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Metagenomic next-generation sequencing for the diagnosis of oral and maxillofacial space infections.Journal of Dental Sciences Jul 2023Metagenomic next-generation sequencing (mNGS) has been widely used for the detection of pathogens causing infectious diseases. This study aimed to evaluate the potential...
BACKGROUND/PURPOSE
Metagenomic next-generation sequencing (mNGS) has been widely used for the detection of pathogens causing infectious diseases. This study aimed to evaluate the potential ability of mNGS to detect pathogens causing oral and maxillofacial space infection (OMSI) and compare the results with those of the traditional diagnostic microbial culture method.
MATERIALS AND METHODS
We retrospectively reviewed the data of 218 patients diagnosed with OMSI who underwent microbial culture and mNGS at the Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, from July 2020 to January 2022.
RESULTS
The positivity rate of mNGS (216 cases) was significantly higher than that of microbial culture (123 cases). The most frequently detected bacteria were different between these two detection methods. (16.05%, 35), (15.69%, 34) and (6.88%, 15) were the most commonly isolated bacteria by culture. However, (61.47%, 134), (68.35%, 149) and (57.34%, 125) were the most commonly detected bacteria by mNGS. mNGS also has advantages in diagnosing viral infections. The optimal numbers of diagnostic reads were 1162 and 588 for the diagnosis of and infections, respectively. Read numbers were significantly correlated with C-reactive protein (CRP), procalcitonin (PCT), and blood glucose levels and neutrophil percentage (NEUT%).
CONCLUSION
For pathogens causing OMSI, mNGS had a higher rate of microbial pathogen detection and remarkable advantages in identifying coinfections involving viruses and fungi. The read numbers for mNGS are important for diagnostic accuracy and disease severity evaluation.
PubMed: 37404664
DOI: 10.1016/j.jds.2022.09.002 -
Frontiers in Microbiology 2023The aim of our study was to investigate the impact of long-term exposure to heavy metals on the microbiome of the buccal mucosa, to unveil the link between environmental...
OBJECTIVES
The aim of our study was to investigate the impact of long-term exposure to heavy metals on the microbiome of the buccal mucosa, to unveil the link between environmental contamination and the oral microbial ecosystem, and to comprehend its potential health implications.
METHODS
Subjects were divided into two groups: the exposure group and the control group. We collected samples of buccal mucosa, soil, and blood, and conducted microbial diversity analysis on both groups of oral samples using 16S rRNA gene sequencing. The concentrations of heavy metals in blood and soil samples were also determined. Additionally, microbial networks were constructed for the purpose of topological analysis.
RESULTS
Due to long-term exposure to heavy metals, the relative abundance of , , , and increased, while the abundance of , , , , and decreased. The concentrations of heavy metals in the blood (Pb, Cd, Hg, and Mo) were associated with the growth of , , , and . In addition, the relative abundances of some pathogenic bacteria, such as , , and , were found to be enriched in the exposure group. Compared to the exposure group network, the control group network had a greater number of nodes, modules, interactive species, and keystone taxa. Module hubs and connectors in the control group converted into peripherals in the exposure group, indicating that keystone taxa changed. Metals in the blood (Pb, Cd, Hg, and Mo) were drivers of the microbial network of the buccal mucosa, which can have adverse effects on the network, thus providing conditions for the occurrence of certain diseases.
CONCLUSION
Long-term exposure to multiple metals perturbs normal bacterial communities in the buccal mucosa of residents in contaminated areas. This exposure reduces the complexity and stability of the microbial network and increases the risk of developing various diseases.
PubMed: 37928665
DOI: 10.3389/fmicb.2023.1264619 -
International Journal of Clinical... Sep 2023Microorganisms induce a variety of infections and diseases in the human body and are largely ubiquitous in the nature of the contamination, directly, or indirectly...
To Evaluate and Compare the Antimicrobial Efficacy of Various Disinfecting Agents on K-file against Gram-positive and Gram-negative Bacteria of Endodontic Origin: An Study.
INTRODUCTION
Microorganisms induce a variety of infections and diseases in the human body and are largely ubiquitous in the nature of the contamination, directly, or indirectly leading to transmission of infectious agents. A substantial number of bacterial species have been identified as inhabitants of the oral cavity. Infection control is a major topic of concern in medical and dental healthcare settings.
AIM
To evaluate the disinfecting ability of various herbal extracts on sterilization of endodontic files against endodontic pathogens.
MATERIALS AND METHODS
The study was conducted in three phases to evaluate the disinfecting ability of tea tree, , eucalyptus, and oil on sterilization of endodontic files against , β, specie and .
