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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 -
Microorganisms Jun 2021The importance and abundance of strict anaerobic bacteria in the respiratory microbiota of people with cystic fibrosis (PWCF) is now established through studies based on...
The importance and abundance of strict anaerobic bacteria in the respiratory microbiota of people with cystic fibrosis (PWCF) is now established through studies based on high-throughput sequencing or extended-culture methods. In CF respiratory niche, one of the most prevalent anaerobic genera is , and particularly the species The objective of this study was to evaluate the antibiotic susceptibility of this anaerobic species. Fifty isolates of cultured from sputum of 50 PWCF have been included. Antibiotic susceptibility testing was performed using the agar diffusion method. All isolates were susceptible to the following antibiotics: amoxicillin/clavulanic acid, piperacillin/tazobactam, imipenem and metronidazole. A total of 96% of the isolates (48/50) were resistant to amoxicillin (indicating beta-lactamase production), 34% to clindamycin (17/50) and 24% to moxifloxacin (12/50). Moreover, 10% (5/50) were multidrug-resistant. A significant and positive correlation was found between clindamycin resistance and chronic azithromycin administration. This preliminary study on a predominant species of the lung "anaerobiome" shows high percentages of resistance, potentially exacerbated by the initiation of long-term antibiotic therapy in PWCF. The anaerobic resistome characterization, focusing on species rather than genera, is needed in the future to better prevent the emergence of resistance within lung microbiota.
PubMed: 34208093
DOI: 10.3390/microorganisms9061275 -
Frontiers in Microbiology 2023The management of infectious diseases has become more critical due to the development of novel pathogenic strains with enhanced resistance. , a gram-negative bacterium,...
The management of infectious diseases has become more critical due to the development of novel pathogenic strains with enhanced resistance. , a gram-negative bacterium, was found to be involved in various infections of the respiratory tract, aerodigestive tract, and gastrointestinal tract. The need to explore novel drug and vaccine targets against this pathogen was triggered by the emergence of antimicrobial resistance against reported antibiotics to combat infections. The study involves core genes acquired from 14 complete strain genome sequences, where promiscuous drug and vaccine candidates were explored by state-of-the-art subtractive proteomics and reverse vaccinology approaches. A stringent bioinformatics analysis enlisted 18 targets as novel, essential, and non-homologous to humans and having druggability potential. Moreover, the extracellular and outer membrane proteins were subjected to antigenicity, allergenicity, and physicochemical analysis for the identification of the candidate proteins to design multi-epitope vaccines. Two candidate proteins (ADK95685.1 and ADK97014.1) were selected as the best target for the designing of a vaccine construct. Lead B- and T-cell overlapped epitopes were joined to generate potential chimeric vaccine constructs in combination with adjuvants and linkers. Finally, a prioritized vaccine construct was found to have stable interactions with the human immune cell receptors as confirmed by molecular docking and MD simulation studies. The vaccine construct was found to have cloning and expression ability in the bacterial cloning system. Immune simulation ensured the elicitation of significant immune responses against the designed vaccine. In conclusion, our study reported novel drug and vaccine targets and designed a multi-epitope vaccine against the infection. Further experimental validation will help open new avenues in the treatment of this multi-drug-resistant pathogen.
PubMed: 37808310
DOI: 10.3389/fmicb.2023.1271798 -
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 -
British Medical Journal (Clinical... Mar 1982To assess the causative role of non-sporing anaerobes in cass of erosive balanoposthitis, anaerobic culture was performed on purulent discharges from 104 patients with...
To assess the causative role of non-sporing anaerobes in cass of erosive balanoposthitis, anaerobic culture was performed on purulent discharges from 104 patients with penile ulceration, a foul-smelling discharge, and a mixed and motile bacterial flora. Most of 29 culturally confirmed infections were due to mixed anaerobes and eight to single anaerobes. A rapid response to treatment with metronidazole also confirmed the anaerobic cause of the infection. Thus, acute anaerobic balanoposthitis can be readily diagnosed clinically and is easily treated.
