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Microbial Genomics Feb 2022Cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are characterized by increasingly frequent acute pulmonary exacerbations that reduce life quality...
Cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) are characterized by increasingly frequent acute pulmonary exacerbations that reduce life quality and length. Human airways are home to a rich polymicrobial environment, which includes members of the obligately anaerobic genus . Despite their commonness, surprisingly little is known about the prevalence, role, genomic diversity and antimicrobial resistance (AMR) potential of species and strains in healthy and diseased airways. Here, we used comparative genomics to develop a real-time PCR assay to permit rapid species identification and quantification from cultures and clinical specimens. Assay specificity was validated across a panel of and non- species, followed by PCR screening of CF and COPD respiratory-derived cultures. Next, 35 PCR-positive isolates were subjected to whole-genome sequencing. Of eight identified species, , , , and overlapped between participant cohorts. Phylogenomic analysis revealed considerable interhost but limited intrahost diversity, suggesting patient-specific lineages in the lower airways, probably from oral cavity aspirations. Correlation of phenotypic AMR profiles with AMR genes identified excellent correlation between presence and decreased doxycycline susceptibility, and presence and decreased azithromycin susceptibility and clindamycin resistance. AMR rates were higher in the CF isolates, reflecting greater antibiotic use in this cohort. All tested isolates were tobramycin-resistant, providing a potential selection method to improve culture retrieval rates. Our addition of 35 airway-derived genomes to public databases will enhance ongoing efforts to unravel the role of this diverse and enigmatic genus in both diseased and healthy lungs.
Topics: Anti-Bacterial Agents; Cystic Fibrosis; Drug Resistance, Bacterial; Genomics; Humans; Lung; Microbial Sensitivity Tests; Prevotella; Pulmonary Disease, Chronic Obstructive; Sputum
PubMed: 35113778
DOI: 10.1099/mgen.0.000754 -
The Journal of Heart and Lung... Jan 2023Long term outcomes of lung transplantation are impacted by the occurrence of chronic lung allograft dysfunction (CLAD). Recent evidence suggests a role for the lung...
BACKGROUND
Long term outcomes of lung transplantation are impacted by the occurrence of chronic lung allograft dysfunction (CLAD). Recent evidence suggests a role for the lung microbiome in the occurrence of CLAD, but the exact mechanisms are not well defined. We hypothesize that the lung microbiome inhibits epithelial autophagic clearance of pro-fibrotic proteins in an IL-33 dependent manner, thereby augmenting fibrogenesis and risk for CLAD.
METHODS
Autopsy derived CLAD and non-CLAD lungs were collected. IL-33, P62 and LC3 immunofluorescence was performed and assessed using confocal microscopy. Pseudomonas aeruginosa (PsA), Streptococcus Pneumoniae (SP), Prevotella Melaninogenica (PM), recombinant IL-33 or PsA-lipopolysaccharide was co-cultured with primary human bronchial epithelial cells (PBEC) and lung fibroblasts in the presence or absence of IL-33 blockade. Western blot analysis and quantitative reverse transcription (qRT) PCR was performed to evaluate IL-33 expression, autophagy, cytokines and fibroblast differentiation markers. These experiments were repeated after siRNA silencing and upregulation (plasmid vector) of Beclin-1.
RESULTS
Human CLAD lungs demonstrated markedly increased expression of IL-33 and reduced basal autophagy compared to non-CLAD lungs. Exposure of co-cultured PBECs to PsA, SP induced IL-33, and inhibited PBEC autophagy, while PM elicited no significant response. Further, PsA exposure increased myofibroblast differentiation and collagen formation. IL-33 blockade in these co-cultures recovered Beclin-1, cellular autophagy and attenuated myofibroblast activation in a Beclin-1 dependent manner.
CONCLUSION
CLAD is associated with increased airway IL-33 expression and reduced basal autophagy. PsA induces a fibrogenic response by inhibiting airway epithelial autophagy in an IL-33 dependent manner.
Topics: Humans; Beclin-1; Pseudomonas; Interleukin-33; Arthritis, Psoriatic; Lung; Autophagy
PubMed: 37014805
DOI: 10.1016/j.healun.2022.09.018 -
Journal of Investigative Medicine : the... Mar 2022Recurrent aphthous stomatitis (RAS) is a common recurrent ulcerative disease of the oral mucosa which is closely related to oral microbial composition. However, the...