RESULTS
Colony-forming units (CFU) of all tested bacteria among group I (tea tree oil) were found to be significantly lower than that among group II ( oil), group III (eucalyptus oil), and group IV ( oil), respectively.
CONCLUSION
The antimicrobial activity among all the essential oils was found to be maximum for tea tree oil, followed in descending order by , eucalyptus, and oils. Hence, the incorporation of these herbs in dental practice will prove to be a valuable adjunct in dental treatment.
CLINICAL SIGNIFICANCE
Herbs have also been long used in various endodontic medicaments and dressings with obtundent and soothing effects and exhibited a great microbial inhibition potential against the tested endodontic pathogens.
HOW TO CITE THIS ARTICLE
Opi K, Dhinsa K, Tripathi AM, To Evaluate and Compare the Antimicrobial Efficacy of Various Disinfecting Agents on K-file against Gram-positive and Gram-negative Bacteria of Endodontic Origin: An Study. Int J Clin Pediatr Dent 2023;16(S-2):S161-S167.
PubMed: 38078027
DOI: 10.5005/jp-journals-10005-2646 -
BMC Microbiology May 2024Intra-oral halitosis (IOH) is bad breath produced locally by the mouth in addition to systemic diseases and is one of the main causes of interpersonal communication and...
BACKGROUND
Intra-oral halitosis (IOH) is bad breath produced locally by the mouth in addition to systemic diseases and is one of the main causes of interpersonal communication and psychological disorders in modern society. However, current treatment modalities still only alleviate IOH and do not eradicate it. Therefore, based on the differential performance of oral microecology in IOH patients, we propose a microbiota transplantation treatment aimed at restoring oral microecological balance and analyze its feasibility by oral flora colonization test in Wistar rats.
OBJECTIVE
Saliva flora samples were collected from IOH patients and healthy subjects to analyze the feasibility of oral microbiota transplantation (OMT) for the treatment of IOH by the Wistar rat oral flora colonization test.
METHODS
Seven patients with IOH who visited the First Affiliated Hospital of Xinjiang Medical University from June 2017 to June 2022 with the main complaint of halitosis and three healthy subjects were randomly selected. A Halimeter portable breath detector was used to record breath values and collect saliva flora samples. Sixteen SPF-grade male Wistar rats were housed in the Animal Experiment Center of Xinjiang Medical University and randomly divided into an experimental group (Group E) and a control group (Group C) for the oral flora colonization test. Species composition and associated metabolic analysis of oral flora during the Wistar rat test using 16SrRNA sequencing technology and PICRUSt metabolic analysis. Also, the changes in the breath values of the rats were recorded during the test.
RESULTS
The proportion of Porphyromonas, Fusobacterium, Leptotrichia, and Peptostreptococcus was significantly higher in group E compared to group C after colonization of salivary flora of IOH patients (all P < 0.05), and the abundance with Gemella was zero before colonization, while no colonization was seen in group C after colonization compared to baseline. PICRUSt metabolic analysis also showed significantly enhanced IOH-related metabolic pathways after colonization in group E (all P < 0.05), as well as significantly higher breath values compared to baseline and group C (all P < 0.0001). After colonization by salivary flora from healthy subjects, group E rats showed a decrease in the abundance of associated odor-causing bacteria colonization, a reduction in associated metabolism, and a significant decrease in breath values. In contrast, group C also showed differential changes in flora structure and breath values compared to baseline after salivary flora colonization of IOH patients.
CONCLUSIONS
OMT for IOH is a promising green treatment option, but the influence of environmental factors and individual differences still cannot be ignored.
Topics: Animals; Halitosis; Rats, Wistar; Male; Rats; Humans; Microbiota; Saliva; Mouth; Feasibility Studies; Bacteria; Adult; Female; RNA, Ribosomal, 16S; Middle Aged
PubMed: 38760711
DOI: 10.1186/s12866-024-03322-4 -
Microbiology Resource Announcements Jun 2024is a recently described bacterium belonging to the family, which was isolated in 2016 from pig intestine. Herein, we report the complete genome sequence of a clinical...
is a recently described bacterium belonging to the family, which was isolated in 2016 from pig intestine. Herein, we report the complete genome sequence of a clinical isolate of (GAI11004) obtained from porcine endocarditis in Japan. The genome contains a 2.4-Mb circular chromosome.
PubMed: 38842319
DOI: 10.1128/mra.00201-24 -
The Korean Journal of Internal Medicine Jun 2024Recent research has increasingly focused on the role of the gastric microbiome in the development of gastric cancer. We aimed to investigate the changes in the...
