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Journal of Environmental and Public... 2023This study was conducted at one of the largest poultry companies in Kuwait during November and December 2019 to evaluate the microbiological threats of (APEC), spp.,...
This study was conducted at one of the largest poultry companies in Kuwait during November and December 2019 to evaluate the microbiological threats of (APEC), spp., and to chickens in fattening houses by counting and identifying the microorganisms by culturing and pyrosequencing analysis. During the fattening cycle, the temperature and humidity ranged between 23.6°C and 29°C and 64.1% and 87.1%, respectively. The total bacterial population and measured in the indoor and outdoor air exhibited a linear relationship during the fattening cycle. The total bacterial and concentrations determined during the cycle ranged between 150 and 2000 CFU/m and 0 and 1000 CFU/m, respectively. and spp. concentrations determined during the cycle ranged between 1 and 220 CFU/m and 4 and 110 CFU/m, respectively. Pyrosequencing analysis of the air inside the houses at the end of the cycle revealed extensive biodiversity in the microorganisms, detecting 32 bacterial genera and 14 species. The identified species belonging to the genera , , , , and were identified as potentially affecting human and broiler health. The emission of potentially pathogenic bacteria to the outdoor environment from chicken housing can pose a considerable risk to human health and environmental microbial pollution. This study could guide the development of integrated control devices for monitoring microbes in broiler production facilities during chicken collection for transport to slaughterhouses.
Topics: Humans; Animals; Chickens; Escherichia coli; Air Pollution, Indoor; Air Microbiology; Air Pollution; Aspergillus; Bacteria; Environmental Monitoring; Fungi
PubMed: 37283812
DOI: 10.1155/2023/3512328 -
American Journal of Respiratory and... Jul 2023Children with preschool wheezing or school-age asthma are reported to have airway microbial imbalances. To identify clusters in children with asthma or wheezing using...
Children with preschool wheezing or school-age asthma are reported to have airway microbial imbalances. To identify clusters in children with asthma or wheezing using oropharyngeal microbiota profiles. Oropharyngeal swabs from the U-BIOPRED (Unbiased Biomarkers for the Prediction of Respiratory Disease Outcomes) pediatric asthma or wheezing cohort were characterized using 16S ribosomal RNA gene sequencing, and unsupervised hierarchical clustering was performed on the Bray-Curtis β-diversity. Enrichment scores of the Molecular Signatures Database hallmark gene sets were computed from the blood transcriptome using gene set variation analysis. Children with severe asthma or severe wheezing were followed up for 12-18 months, with assessment of the frequency of exacerbations. Oropharyngeal samples from 241 children (age range, 1-17 years; 40% female) revealed four taxa-driven clusters dominated by , , , and . The clusters showed significant differences in atopic dermatitis, grass pollen sensitization, FEV% predicted after salbutamol, and annual asthma exacerbation frequency during follow-up. The cluster was the most allergic and included the highest percentage of children with two or more exacerbations per year during follow-up. The oropharyngeal clusters were different in the enrichment scores of TGF-β (transforming growth factor-β) (highest in the cluster) and Wnt/β-catenin signaling (highest in the cluster) transcriptomic pathways in blood (all values <0.05). Analysis of the oropharyngeal microbiota of children with asthma or wheezing identified four clusters with distinct clinical characteristics (phenotypes) that associate with risk for exacerbation and transcriptomic pathways involved in airway remodeling. This suggests that further exploration of the oropharyngeal microbiota may lead to novel pathophysiologic insights and potentially new treatment approaches.
Topics: Female; Male; Humans; Transcriptome; Respiratory Sounds; Asthma; Hypersensitivity; Microbiota
PubMed: 37163754
DOI: 10.1164/rccm.202211-2107OC -
Frontiers in Cellular and Infection... 2021Autoimmune hepatitis (AIH) is a common cause of liver cirrhosis. To identify the characteristics of the oral microbiome in patients with AIH, we collected 204 saliva... (Randomized Controlled Trial)
Randomized Controlled Trial
Autoimmune hepatitis (AIH) is a common cause of liver cirrhosis. To identify the characteristics of the oral microbiome in patients with AIH, we collected 204 saliva samples including 68 AIH patients and 136 healthy controls and performed microbial MiSeq sequencing after screening. All samples were randomly divided into discovery cohorts (46 AIH and 92 HCs) and validation cohorts (22 AIH and 44 HCs). Moreover, we collected samples of 12 AIH patients from Hangzhou for cross-regional validation. We described the oral microbiome characteristics of AIH patients and established a diagnostic model. In the AIH group, the oral microbiome diversity was significantly increased. The microbial communities remarkably differed between the two groups. Seven genera, mainly and , were dominant in the HC group, while 51 genera, and , were enriched in the AIH group. Notably, we found 23 gene functions, including Membrane Transport, Carbohydrate Metabolism, and Glycerolipid metabolism that were dominant in AIH and 31 gene functions that prevailed in HCs. We further investigated the correlation between the oral microbiome and clinical parameters. The optimal 5 microbial markers were figured out through a random forest model, and the distinguishing potential achieved 99.88% between 46 AIH and 92 HCs in the discovery cohort and 100% in the validation cohort. Importantly, the distinguishing potential reached 95.55% in the cross-regional validation cohort. In conclusion, this study is the first to characterize the oral microbiome in AIH patients and to report the successful establishment of a diagnostic model and the cross-regional validation of microbial markers for AIH. Importantly, oral microbiota-targeted biomarkers may be able to serve as powerful and noninvasive diagnostic tools for AIH.