Recurrent aphthous stomatitis (RAS) is a common recurrent ulcerative disease of the oral mucosa which is closely related to oral microbial composition. However, the specific effect and the mechanism of smoking in RAS are unclear. In this study, 16S rRNA sequencing technology was used to compare the differences in saliva microbial community between 28 non-smoking healthy controls (NSctrl), 31 non-smoking RAS patients (NSras), and 19 smoking RAS patients (Sras). The results showed that the bacterial community diversity in patients with RAS (NSras and Sras) was lower than that of NSctrl. The microbial community in smoking-associated RAS is less diverse and distinct from that of non-smokers. The RAS groups have higher abundance of , , and and lower abundance of , , , , , and at the genera level. A significantly different abundance of , , , , , and was observed between the Sras and the NSras group. Notably, there was a significant difference in many species from the genus and between the NSras and the Sras group. Further, the relative abundance of several taxa is correlated with smoking age or frequency, including , , , and at the genera level, and , , , , , , , and at the species level. Among patients with RAS, smoking aggravated the pathways of respiration and human pathogens. Our results suggest that smoking is closely related to changes in the oral microbiota, which may contribute an opposite effect to the pathogenesis of RAS. This study provides new insight and theoretical basis for the cause and pathogenesis of RAS and better prevention and treatment.
Topics: Bacteria; Cigarette Smoking; Humans; Microbiota; RNA, Ribosomal, 16S; Stomatitis, Aphthous
PubMed: 34824153
DOI: 10.1136/jim-2021-002119 -
Frontiers in Cellular and Infection... 2021The oral microbiota has been observed to be influenced by cigarette smoking and linked to several human diseases. However, research on the effect of cigarette smoking on...
The oral microbiota has been observed to be influenced by cigarette smoking and linked to several human diseases. However, research on the effect of cigarette smoking on the oral microbiota has not been systematically conducted in the Chinese population. We profiled the oral microbiota of 316 healthy subjects in the Chinese population by 16S rRNA gene sequencing. The alpha diversity of oral microbiota was different between never smokers and smokers ( = 0.002). Several bacterial taxa were first reported to be associated with cigarette smoking by LEfSe analysis, including ( = 1.56E-04), ( = 1.65E-06), and ( = 3.52E-02) at the genus level and ( = 1.55E-02), ( = 8.48E-08), ( = 4.13E-03), ( = 1.79E-06), ( = 3.83E-06), ( = 2.28E-04), and ( = 4.82E-02) at the species level. Two nitrite-producing bacteria that can increase the acidity of the oral cavity, and , were also enriched in smokers with FDR-adjusted -values of 3.62E-06 and 1.10E-06, respectively. Notably, we observed that two acid production-related pathways, amino acid-related enzymes ( = 6.19E-05) and amino sugar and nucleotide sugar metabolism ( = 2.63E-06), were increased in smokers by PICRUSt analysis. Finally, the co-occurrence analysis demonstrated that smoker-enriched bacteria were significantly positively associated with each other and were negatively correlated with the bacteria decreased in smokers. Our results suggested that cigarette smoking may affect oral health by creating a different environment by altering bacterial abundance, connections among oral microbiota, and the microbiota and their metabolic function.
Topics: China; Cigarette Smoking; Humans; Microbiota; Micrococcaceae; Prevotella; RNA, Ribosomal, 16S
PubMed: 34123872
DOI: 10.3389/fcimb.2021.658203 -
International Journal of Molecular... Jul 2022A complex balanced equilibrium of the bacterial ecosystems exists in the oral cavity that can be altered by tobacco smoking, psychological stressors, bad dietary habit,... (Review)
Review
A complex balanced equilibrium of the bacterial ecosystems exists in the oral cavity that can be altered by tobacco smoking, psychological stressors, bad dietary habit, and chronic periodontitis. Oral dysbiosis can promote the onset and progression of oral squamous cell carcinoma (OSCC) through the release of toxins and bacterial metabolites, stimulating local and systemic inflammation, and altering the host immune response. During the process of carcinogenesis, the composition of the bacterial community changes qualitatively and quantitatively. Bacterial profiles are characterized by targeted sequencing of the 16S rRNA gene in tissue and saliva samples in patients with OSCC. , , , , , and are the significantly increased bacteria in salivary samples. These have a potential diagnostic application to predict oral cancer through noninvasive salivary screenings. Oral lactic acid bacteria, which are commonly used as probiotic therapy against various disorders, are valuable adjuvants to improve the response to OSCC therapy.
