scholarly journals Clinical Detection of Chronic Rhinosinusitis through Next-Generation Sequencing of the Oral Microbiota

2020 ◽  
Vol 8 (6) ◽  
pp. 959 ◽  
Author(s):  
Ben-Chih Yuan ◽  
Yao-Tsung Yeh ◽  
Ching-Chiang Lin ◽  
Cheng-Hsieh Huang ◽  
Hsueh-Chiao Liu ◽  
...  
Keyword(s):  
16S Rrna ◽  
Chronic Rhinosinusitis ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Upper Respiratory Tract ◽  
Aerobic Culture ◽  
Β Diversity ◽  
Α Diversity ◽  
Significant Difference ◽  
Anaerobic Infections

Chronic rhinosinusitis (CRS) is the chronic inflammation of the sinus cavities of the upper respiratory tract, which can be caused by a disrupted microbiome. However, the role of the oral microbiome in CRS is not well understood. Polymicrobial and anaerobic infections of CRS frequently increased the difficulty of cultured and antibiotic therapy. This study aimed to elucidate the patterns and clinical feasibility of the oral microbiome in CRS diagnosis. Matched saliva and nasal swabs were collected from 18 CRS patients and 37 saliva specimens from normal volunteers were collected for 16S rRNA sequencing. The α-diversity of the saliva displayed no significant difference between control and CRS patients, whereas the β-diversity was significantly different (p = 0.004). Taxonomic indices demonstrated that Veillonella dispar, Rothia mucilaginosa, and Porphyromonas endodontalis were enriched, while Campylobacter and Cardiobacterium were reduced in the saliva of CRS patients. These microbial markers could significantly distinguish CRS patients from control (AUC = 0.939). It is noted that the 16S rRNA results of the nasal swab were consistent with the nasopharynx aerobic culture, and additionally detected multiple pathogens in CRS patients. In summary, these results indicated these oral microbiomes may provide a novel signal for CRS detection and that NGS may be an alternative approach for CRS diagnosis.

scholarly journals The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 878 ◽  
Author(s):  
Maria A. Sierra ◽  
Qianhao Li ◽  
Smruti Pushalkar ◽  
Bidisha Paul ◽  
Tito A. Sandoval ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oral Microbiome ◽  
Data Curation ◽  
Ribosomal Database Project ◽  
Β Diversity ◽  
Bioinformatics Tools ◽  
Large Databases ◽  
Α Diversity ◽  
Reference Databases ◽  
Taxonomical Classification

There is currently no criterion to select appropriate bioinformatics tools and reference databases for analysis of 16S rRNA amplicon data in the human oral microbiome. Our study aims to determine the influence of multiple tools and reference databases on α-diversity measurements and β-diversity comparisons analyzing the human oral microbiome. We compared the results of taxonomical classification by Greengenes, the Human Oral Microbiome Database (HOMD), National Center for Biotechnology Information (NCBI) 16S, SILVA, and the Ribosomal Database Project (RDP) using Quantitative Insights Into Microbial Ecology (QIIME) and the Divisive Amplicon Denoising Algorithm (DADA2). There were 15 phyla present in all of the analyses, four phyla exclusive to certain databases, and different numbers of genera were identified in each database. Common genera found in the oral microbiome, such as Veillonella, Rothia, and Prevotella, are annotated by all databases; however, less common genera, such as Bulleidia and Paludibacter, are only annotated by large databases, such as Greengenes. Our results indicate that using different reference databases in 16S rRNA amplicon data analysis could lead to different taxonomic compositions, especially at genus level. There are a variety of databases available, but there are no defined criteria for data curation and validation of annotations, which can affect the accuracy and reproducibility of results, making it difficult to compare data across studies.

scholarly journals Salivary microbiome profiling reveals a dysbiotic schizophrenia-associated microbiota

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Ying Qing ◽  
Lihua Xu ◽  
Gaoping Cui ◽  
Liya Sun ◽  
Xiaowen Hu ◽  
...  
Keyword(s):  
16S Rrna Gene Sequencing ◽  
Oral Microbiome ◽  
Disease Stage ◽  
First Episode ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
Β Diversity ◽  
Metabolic Functions ◽  
Α Diversity ◽  
Rrna Gene Sequencing