Topics: Cohort Studies; Hepatitis, Autoimmune; Humans; Microbiota; Saliva; Veillonella
PubMed: 34094998
DOI: 10.3389/fcimb.2021.656674 -
Pediatric Research Dec 2021Tobacco smoke contains numerous toxic chemicals that accumulate in indoor environments creating thirdhand smoke (THS). We investigated if THS-polluted homes differed in...
INTRODUCTION
Tobacco smoke contains numerous toxic chemicals that accumulate in indoor environments creating thirdhand smoke (THS). We investigated if THS-polluted homes differed in children's human and built-environment microbiomes as compared to THS-free homes.
METHODS
Participants were n = 19 THS-exposed children and n = 10 unexposed children (≤5 years) and their caregivers. Environmental and biological samples were analyzed for THS pollutants and exposure. Swab samples were collected from the built-environment (floor, table, armrest, bed frame) and child (finger, nose, mouth, and ear canal), and 16S ribosomal RNA genes were analyzed for bacterial taxa using high-throughput DNA sequencing.
RESULTS
Phylogenetic α-diversity was significantly higher for the built-environment microbiomes in THS-polluted homes compared to THS-free homes (p < 0.014). Log2-fold comparison found differences between THS-polluted and THS-free homes for specific genera in samples from the built-environment (e.g., Acinetobacter, Bradyrhizobium, Corynebacterium, Gemella, Neisseria, Staphylococcus, Streptococcus, and Veillonella) and in samples from children (esp. Corynebacterium, Gemella, Lautropia, Neisseria, Rothia, Staphylococcus, and Veillonella).
CONCLUSION
When exposed to THS, indoor and children microbiomes are altered in an environment-specific manner. Changes are similar to those reported in previous studies for smokers and secondhand smoke-exposed persons. THS-induced changes in child and built-environmental microbiomes may play a role in clinical outcomes in children.
IMPACT
Despite smoking bans, children can be exposed to tobacco smoke residue (i.e., thirdhand smoke) that lingers on surfaces and in settled house dust. Thirdhand smoke exposure is associated with changes in the microbiomes of the home environment and of the children living in these homes. Thirdhand smoke is associated with increased phylogenetic diversity of the home environment and changes in the abundances of several genera of the child microbiome known to be affected by active smoking and secondhand smoke (e.g., Corynebacterium, Staphylococcus, Streptococcus). Thirdhand smoke exposure by itself may induce alterations in the microbiome that play a role in childhood pathologies.
Topics: Bacteria; Child, Preschool; Family Characteristics; Humans; Microbiota; Species Specificity; Tobacco Smoke Pollution
PubMed: 33654287
DOI: 10.1038/s41390-021-01400-1 -
Frontiers in Cellular and Infection... 2024Graves' disease (GD) is the most common cause of hyperthyroidism, and its pathogenesis remains incompletely elucidated. Numerous studies have implicated the gut...
BACKGROUND
Graves' disease (GD) is the most common cause of hyperthyroidism, and its pathogenesis remains incompletely elucidated. Numerous studies have implicated the gut microbiota in the development of thyroid disorders. This study employs Mendelian randomization analysis to investigate the characteristics of gut microbiota in GD patients, aiming to offer novel insights into the etiology and treatment of Graves' disease.
METHODS
Two-sample Mendelian randomization (MR) analysis was employed to assess the causal relationship between Graves' disease and the gut microbiota composition. Gut microbiota data were sourced from the international consortium MiBioGen, while Graves' disease data were obtained from FINNGEN. Eligible single nucleotide polymorphisms (SNPs) were selected as instrumental variables. Multiple analysis methods, including inverse variance-weighted (IVW), MR-Egger regression, weighted median, weighted mode, and MR-RAPS, were utilized. Sensitivity analyses were conducted employing MR-Egger intercept test, Cochran's Q test, and leave-one-out analysis as quality control measures.