Topics: Bacteria; Carcinoma, Squamous Cell; Humans; Microbiota; Mouth Neoplasms; RNA, Ribosomal, 16S
PubMed: 35955456
DOI: 10.3390/ijms23158323 -
Journal of Periodontal Research May 2024This systematic review aims to investigate the microbial basis underlying the association between oral microbiota and colorectal cancer. A comprehensive search was... (Review)
Review
This systematic review aims to investigate the microbial basis underlying the association between oral microbiota and colorectal cancer. A comprehensive search was conducted across four databases, encompassing potentially relevant studies published up to April 2024 related to the PECO question: "Is there a differentiation in oral microbial composition between adult patients diagnosed with colorectal cancer compared to healthy patients?". The Newcastle-Ottawa Scale was used to evaluate the quality of the studies included. The level of evidence was assessed through the GRADE (Grading of Recommendations, Assessment, Development and Evaluation) tool. Sixteen studies fulfilled the eligibility criteria. Based on low to moderate evidence profile, high levels of certain subspecies within Firmicutes (such as Streptococcus anginosus, Peptostreptococcus stomatis, S. koreensis, and S. gallolyticus), Prevotella intermedia, Fusobacterium nucleatum, and Neisseria oralis were found to be associated with colorectal cancer. Conversely, certain bacteria (e.g., Lachnospiraceae, F. periodonticum, and P. melaninogenica) could exert a symbiotic protective effect against colorectal cancer. Based on existing evidence, it appears that variations in oral microbiota composition exist among individuals with and without colorectal cancer. However, further research is necessary to determine the mechanisms of oral dysbiosis in colorectal carcinogenesis.
PubMed: 38775019
DOI: 10.1111/jre.13289 -
International Journal of Environmental... May 2022The dysbiosis of oral microbiota is linked to numerous diseases and is associated with personal lifestyles, such as alcohol drinking. However, there is inadequate data...
The dysbiosis of oral microbiota is linked to numerous diseases and is associated with personal lifestyles, such as alcohol drinking. However, there is inadequate data to study the effect of alcohol drinking on oral microbiota from the Chinese population. Here, we profiled the oral microbiota of 150 healthy subjects in the Chinese population by 16S rRNA gene sequencing. The results showed that drinkers had significantly higher alpha diversity than non-drinkers. A significant difference in overall microbiota composition was observed between non-drinkers and drinkers. Additionally, using DESeq analysis, we found genus and , and species and were significantly enriched in drinkers; meanwhile, the genus , and , and species were significantly depleted in drinkers. PICRUSt analysis showed that significantly different genera were mainly related to metabolism pathways. The oxygen-independent pathways, including galactose, fructose and mannose metabolism pathways, were enriched in drinkers and positively associated with genera enriched in drinkers; while the pyruvate metabolism pathway, an aerobic metabolism pathway, was decreased in drinkers and negatively associated with genera enriched in drinkers. Our results suggested that alcohol drinking may affect health by altering oral microbial composition and potentially affecting microbial functional pathways. These findings may have implications for better understanding the potential role those oral bacteria play in alcohol-related diseases.
Topics: Alcohol Drinking; China; Dysbiosis; Humans; Microbiota; RNA, Ribosomal, 16S
PubMed: 35565124
DOI: 10.3390/ijerph19095729 -
A Review on Microbial Species for Forensic Body Fluid Identification in Healthy and Diseased Humans.Current Microbiology Jul 2023Microbial communities present in body fluids can assist in distinguishing between types of body fluids. Metagenomic studies have reported bacterial genera which are core... (Review)
Review
Microbial communities present in body fluids can assist in distinguishing between types of body fluids. Metagenomic studies have reported bacterial genera which are core to specific body fluids and are greatly influenced by geographical location and ethnicity. Bacteria in body fluids could also be due to bacterial infection; hence, it would be worthwhile taking into consideration bacterial species associated with diseases. The present review reports bacterial species characteristic of diseased and healthy body fluids across geographical locations, and bacteria described in forensic studies, with the aim of collating a set of bacteria to serve as the core species-specific markers for forensic body fluid identification. The most widely reported saliva-specific bacterial species are Streptococcus salivarius, Prevotella melaninogenica, Neisseria flavescens, with Fusobacterium nucleatum associated with increased diseased state. Lactobacillus crispatus and Lactobacillus iners are frequently dominant in the vaginal microbiome of healthy women. Atopobium vaginae, Prevotella bivia, and Gardnerella vaginalis are more prevalent in women with bacterial vaginosis. Semen and urine-specific bacteria at species level have not been reported, and menstrual blood bacteria are indistinguishable from vaginal fluid. Targeting more than one bacterial species is recommended for accurate body fluid identification. Although metagenomic sequencing provides information of a broad microbial profile, the specific bacterial species could be used to design biosensors for rapid body fluid identification. Validation of microbial typing methods and its application in identifying body fluids in a mixed sample would allow regular use of microbial profiling in a forensic workflow.