AbstractSchizophrenia is a debilitating mental disorder and often has a prodromal period, referred to as clinical high risk (CHR) for psychosis, prior to the first episode. The etiology and pathogenesis of schizophrenia remain unclear. Despite the human gut microbiome being associated with schizophrenia, the role of the oral microbiome, which is a vital player in the mouth–body connection, is not well understood. To address this, we performed 16S rRNA gene sequencing to investigate the salivary microbiome in 85 patients with drug-naïve first-episode schizophrenia (FES), 43 individuals at CHR, and 80 healthy controls (HCs). The salivary microbiome of FES patients was characterized by higher α-diversity and lower β-diversity heterogeneity than those of CHR subjects and HCs. Proteobacteria, the predominant phylum, was depleted, while Firmicutes and the Firmicutes/Proteobacteria ratio was enriched, in a stepwise manner from HC to CHR to FES. H2S-producing bacteria exhibited disease-stage-specific enrichment and could be potential diagnostic biomarkers for FES and CHR. Certain salivary microbiota exhibited disease-specific correlation patterns with symptomatic severities, peripheral pro-inflammatory cytokines, thioredoxin, and S100B in FES. Furthermore, the metabolic functions from inferred metagenomes of the salivary microbiome were disrupted in FES, especially amino acid metabolism, carbohydrate metabolism, and xenobiotic degradation. This study has established a link between salivary microbiome alterations and disease initiation and provided the hypothesis of how the oral microbiota could influence schizophrenia.

scholarly journals Frequency of Selenomonas Noxia in Oral Microbiota of Obese and Normal Weight People in Duhok-Iraq

2019 ◽  
Vol 7 (4) ◽  
pp. 120-124
Author(s):  
Roshna M. Qadir ◽  
Mahde S. Abdulrahman
Keyword(s):  
Oral Bacteria ◽  
Normal Weight ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Obese People ◽  
Overweight People ◽  
Significant Difference ◽  
Overweight Group ◽  
Oral Carriage ◽  
Selenomonas Noxia

Obesity represents one of the major problematic health issues worldwide. Recent evidences suggest that obesity is related with the alteration of the oral microbiome. The aim of this study was to measure the salivary bacterial Selenomonas noxia in Duhok population. A total of 155 saliva samples were collected from individuals (aged between 19-35 years) of both genders (86 females and 69 males). The individuals were divided into three groups (obese, overweight, and normal weight) based on their body mass index. Bacterial genomic DNA was extracted from saliva samples. Molecular detections of Selenomonas noxia were performed by the polymerase chain reaction. Among the 155 participants, 34.1% were obese, 26.4% overweight and 39.3% normal weight individuals. The prevalence rate of oral S. noxia among all people was 82.6%. The highest rate of S. noxia was in obese people (86.8%), followed by overweight (85.4%) and normal weight people (77%). The prevalence of S. noxia in overweight people was statistically significant in compare with the normal weight people (p<0.0001). Moreover, the oral carriage of S. noxia was highest among the overweight females (94.5%) followed by obese females (88.9%). However, no significant difference was found compared to males. The result revealed that it is possible to assume that the expansion of S. noxia in saliva is due to obesity. Moreover, the composition of salivary microbiome may lead to the risk that the overweight group is at risk of future obesity. However, further investigations are required with larger sample and participants with different socioeconomic status in order to address the exact link between obesity and oral bacteria. This could lead to a new and promising therapeutic way for improving human's health.  

The microbial characteristics of patients with esophageal squamous cell carcinoma before and after immunotherapy.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. e16016-e16016
Author(s):  
Jing Zuo ◽  
Wenjing Lv ◽  
Yudong Wang ◽  
Zhisong Fan ◽  
Li Feng ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
16S Rrna ◽  
Esophageal Squamous Cell Carcinoma ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Fecal Samples ◽  
Β Diversity ◽  
Α Diversity ◽  
Before And After ◽  
New Ideas

