alpha and beta diversity measures. Linear discriminant analysis effect size identified taxa discriminating between RA versus non-RA and across TAS2R38 genotypes. TAS2R38 genotype frequency was similar between RA and non-RA controls (PAV/PAV; PAV/AVI; AVI/AVI: RA 42.9%; 45.7%; 11.4% versus controls 32.8%; 48.4%; 18.8%, chi-square (2, N = 99) = 2.1, p = 0.35). The relative abundance of Porphyromonas, among others, differed between RA and non-RA controls. The relative abundance of several bacterial species also differed across TAS2R38 genotypes. These findings suggest an association between T2R38 polymorphisms and RA buccal microbial composition. However, further research is needed to understand the impact of T2R38 in oral health and RA development.

Download Full-text

Niche-Specialist And Age-Related Microbial Ecosystem: Correlation Analysis With Immune Cells In Oral Homeostasis

10.21203/rs.3.rs-829179/v1 ◽

2021 ◽

Author(s):

Dongjia Lin ◽

Lisa Yang ◽

Qiannan Hu ◽

Dikan Wang ◽

Wenxiao Dai ◽

...

Keyword(s):

Correlation Analysis ◽

Immune Cells ◽

Immune Cell ◽

Oral Bacteria ◽

Oral Microbiome ◽

Rrna Gene ◽

Oral Microbiota ◽

Life Stages ◽

Microbial Ecosystem ◽

Age Related

Abstract Background: The oral microbial ecosystem, with distinct characteristics in structure and evolution, plays an important role in the mucosal homeostasis. The characterization of baseline microbial and functional diversity in the oral microbiome has been discussed, yet the taxon-taxon relationships, and the role of the microbes themselves to the host mucosa are still lack of discussing. In addition, the current literature seems insufficient to draw a definitive conclusion about a possible impact of ageing on the oral microbiota. Therefore, the study focuses on the spatial and temporal characteristics of the oral microbial ecosystem, and its correlation with immune cell in oral homeostasis. Results: The V3V4 region of 16S rRNA gene of 30 samples from different sites (gingiva, palate, buccal, tongue) and life stages (adult, old) was analyzed. Flow cytometry was used to investigate the residing immune cells. The niche-specialist and age-related communities, characterized by alterations in microbiota structure, taxon-taxon relationship, microbial functions, and immune cell inhabiting, have been addressed. Interestingly, network analysis shows more antagonistic interactions in gingiva, palatal site, and old mice saliva, where harbor a richer diversity. While in buccal mucosa and tongue, it appears more synergic interactions to maintain the ecosystem balance. Functional analysis reveals that the significant factor that determines the niche for a microbe is its local habitat in the content of one specific age, which includes its immediate neighbors. Correlation analysis suggests strong associations between distinct oral bacteria and Th cells exist in different life stages. Conclusions: Our findings propose that the oral microbial ecosystem, with niche-specialist and age-related characteristics, has unique evolution and co-evolution with the host to maintain oral homeostasis, which provides critical insights on mucosal microbiology.

Download Full-text