BACKGROUND/AIMS
Recent research has increasingly focused on the role of the gastric microbiome in the development of gastric cancer. We aimed to investigate the changes in the microbiome during gastric carcinogenesis in structural and functional aspects, with a specific focus on the association between oral and gastric microbiomes.
METHODS
We collected saliva, gastric juice, and gastric tissue samples from 141 patients at different stages of gastric carcinogenesis and processed them for microbiome analysis using 16S rRNA gene profiling. The alpha and beta diversities were analyzed, and the differences in microbiome composition and function profiles were analyzed among the groups, as well as the correlation between changes in the oral and gastric microbiomes during carcinogenesis.
RESULTS
We observed significant differences in microbial diversity and composition between the disease and control groups, primarily in the gastric juice. Specific bacterial strains, including Schaalia odontolytica, Streptococcus cristatus, and Peptostreptococcus stomatis, showed a significant increase in abundance in the gastric juice in the low-grade dysplasia and gastric cancer groups. Notably, the correlation between the oral and gastric microbiota compositions, increased as the disease progressed. Predictive analysis of the metagenomic functional profiles revealed changes in functional pathways that may be associated with carcinogenesis (ABC transport and two-component systems).
CONCLUSIONS
During gastric carcinogenesis, the abundance of oral commensals associated with cancer increased in the stomach. The similarity in microbial composition between the stomach and oral cavity also increased, implying a potential role of oral-gastric bacterial interactions in gastric cancer development.
PubMed: 38910513
DOI: 10.3904/kjim.2023.490 -
Microbiology Spectrum Jun 2024Malignant central airway stenosis is treated with airway stent placement, but post-placement microbial characteristics remain unclear. We studied microbial features in...
UNLABELLED
Malignant central airway stenosis is treated with airway stent placement, but post-placement microbial characteristics remain unclear. We studied microbial features in 60 patients post-stent placement, focusing on changes during granulation tissue proliferation. Samples were collected before stent ( = 29), after stent on day 3 ( = 20), and after granulation tissue formation (AS-GTF, = 43). Metagenomic sequencing showed significant respiratory tract microbiota changes with granulation tissue. The microbiota composition, dominated by , , and , was similar among the groups. At the species level, the AS-GTF group exhibited significant differences, with and enriched. Analysis based on tracheoesophageal fistula presence identified and as the main differential species, enriched in the fistula subgroup. Viral and fungal detection showed and as the main species, respectively. These findings highlight microbiota changes after stent placement, potentially associated with granulation tissue proliferation, informing stent placement therapy and anti-infective treatment optimization.
IMPORTANCE
Malignant central airway stenosis is a life-threatening condition that can be effectively treated with airway stent placement. However, despite its clinical importance, the microbial characteristics of the respiratory tract following stent insertion remain poorly understood. This study addresses this gap by investigating the microbial features in patients with malignant central airway stenosis after stent placement, with a specific focus on microbial changes during granulation tissue proliferation. The findings reveal significant alterations in the diversity and structure of the respiratory tract microbiota following the placement of malignant central airway stents. Notably, certain bacterial species, including and , exhibit distinct patterns in the after-stent granulation tissue formation group. Additionally, the presence of tracheoesophageal fistula further influences the microbial composition. These insights provide valuable references for optimizing stent placement therapy and enhancing clinical anti-infective strategies.
Topics: Humans; Stents; Female; Male; Microbiota; Middle Aged; Aged; Bacteria; Airway Obstruction; Respiratory System; Granulation Tissue; Adult; Aged, 80 and over; Tracheoesophageal Fistula
PubMed: 38747599
DOI: 10.1128/spectrum.03472-23 -
NPJ Biofilms and Microbiomes Apr 2024Dysbiosis of the human oral microbiota has been reported to be associated with oral cavity squamous cell carcinoma (OSCC) while the host-microbiota interactions with...