e16016 Background: Esophageal squamous cell carcinoma (ESCC) is a common malignancy without effective therapy. Immune checkpoint–oriented immunotherapies have shown considerable promise and the advent of esophageal microbiome provides researchers with new ideas. Methods: DNA was extracted from blood, oral mucosal, saliva, urine, fecal samples from 20 ESCC patients before and after immunotherapy. Total microbial genomic DNA samples were extracted using an OMEGA Soil DNA Kit (D5625-01). The V3–V4 regions of bacterial 16S rRNA genes were amplified by PCR using the forward primer and the reverse primer and were sequenced with Illumina MiSeq platform. In order to comprehensively evaluate the α diversity of microbial communities, we used Chao1 and Observed Species indices to characterize the richness, Shannon and Simpson indices to characterize the diversity. PCoA were used to analyze differences in β diversity. Functions of 16S rRNA sequences were predicted using the PICRUSt2 and KEGG databases. Results: A comparison of blood, oral mucosal, saliva, urine, fecal samples of ESCC patients before and after immunotherapy showed that α diversity was not statistically significant. In terms of β diversity, no statistically significant differences were detected within blood, oral mucosal, saliva, urine, fecal samples of ESCC patients before and after immunotherapy. In ESCC patients treated before immunotherapy, the α diversity and β diversity of blood, oral mucosal, saliva, urine, fecal samples were different, and in ESCC patients treated after immunotherapy had the same rule. At the phylum level, the top 5 microbes in ESCC patients before and after immunotherapy were Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria. At the genus level, the top 5 microbes in ESCC patients before immunotherapy were Aquabacterium, Streptococcus, Prevotella, Veillonella, Bacteroides, and in ESCC patients after immunotherapy were Aquabacterium, Streptococcus, Prevotella, Faecalibacterium, Veillonella. In terms of the microbial functions in ESCC patients before and after immunotherapy, the metabolic pathways accounted for the most. Conclusions: This study is conducive to exploring new mechanisms for tumor cells to evade host immune surveillance, providing new ideas and new strategies for the microecology-based immunotherapy of ESCC.

scholarly journals Salivary Microbiome in Children With Down Syndrome

2021 ◽  
Author(s):  
Seiji Morishima ◽  
Kaori Takeda ◽  
Setsue Greenan ◽  
Yoshinobu Maki
Keyword(s):  
Down Syndrome ◽  
Relative Abundance ◽  
Quantitative Polymerase Chain Reaction ◽  
Genetic Disorder ◽  
Oral Microbiome ◽  
Mixed Dentition ◽  
Oral Diseases ◽  
16S Sequencing ◽  
Α Diversity ◽  
Significant Difference

Abstract Down syndrome (DS), a most frequently occurring genetic disorder, is associated with oral morphological abnormalities and higher incidence rates of oral diseases. Recent studies have analyzed the oral microbiome to elucidate their relationships with oral diseases and general health; however, reports on the oral microbiome in individuals with DS are scarce. This study aimed to characterize the oral microbiome in children with DS. The salivary microbiomes of children with DS (DS) and children without DS (ND) aged 1 to 12 years were compared. Results of culture and quantitative polymerase chain reaction (qPCR) detection tests for cariogenic and periodontopathic bacteria showed no significant differences in the detected bacteria between the DS and ND groups, with the exception of a significantly higher detection rate of Candida albicans in children with DS with mixed dentition. A comparison of the salivary microbiomes by 16S sequencing showed no significant difference in α diversity; however, it showed a significant difference in β diversity. Children with DS had a higher relative abundance of Corynebacterium and Cardiobacterium, and lower relative abundance of TM7. This study provided basic data on the salivary microbiome of children with DS and further identified a characteristic microbiological marker of children with DS.

scholarly journals The Dynamics of Respiratory Microbiota during Mechanical Ventilation in Patients with Pneumonia

2020 ◽  
Vol 9 (3) ◽  
pp. 638 ◽  
Author(s):  
Seongji Woo ◽  
So-Yeong Park ◽  
Youngmi Kim ◽  
Jin Pyeong Jeon ◽  
Jae Jun Lee ◽  
...  
Keyword(s):  
Mechanical Ventilation ◽  
Intensive Care ◽  
Clinical Outcomes ◽  
Extubation Failure ◽  
Shannon Index ◽  
Β Diversity ◽  
Α Diversity ◽  
Significant Difference ◽  
Respiratory Microbiome ◽  
Successful Extubation