RESULTS
The Mendelian randomization study conducted in a European population revealed a decreased risk of Graves' disease associated with (Odds ratio (OR) [95% confidence interval (CI)]: 0.89 [0.89 ~ 0.90], adjusted value: <0.001), (OR: [95% CI]: 0.555 [0.437 ~ 0.706], adjusted value: <0.001), and (OR [95% CI]: 0.632 [0.492 ~ 0.811], adjusted value: 0.016). No significant evidence of heterogeneity, or horizontal pleiotropy was detected. Furthermore, the preliminary MR analysis identified 13 bacterial species including group and group, exhibiting significant associations with Graves' disease onset, suggesting potential causal effects.
CONCLUSION
A causal relationship exists between gut microbiota and Graves' disease. , , and emerge as protective factors against Graves' disease development. Prospective probiotic supplementation may offer a novel avenue for adjunctive treatment in the management of Graves' disease in the future.
Topics: Humans; Bacteroidaceae; Bacteroides; Veillonella; Prospective Studies; Graves Disease; Genome-Wide Association Study
PubMed: 38404289
DOI: 10.3389/fcimb.2024.1288222 -
Frontiers in Oral Health 2021In light of recent technological advances in Next-generation sequencing (NGS) and the accumulation of large, publicly available oral microbiome datasets, the need for...
In light of recent technological advances in Next-generation sequencing (NGS) and the accumulation of large, publicly available oral microbiome datasets, the need for meta-analysing data on caries microbiome is becoming feasible and essential. A consensus on the identification of enriched organisms in cariogenic dysbiotic biofilms would be reached. For example, members of the genus have been detected in caries biofilms, and may have an underestimated contribution to the dysbiotic process. Hence, we aimed to determine the abundance of species in dental caries in studies using NGS data. Analysis was performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (registered at PROSPERO: CRD42020204150). Studies investigating microbial composition in saliva, dental biofilm, or carious dentin were included. Six databases and grey literature were searched. Two independent reviewers selected the papers and assessed the methodological quality. Searches retrieved 1,323 titles, from which 38 studies were included in a qualitative synthesis, comprising a total of 1,374 caries and 745 caries-free individuals. Most studies analysed 16S rRNA amplicons, and only 5 studies used shotgun metagenomics and metatranscriptomics. A geographical bias was observed. The methodological quality was downrated in 81.5% of the studies due to the lack of criteria for defining cases and standard criteria used for measurement of the condition in a reliable way. Six studies on early childhood caries (ECC) were meta-analysed, confirming a significant enrichment of spp. in caries-associated biofilms (but not saliva) when compared to caries-free controls [mean difference: 2.22 (0.54-3.90); = 0.01]. . is more abundant in individuals suffering with ECC when compared to caries-free controls (very low evidence certainty), and should be considered for further studies to observe their metabolism in dental caries. There is an urgent need for a consensus in methodologies used to allow for more rigorous comparison between NGS studies, particularly including clinical data and details of caries diagnosis, as they are currently scarce. Inconsistent reporting on the NGS data affected the cross-study comparison and the biological connexions of the relative abundances on caries microbiome.
PubMed: 35048071
DOI: 10.3389/froh.2021.770917 -
Dental Materials Journal Aug 2023Adhesion of the most common dental biofilm bacteria to alloys used in orthodontics in relation to surface characteristics was analyzed. Streptococcus mutans (S. mutans),...
Adhesion of the most common dental biofilm bacteria to alloys used in orthodontics in relation to surface characteristics was analyzed. Streptococcus mutans (S. mutans), Streptococcus oralis (S. oralis), Veillonella parvula (V. parvula), and Aggregatibacter actinomycetemcomitans (A. actynomicetemcomitans) were incubated for 4 h with nickel-titanium (NiTi) and stainless-steel (SS) wires. The surface roughness and free energy of the alloys, as well as the hydrophobicity of the alloys and bacteria, were assessed. NiTi had higher surface free energy and rougher (p<0.001) and more hydrophilic surfaces than SS (p<0.001). The hydrophobic properties of the bacteria decreased in the following order: V. parvula>S. oralis>S. mutans>A. actynomicetemcomitans. Bacterial adhesion generally increased over time, though this pattern was influenced by the type of alloy and the bacteria present (p<0.001). In a multiple linear regression, the principal predictor of adhesion was bacterial hydrophobicity (p<0.001), followed by time (p<0.001); alloy surface characteristics had a low influence.
Topics: Dental Alloys; Orthodontic Wires; Surface Properties; Orthodontic Appliances; Alloys; Streptococcus mutans; Titanium; Stainless Steel
PubMed: 37271541
DOI: 10.4012/dmj.2022-235 -
Frontiers in Immunology 2021Biliary atresia is the most common cause of liver disease and liver transplantation in children. The accumulation of bile acids in hepatocytes and the stimulation of the...