Topics: Balanitis; Eikenella corrodens; Fusobacterium; Humans; Male; Metronidazole; Prevotella melaninogenica
PubMed: 6121604
DOI: 10.1136/bmj.284.6319.859 -
Frontiers in Cellular and Infection... 2022Periodontal disease in pregnancy is considered a risk factor for adverse birth outcomes. Periodontal disease has a microbial etiology, however, the current state of...
BACKGROUND
Periodontal disease in pregnancy is considered a risk factor for adverse birth outcomes. Periodontal disease has a microbial etiology, however, the current state of knowledge about the subgingival microbiome in pregnancy is not well understood.
OBJECTIVE
To characterize the structure and diversity of the subgingival microbiome in early and late pregnancy and explore relationships between the subgingival microbiome and preterm birth among pregnant Black women.
METHODS
This longitudinal descriptive study used 16S rRNA sequencing to profile the subgingival microbiome of 59 Black women and describe microbial ecology using alpha and beta diversity metrics. We also compared microbiome features across early (8-14 weeks) and late (24-30 weeks) gestation overall and according to gestational age at birth outcomes (spontaneous preterm, spontaneous early term, full term).
RESULTS
In this sample of Black pregnant women, the top twenty bacterial taxa represented in the subgingival microbiome included a spectrum representative of various stages of biofilm progression leading to periodontal disease, including known periopathogens and Other organisms associated with periodontal disease reflected in the subgingival microbiome included several spp., and spp. Measures of alpha or beta diversity did not distinguish the subgingival microbiome of women according to early/late gestation or full term/spontaneous preterm birth; however, alpha diversity differences in late pregnancy between women who spontaneously delivered early term and women who delivered full term were identified. Several taxa were also identified as being differentially abundant according to early/late gestation, and full term/spontaneous early term births.
CONCLUSIONS
Although the composition of the subgingival microbiome is shifted toward complexes associated with periodontal disease, the diversity of the microbiome remains stable throughout pregnancy. Several taxa were identified as being associated with spontaneous early term birth. Two, in particular, are promising targets of further investigation. Depletion of the oral commensal in early pregnancy and elevated levels of in late pregnancy were both associated with spontaneous early term birth.
Topics: Female; Humans; Infant, Newborn; Microbiota; Periodontal Diseases; Porphyromonas gingivalis; Pregnancy; Premature Birth; RNA, Ribosomal, 16S; Term Birth
PubMed: 35646730
DOI: 10.3389/fcimb.2022.873683 -
Revista Espanola de Quimioterapia :... Oct 2015Noma is an aggressive orofacial gangrenous pathology that damages hard and soft tissues of the mouth and the face. Throughout the centuries it has been present around... (Review)
Review
Noma is an aggressive orofacial gangrenous pathology that damages hard and soft tissues of the mouth and the face. Throughout the centuries it has been present around the globe, but nowadays it has practically disappeared from developed countries and mainly affects children from the most disadvantaged places, especially in Africa. Noma disease is a multifactorial process; malnutrition, debilitating diseases (bacterial or viral systemic diseases, HIV-associated immunosuppression, etc.) and intraoral infections are some of the factors implied. The characteristic tissue necrosis is produced by a polymicrobial infection. Fusobacterium necrophorum, Prevotella intermedia, Prevotella melaninogenica, Fusobacterium nucleatum, Bacteroides fragilis, Bacillus cereus, Trueperella pyogenes, spyrochetes, etc, are some of the species that have been isolated from the affected areas. Without treatment, noma is lethal in a short period of time, and the patients that survive show severe sequelae that hinder their life and interpersonal relationships. The aim of this paper is to unify the existing information and to promote wider knowledge and awareness among the population.
Topics: Africa; Humans; Neglected Diseases; Noma; Quality of Life; Risk Factors
PubMed: 26437752
DOI: No ID Found -
Microbiology Spectrum Feb 2023Several previous studies have shown that oral microbial disorders may be closely related to the occurrence and development of type 2 diabetes mellitus (T2DM). However,...