Bacterial pneumonia is a major cause of mechanical ventilation in intensive care units. We hypothesized that the presence of particular microbiota in endotracheal tube aspirates during the course of intubation was associated with clinical outcomes such as extubation failure or 28-day mortality. Sixty mechanically ventilated ICU (intensive care unit) patients (41 patients with pneumonia and 19 patients without pneumonia) were included, and tracheal aspirates were obtained on days 1, 3, and 7. Gene sequencing of 16S rRNA was used to measure the composition of the respiratory microbiome. A total of 216 endotracheal aspirates were obtained from 60 patients. A total of 22 patients were successfully extubatedwithin3 weeks, and 12 patients died within 28days. Microbiota profiles differed significantly between the pneumonia group and the non-pneumonia group (Adonis, p < 0.01). While α diversity (Shannon index) significantly decreased between day 1 and day 7 in the successful extubation group, it did not decrease in the failed extubation group among intubated patients with pneumonia. There was a significant difference in the change of βdiversity between the successful extubation group and the failed extubation group for Bray-Curtis distances (p < 0.001). At the genus level, Rothia, Streptococcus, and Prevotella correlated with the change of β diversity. A low relative abundance of Streptococci at the time of intubation was strongly associated with 28-day mortality. The dynamics of respiratory microbiome were associated with clinical outcomes such as extubation failure and mortality. Further large prospective studies are needed to test the predictive value of endotracheal aspirates in intubated patients.

scholarly journals The Gut Microbiome of Heart Failure With Preserved Ejection Fraction

2021 ◽  
Author(s):  
Anna L. Beale ◽  
Joanne A. O’Donnell ◽  
Michael E. Nakai ◽  
Shane Nanayakkara ◽  
Donna Vizi ◽  
...  
Keyword(s):  
Risk Factors ◽  
Heart Failure ◽  
Ejection Fraction ◽  
Gut Microbiota ◽  
Gut Microbiome ◽  
Short Chain ◽  
Preserved Ejection Fraction ◽  
Β Diversity ◽  
Α Diversity ◽  
Significant Difference

Background Risk factors for heart failure with preserved ejection fraction (HFpEF) include hypertension, age, sex, and obesity. Emerging evidence suggests that the gut microbiota independently contributes to each one of these risk factors, potentially mediated via gut microbial‐derived metabolites such as short‐chain fatty acids. In this study, we determined whether the gut microbiota were associated with HFpEF and its risk factors. Methods and Results We recruited 26 patients with HFpEF and 67 control participants from 2 independent communities. Patients with HFpEF were diagnosed by exercise right heart catheterization. We assessed the gut microbiome by bacterial 16S rRNA sequencing and food intake by the food frequency questionnaire. There was a significant difference in α‐diversity (eg, number of microbes) and β‐diversity (eg, type and abundance of microbes) between both cohorts of controls and patients with HFpEF ( P =0.001). We did not find an association between β‐diversity and specific demographic or hemodynamic parameters or risk factors for HFpEF. The Firmicutes to Bacteroidetes ratio, a commonly used marker of gut dysbiosis, was lower, but not significantly so ( P =0.093), in the patients with HFpEF. Compared with controls, the gut microbiome of patients with HFpEF was depleted of bacteria that are short‐chain fatty acid producers. Consistent with this, participants with HFpEF consumed less dietary fiber (17.6±7.7 versus 23.2±8.8 g/day; P =0.016). Conclusions We demonstrate key changes in the gut microbiota in patients with HFpEF, including the depletion of bacteria that generate metabolites known to be important for cardiovascular homeostasis. Further studies are required to validate the role of these gut microbiota and metabolites in the pathophysiology of HFpEF.

Host Genetic Associations with Salivary Microbiome in Oral Cancer

2021 ◽  
pp. 002203452110519
Author(s):  
S.F. Yang ◽  
C.W. Lin ◽  
C.Y. Chuang ◽  
Y.C. Lee ◽  
W.H. Chung ◽  
...  
Keyword(s):  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Genetic Effect ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Oral Diseases ◽  
Genetic Associations ◽  
Β Diversity ◽  
Host Genetic ◽  
Discovery Stage

Despite the growing recognition of a host genetic effect on shaping gut microbiota composition, the genetic determinants of oral microbiota remain largely unexplored, especially in the context of oral diseases. Here, we performed a microbiome genome-wide association study in 2 independent cohorts of patients with oral squamous cell carcinoma (OSCC, n = 144 and 67) and an additional group of noncancer individuals ( n = 104). Besides oral bacterial dysbiosis and signatures observed in OSCC, associations of 3 loci with the abundance of genus-level taxa and 4 loci with β diversity measures were detected ( q < 0.05) at the discovery stage. The most significant hit (rs10906082 with the genus Lachnoanaerobaculum, P = 3.55 × 10–9 at discovery stage) was replicated in a second OSCC cohort. Moreover, the other 2 taxonomical associations, rs10973953 with the genus Kingella ( P = 1.38 × 10–9) and rs4721629 with the genus Parvimonas ( P = 3.53 × 10–8), were suggestive in the meta-analysis combining 2 OSCC cohorts. Further pathway analysis revealed that these loci were enriched for genes in regulation of oncogenic and angiogenic responses, implicating a genetic anchor to the oral microbiome in estimation of casual relationships with OSCC. Our findings delineate the role of host genotypes in influencing the structure of oral microbial communities.