Dysbiosis of the human oral microbiota has been reported to be associated with oral cavity squamous cell carcinoma (OSCC) while the host-microbiota interactions with respect to the potential impact of pathogenic bacteria on host genomic and epigenomic abnormalities remain poorly studied. In this study, the mucosal bacterial community, host genome-wide transcriptome and DNA CpG methylation were simultaneously profiled in tumors and their adjacent normal tissues of OSCC patients. Significant enrichment in the relative abundance of seven bacteria species (Fusobacterium nucleatum, Treponema medium, Peptostreptococcus stomatis, Gemella morbillorum, Catonella morbi, Peptoanaerobacter yurli and Peptococcus simiae) were observed in OSCC tumor microenvironment. These tumor-enriched bacteria formed 254 positive correlations with 206 up-regulated host genes, mainly involving signaling pathways related to cell adhesion, migration and proliferation. Integrative analysis of bacteria-transcriptome and bacteria-methylation correlations identified at least 20 dysregulated host genes with inverted CpG methylation in their promoter regions associated with enrichment of bacterial pathogens, implying a potential of pathogenic bacteria to regulate gene expression, in part, through epigenetic alterations. An in vitro model further confirmed that Fusobacterium nucleatum might contribute to cellular invasion via crosstalk with E-cadherin/β-catenin signaling, TNFα/NF-κB pathway and extracellular matrix remodeling by up-regulating SNAI2 gene, a key transcription factor of epithelial-mesenchymal transition (EMT). Our work using multi-omics approaches explored complex host-microbiota interactions and provided important insights into genetic and functional basis in OSCC tumorigenesis, which may serve as a precursor for hypothesis-driven study to better understand the causational relationship of pathogenic bacteria in this deadly cancer.
Topics: Humans; Squamous Cell Carcinoma of Head and Neck; Epigenomics; Dysbiosis; Mouth Neoplasms; Carcinoma, Squamous Cell; Bacteria; Fusobacterium nucleatum; Head and Neck Neoplasms; Epigenesis, Genetic; Microbiota; Tumor Microenvironment
PubMed: 38589501
DOI: 10.1038/s41522-024-00511-x -
Children (Basel, Switzerland) Nov 2023The role of diet in shaping oral microbiota and its potential contribution to the development of periodontal pathogens cannot be understated. This study aimed to explore...
The role of diet in shaping oral microbiota and its potential contribution to the development of periodontal pathogens cannot be understated. This study aimed to explore the correlation between dietary habits and the prevalence of 11 periodontal pathogens among children and adolescents in Oradea, Romania. The identification of these pathogens was performed using the micro-IDent test kit, capable of detecting 11 specific periodontal pathogens. Bacterial sampling was conducted from the crevicular fluid in the morning, prior to brushing, followed by the completion of a brief questionnaire by parents. The questionnaire captured various aspects of the children's eating habits, including meal frequency, consumption of sweets, and hydration levels. The collected samples were dispatched to the laboratory for analysis, which provided insights into the abundance of microorganisms. The study encompassed 60 participants aged between 2 and 18 years, with the majority reported by their parents to have regulated meal timings, frequent sugar intake, and adequate hydration. The findings revealed significant associations between certain dietary factors and the presence of specific periodontal pathogens. Notably, the absence of breastfeeding was linked with the detection of and . Furthermore, frequent consumption of sweets corresponded with the presence of spp., which was particularly observed in individuals consuming sweets 2-3 times a day. Insufficient age-appropriate hydration showed an association with the prevalence of , , and spp. In this sample, it became evident that eating habits and diet influenced the presence of several periodontal pathogens. The lack of breastfeeding was predominantly associated with positive results for and , while inadequate hydration correlated more frequently with the presence of and Moreover, frequent consumption of sweets was linked to the presence of spp.
PubMed: 38002870
DOI: 10.3390/children10111779 -
Biomedicines Aug 2023The oral microbiome can be influenced by many factors and its dysbiosis can have negative effects on oral and general health. The purpose of this study was to analyze...
The oral microbiome can be influenced by many factors and its dysbiosis can have negative effects on oral and general health. The purpose of this study was to analyze the intensity of 11 periodontal pathogenic microorganisms identified in the oral cavity of a sample of children and adolescents from Oradea, Romania and to investigate the association of some variables (age, gender, body mass index, diet, and salivary pH) with the identified microorganisms. The cross-sectional study was conducted on a group of clinically healthy patients under the age of 18 years from Oradea, Romania. For the analysis of the periodontal pathogens, the micro-IDent kit was used, which determines 11 bacterial markers for periodontitis and peri-implantitis. The kit is based on the polymerase chain reaction (PCR). Bacterial sampling was carried out according to the manufacturer's instructions. A total of 60 children (23 male, 37 female) were included in this study, and were divided into three different age categories. No statistically significant results were identified for gender. However statistically significant results were obtained for other variables. Positive results for and were associated with ages between 13 and 18 years, while positive results for spp. were associated with ages between 2 and 5 years. Positive results for , , , and were associated with an overweight BMI. Negative results for and were associated with a natural diet in the first 6 months of life. Positive results for and were associated with an acidic salivary pH. In this study, the identified periodontal pathogens were associated with age, body mass index, diet in the first 6 months of life, and salivary pH.
PubMed: 37760818
DOI: 10.3390/biomedicines11092374