Several previous studies have shown that oral microbial disorders may be closely related to the occurrence and development of type 2 diabetes mellitus (T2DM). However, whether the function of oral microorganisms and their metabolites have changed in patients with T2DM who have not suffered from any oral diseases has not been reported. We performed metagenomic analyses and nontargeted metabolic analysis of saliva and supragingival plaque samples from patients with T2DM who have not suffered any oral diseases and normal controls. We found that periodontal pathogens such as Porphyromonas gingivalis and Prevotella melaninogenica were significantly enriched, while the abundances of dental caries pathogens such as Streptococcus mutans and Streptococcus sobrinus were not significantly different in patients with T2DM compared to those in normal controls. Metabolomic analyses showed that the salivary levels of cadaverine and L-(+)-leucine of patients with T2DM were significantly higher than those of normal controls, while the supragingival plaque levels of N-acetyldopamine and 3,4-dimethylbenzoic acid in patients with T2DM were significantly higher than those in the normal controls. Additionally, we identified the types of oral microorganisms related to the changes in the levels of circulating metabolites, and the oral microorganisms were involved in the dysregulation of harmful metabolites such as cadaverine and n, n-dimethylarginine. Overall, our study first described the changes in the composition of oral microorganisms and their metabolites in patients with T2DM who have not suffered any oral diseases, which will provide a direct basis for finding oral biomarkers for early warning of oral diseases in T2DM. The incidence of oral diseases in type 2 diabetic patients might increase, and the severity might also be more serious. At present, the relationship between oral microorganisms and type 2 diabetes mellitus (T2DM) has become a hot topic in systemic health research. However, whether the function of oral microorganisms and their metabolites have changed in patients with T2DM who have not suffered from any oral diseases has not been reported. We found that even if the oral condition of T2DM is healthy, their oral microbes and metabolites have changed, thus increasing the risk of periodontal disease. Our study first described the changes in the composition of oral microorganisms and their metabolites in T2DM who have not suffered any oral diseases and revealed the correlation between oral microorganisms and their metabolites, which will provide a direct basis for finding oral biomarkers for early warning of oral diseases in patients with T2DM.
Topics: Humans; Diabetes Mellitus, Type 2; Dysbiosis; Cadaverine; Dental Caries; Microbiota
PubMed: 36625596
DOI: 10.1128/spectrum.03796-22 -
Journal of Oral Microbiology 2023The current study aimed to test the hypothesis that Parkinson's disease exacerbates periodontitis by altering its microbiome.
AIM
The current study aimed to test the hypothesis that Parkinson's disease exacerbates periodontitis by altering its microbiome.
MATERIALS AND METHODS
Clinical periodontal parameters were recorded. Subgingival samples from healthy controls, periodontitis patients (PD), and Parkinson's patients with periodontitis (PA+PD) were analyzed using the checkerboard DNA-DNA hybridization technique for targeting 40 bacterial species typically associated with periodontal disease and health. Next-generation sequencing (NGS) of the 16S ribosomal RNA gene (V1-V3 regions) was performed to analyze the microbiome comprehensively.
RESULTS
Parkinson's patients had mild-to-moderate motor dysfunctions. Bleeding on probing was significantly increased in the PA+PD group compared to PD ( < 0.05). With checkerboard analysis, PA was associated with increased ( = 0.0062), ( = 0.0439), ( < 0.0001), ( = 0.0002), ( < 0.0001), and ( = 0.0020). ( = 0.0042), ( = 0.0022), ( = 0.0002), ( = 0.0045), ( = 0.0267), ( = 0.0017), ( = 0.0020), and ( = 0.0002) were higher; ( = 0.0072) was lower in deep pockets in the PA+PD compared to PD. ( = 0.0351) and ( = 0.002) were lower; ( = 0.0002), ( = 0065), ( = 0.0151), ( = 0.0141), ( = 0.0057), and ( = 0.0316) were higher in shallow pockets in the PA+PD. Diversity decreased in PD ( = 0.001) and PA+PD ( = 0.026) compared to control, with minimal differences in alpha and beta diversities among PD and PA+PD based on NGS results.
CONCLUSION
These data demonstrated that Parkinson's disease modifies PD-associated subgingival microbiome.
PubMed: 37649970
DOI: 10.1080/20002297.2023.2250650 -
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