scholarly journals Microbiome Profiles of Ligature-Induced Periodontitis in Nonhuman Primates across the Life Span

2019 ◽  
Vol 87 (6) ◽  
Author(s):  
Sreenatha Kirakodu ◽  
Jin Chen ◽  
Janis Gonzalez Martinez ◽  
Octavio A. Gonzalez ◽  
Jeffrey Ebersole
Keyword(s):  
Nonhuman Primates ◽  
Age Groups ◽  
Amplicon Sequencing ◽  
Young Adolescent ◽  
Oral Microbiome ◽  
Host Responses ◽  
Content Type ◽  
Β Diversity ◽  
16S Amplicon Sequencing ◽  
Α Diversity

ABSTRACT This investigation compared the microbiomes colonizing teeth during the initiation, progression, and resolution of periodontitis in nonhuman primates (Macaca mulatta) at different ages. Subgingival plaque samples were collected at baseline; 0.5, 1, and 3 months following ligature-induced periodontitis; and following naturally occurring disease resolution at 5 months. Samples were analyzed using 16S amplicon sequencing to identify bacterial profiles across age groups: young (<3 years of age), adolescent (3 to 7 years), adult (12 to 15 years), and aged (17 to 23 years). α-Diversity of the microbiomes was greater in the adult/aged samples than in the young/adolescent samples. β-Diversity of the samples demonstrated clear age group differences, albeit individual variation in microbiomes between animals within the age categories was noted. Phylum distributions differed between the young/adolescent animals and the adult/aged animals at each of the time points, showing an enrichment of the phyla Spirochetes, Fusobacteria, and Bacteroidetes associated with periodontitis. Major differences in the top 50 operational taxonomic units (OTUs) were noted in the young and adolescent microbiomes during initiation and progression postligation compared to the adult and aged animals. The proportions of a large number of species in the top 50 OTUs were lower at baseline and in resolved disease microbiomes in the young samples, while profiles in adolescent animals were more consistent with the disease microbiomes. Microbiome profiles for resolution for adults and aged animals appeared more resilient and generally maintained a pattern similar to that of disease. Use of the model can expand our understanding of the crucial interactions of the oral microbiome and host responses in periodontitis.

scholarly journals The Human Oral Microbiome

2010 ◽  
Vol 192 (19) ◽  
pp. 5002-5017 ◽  
Author(s):  
Floyd E. Dewhirst ◽  
Tuste Chen ◽  
Jacques Izard ◽  
Bruce J. Paster ◽  
Anne C. R. Tanner ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Species Level ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Oral Microbiota ◽  
16S Rrna Gene Sequences ◽  
Culture Independent ◽  
Health And Disease

ABSTRACT The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome is comprised of over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene sequences into a curated phylogeny-based database, the Human Oral Microbiome Database (HOMD), and make it web accessible (www.homd.org ). The HOMD includes 619 taxa in 13 phyla, as follows: Actinobacteria, Bacteroidetes, Chlamydiae, Chloroflexi, Euryarchaeota, Firmicutes, Fusobacteria, Proteobacteria, Spirochaetes, SR1, Synergistetes, Tenericutes, and TM7. The second aim was to analyze 36,043 16S rRNA gene clones isolated from studies of the oral microbiota to determine the relative abundance of taxa and identify novel candidate taxa. The analysis identified 1,179 taxa, of which 24% were named, 8% were cultivated but unnamed, and 68% were uncultivated phylotypes. Upon validation, 434 novel, nonsingleton taxa will be added to the HOMD. The number of taxa needed to account for 90%, 95%, or 99% of the clones examined is 259, 413, and 875, respectively. The HOMD is the first curated description of a human-associated microbiome and provides tools for use in understanding the role of the microbiome in health and disease.

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