Topics: Humans; Female; Vaginosis, Bacterial; Vagina; Body Fluids; Gardnerella vaginalis; Saliva; Bacteria
PubMed: 37491404
DOI: 10.1007/s00284-023-03413-x -
Oral Diseases May 2024Our previous studies have found that the composition ratio of Prevotella melaninogenica (Pm) on buccal mucosa surface of oral lichen planus (OLP) patients increased...
OBJECTIVE
Our previous studies have found that the composition ratio of Prevotella melaninogenica (Pm) on buccal mucosa surface of oral lichen planus (OLP) patients increased significantly compared with control. Furthermore, Pm could invade the epithelium of OLP patients. This study aimed to further explore the impact of Pm on oral keratinocytes.
MATERIALS AND METHODS
The Pm-human oral keratinocyte (HOK) co-culture model was established to detect monolayer permeability, zona occludens-1 (ZO-1) expression, and intracellular survival of Pm. We performed RNA-seq followed by identification of differentially expressed genes (DEGs) and Gene Ontology (GO) analysis, with a particular focus on myosin light chain kinase (MLCK). An MLCK inhibitor ML-7 was utilized in Pm-HOK co-culture model to assess its effects on monolayer permeability and ZO-1 expression.
RESULTS
HOK monolayer permeability was increased, and ZO-1 expression was decreased after co-culture (p < 0.05). Pm could survive in HOK cells. RNA-seq revealed MLCK was an upregulated common DEG. The expression of MLCK in the Pm-HOK co-culture model was upregulated. Inhibition of MLCK rescued the increased epithelial permeability, and ZO-1 expression was upregulated (p < 0.05).
CONCLUSION
MLCK may be involved in disrupting epithelial barrier function by Pm.
PubMed: 38720551
DOI: 10.1111/odi.14980 -
Frontiers in Cellular and Infection... 2022The aim of this study was to analyze the cultivable oral microbiota of patients with obstructive sleep apnea (OSA) and its association with the periodontal condition.
OBJECTIVE
The aim of this study was to analyze the cultivable oral microbiota of patients with obstructive sleep apnea (OSA) and its association with the periodontal condition.
METHODS
The epidemiology profile of patients and their clinical oral characteristics were determined. The microbiota was collected from saliva, subgingival plaque, and gingival sulcus of 93 patients classified into four groups according to the periodontal and clinical diagnosis: Group 1 ( = 25), healthy patients; Group 2 ( = 17), patients with periodontitis and without OSA; Group 3 ( = 19), patients with OSA and without periodontitis; and Group 4 ( = 32), patients with periodontitis and OSA. Microbiological samples were cultured, classified, characterized macroscopically and microscopically, and identified by MALDI-TOF-MS. The distribution of complexes and categories of microorganisms and correlations were established for inter- and intra-group of patients and statistically evaluated using the Spearman test (-value <0.5) and a multidimensional grouping analysis.
RESULT
There was no evidence between the severity of OSA and periodontitis ( = 0.2813). However, there is a relationship between the stage of periodontitis and OSA ( = 0.0157), with stage III periodontitis being the one with the highest presence in patients with severe OSA (prevalence of 75%; = 0.0157), with more cases in men. The greatest distribution of the complexes and categories was found in oral samples of patients with periodontitis and OSA (Group 4 P-OSA); even spp. were more prevalent in these patients. Periodontitis and OSA are associated with comorbidities and oral conditions, and the microorganisms of the orange and red complexes participate in this association. The formation of the dysbiotic biofilm was mainly related to the presence of these complexes in association with spp.
CONCLUSION
Periodontopathogenic bacteria of the orange complex, such as , and the yeast , altered the cultivable oral microbiota of patients with periodontitis and OSA in terms of diversity, possibly increasing the severity of periodontal disease. The link between yeasts and periodontopathogenic bacteria could help explain why people with severe OSA have such a high risk of stage III periodontitis. Antimicrobial approaches for treating periodontitis in individuals with OSA could be investigated using polymicrobial biofilms, according to our findings.
Topics: Candida; Candida albicans; Causality; Gingiva; Humans; Male; Periodontitis; Sleep Apnea, Obstructive
PubMed: 36189359
DOI: 10.3389/fcimb.2022.934298