BACKGROUND AND AIMS
Biliary atresia is the most common cause of liver disease and liver transplantation in children. The accumulation of bile acids in hepatocytes and the stimulation of the intestinal microbiome can aggravate the disease progression. This study investigated changes in the composition of the gut microbiota and its metabolites in biliary atresia and the possible effects of these changes on disease progression.
METHODS
Stool samples of biliary atresia at different disease stages and matched control individuals were collected (early stage: 16 patients, 16 controls; later stage: 16 patients, 10 controls). Metagenomic sequencing was performed to evaluate the gut microbiota structure. Untargeted metabolomics was performed to detect and analyze the metabolites and bile acid composition.
RESULTS
A disturbed gut microbiota structure occurred in the early and later stages of biliary atresia. , , , and have always been dominant. The abundance of displayed significant changes between the early and later stages of biliary atresia. Combined with clinical indicators, Spearman's analysis showed that and strongly correlated with liver enzymes. had an enormously positive relationship with lithocholic acid derivatives. Metabolites involved in tryptophan metabolism were changed in the patients with biliary atresia, which had a significant association with stool and blood total bilirubin ( < 0.05).
CONCLUSIONS
The liver damage of biliary atresia was directly or indirectly exacerbated by the interaction of enriched (), (), and () with dysmetabolism of tryptophan and bile acid.
Topics: Bile Acids and Salts; Biliary Atresia; Disease Progression; Dysbiosis; Female; Gastrointestinal Microbiome; Humans; Infant; Infant, Newborn; Male; Tryptophan
PubMed: 34630385
DOI: 10.3389/fimmu.2021.698900 -
Scientific Reports Oct 2020Recently, it was suggested that the nitrite (NO) produced from NO by oral bacteria might contribute to oral and general health. Therefore, we aimed to clarify the...
Recently, it was suggested that the nitrite (NO) produced from NO by oral bacteria might contribute to oral and general health. Therefore, we aimed to clarify the detailed information about the bacterial NO-production in the oral biofilm. Dental plaque and tongue-coating samples were collected, then the NO-producing activity was measured. Furthermore, the composition of the NO-producing bacterial population were identified using the Griess reagent-containing agar overlay method and molecular biological method. NO-producing activity per mg wet weight varied among individuals but was higher in dental plaque. Additionally, anaerobic bacteria exhibited higher numbers of NO-producing bacteria, except in the adults' dental plaque. The proportion of NO-producing bacteria also varied among individuals, but a positive correlation was found between NO-producing activity and the number of NO-producing bacteria, especially in dental plaque. Overall, the major NO-producing bacteria were identified as Actinomyces, Schaalia, Veillonella and Neisseria. Furthermore, Rothia was specifically detected in the tongue coatings of children. These results suggest that dental plaque has higher NO-producing activity and that this activity depends not on the presence of specific bacteria or the bacterial compositions, but on the number of NO-producing bacteria, although interindividual differences were detected.
Topics: Actinomyces; Actinomycetaceae; Adolescent; Adult; Bacteria, Anaerobic; Biofilms; Child; Child, Preschool; Dental Plaque; Female; Humans; Male; Microbiota; Micrococcaceae; Mouth; Neisseria; Nitrites; Veillonella; Young Adult
PubMed: 33024169
DOI: 10.1038/s41598-020-73479-1 -
Journal of Clinical Periodontology Sep 2021To study the peri-implant submucosal microbiome in relation to implant disease status, dentition status, smoking habit, gender, implant location, implant system, time of...
AIM
To study the peri-implant submucosal microbiome in relation to implant disease status, dentition status, smoking habit, gender, implant location, implant system, time of functional loading, probing pocket depth (PPD), and presence of bleeding on probing.
MATERIALS AND METHODS
Biofilm samples were collected from the deepest peri-implant site of 41 patients with paper points, and analysed using 16S rRNA gene pyrosequencing.
RESULTS
We observed differences in microbial profiles by PPD, implant disease status, and dentition status. Microbiota in deep pockets included higher proportions of the genera Fusobacterium, Prevotella, and Anaeroglobus compared with shallow pockets that harboured more Rothia, Neisseria, Haemophilus, and Streptococcus. Peri-implantitis (PI) sites were dominated by Fusobacterium and Treponema compared with healthy implants and peri-implant mucositis, which were mostly colonized by Rothia and Streptococcus. Partially edentulous (PE) individuals presented more Fusobacterium, Prevotella, and Rothia, whereas fully edentulous individuals presented more Veillonella and Streptococcus.
CONCLUSIONS
PPD, implant disease status, and dentition status may affect the submucosal ecology leading to variation in composition of the microbiome. Deep pockets, PI, and PE individuals were dominated by Gram-negative anaerobic taxa.
Topics: Cross-Sectional Studies; Dental Implants; Humans; Microbiota; Peri-Implantitis; RNA, Ribosomal, 16S
PubMed: 34101220
DOI: 10.1111/jcpe.13502