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Nefrologia 2024Diabetes, dyslipidemia, older age, gender, urinary tract infections, and recent antibiotic intake have been associated with a decrease in the urobiome richness and other...
INTRODUCTION AND OBJECTIVES
Diabetes, dyslipidemia, older age, gender, urinary tract infections, and recent antibiotic intake have been associated with a decrease in the urobiome richness and other fluctuations in this microbiome. Gut and blood microbiome have been reported to be altered in patients with chronic kidney disease (CKD), and specifically in peritoneal dialysis (PD) patients. Still, there are currently no studies describing the urogenital microbiome in CKD-PD patients. In this study we characterized the urobiome profile in 46 PD patients and analyzed its clinical and inflammatory parameters.
MATERIALS AND METHODS
Mid-stream urine, fecal and blood samples were collected from 46 patients undergoing PD at Centro Hospitalar Universitário de São João (CHUSJ) in Porto, Portugal. Exclusion criteria were age under 18 years old, inability to give informed consent, history of infection in the last three months, and antibiotic intake in the last three months. The microbiome communities were analyzed by amplification and sequencing of the V3-V4 region of the bacterial 16S rRNA gene. Correlations with the patients' clinical data and inflammatory profile were performed.
RESULTS
CKD-PD patients presented a unique urobiome profile dominated by Bacillota, Actinomycetota and Pseudomonadota and characterized by a lower Shannon diversity than fecal and blood microbiome. The taxonomic profiles of urogenital samples were organized in multiple subtypes dominated by populations of Lactobacillus, Staphylococcus, Streptococcus, Gardnerella, Prevotella, Escherichia-Shigella, being similar to other non-PD-CKD patients. Gender, sCD14, residual diuresis and history of peritonitis were significantly associated to variations in the urobiome. Although not reaching statistical significance, diabetes and the time on PD also showed association with particular taxonomic groups. Depletion of Gardnerella, Staphylococcus, Corynebacterium, Lactobacillus or Dermabacter populations correlated with CKD-PD patients with history of diabetes, history of peritonitis and altered levels of sCD14.
CONCLUSIONS
Our results highlight urogenital microbiome as a potential partner and/or marker in the overall health state of CKD-PD patients.
Topics: Humans; Female; Male; Peritoneal Dialysis; Middle Aged; Microbiota; Renal Insufficiency, Chronic; Aged; Urogenital System; Adult; Feces
PubMed: 38697697
DOI: 10.1016/j.nefroe.2024.04.004 -
International Journal of Cosmetic... Jun 2024This study aimed to expound on the correlation between facial skin microbiome and sensitive skin (SS) using a novel sequencing technique.
OBJECTIVE
This study aimed to expound on the correlation between facial skin microbiome and sensitive skin (SS) using a novel sequencing technique.
METHODS
We applied the 2bRAD sequencing for the microbiome, which enables accurate characterization of the low-biomass microbiome at species resolution to profile facial skin microbes in SS and non-SS groups. Further, the bacterial colonies were isolated and cultured from skin surfaces to study the pro-inflammatory effect on human keratinocytes by ELISA.
RESULTS
We accordingly identified 1142 genera and 4436 strains. In the SS group, the proportions of Actinomyces and Microbotryomycetes were significantly increased, whereas that of Acidimicrobiia was decreased. Kruskal-Wallis analysis revealed significant differences in 11 genera and 35 species, among which the proportions of Dermabacter, Chryseobacterium, Rhodotorula and Peptoniphilus A were increased in the SS group. Analysis of the top 10 genera revealed increased proportions of Cutibacterium, Corynebacterium and Staphylococcus. Moreover, the proportion of Dermabacter hominis was significantly increased by 18.9-fold in the SS group, whereas those of many Streptococcus strains were significantly decreased. Focus on the isolated bacterial colonies from skin surfaces, more yellow colonies were found in SS group when cultured in Tryptic Soy Broth medium for 48 h, and more interleukin-8 was detected on keratinocytes after yellow colonies stimulation, such as S.capitis, M.luteus.
CONCLUSIONS
This study suggests that more SS-associated microorganisms can be identified using the 2bRAD technique even with a small sample size. Dermabacter hominis and Chryseobacterium was firstly reported with a significantly increase in SS, and the S.capitis, as well as M.luteus, but not S.aureus, may be associated with skin inflammation.
Topics: Humans; Skin; Microbiota; Face; Adult; Female; Keratinocytes; Middle Aged
PubMed: 38229273
DOI: 10.1111/ics.12941 -
BMC Microbiology Jan 2024Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification...
Novel Organism Verification and Analysis (NOVA) study: identification of 35 clinical isolates representing potentially novel bacterial taxa using a pipeline based on whole genome sequencing.
BACKGROUND
Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS).
RESULTS
We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently.
CONCLUSION
Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define.
Topics: Bacteria; Whole Genome Sequencing; Corynebacterium; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; RNA, Ribosomal, 16S; Bacterial Typing Techniques
PubMed: 38178003
DOI: 10.1186/s12866-023-03163-7 -
Frontiers in Cellular and Infection... 2023To explore the changes of bacterial flora in anophthalmic patients wearing ocular prosthesis (OP) and the microbiome diversity in conditions of different OP materials.
PURPOSE
To explore the changes of bacterial flora in anophthalmic patients wearing ocular prosthesis (OP) and the microbiome diversity in conditions of different OP materials.
METHODS
A cross-sectional clinical study was conducted, involving 19 OP patients and 23 healthy subjects. Samples were collected from the upper, lower palpebral, caruncle, and fornix conjunctiva. 16S rRNA sequencing was applied to identify the bacterial flora in the samples. The eye comfort of each OP patient was determined by a questionnaire. In addition, demographics information of each participant was also collected.
RESULTS
The diversity and richness of ocular flora in OP patients were significantly higher than that in healthy subjects. The results of flora species analysis also indicated that in OP patients, pathogenic microorganisms such as and increased significantly, while the resident flora of and decreased significantly. Within the self-comparison of OP patients, compared with Polymethyl Methacrylate (PMMA), prosthetic material of glass will lead to the increased colonization of opportunistic pathogens such as and , while gender and age have no significant impact on ocular flora.
CONCLUSIONS
The ocular flora of OP patients was significantly different from that of healthy people. Abundant colonization of pathogenic microorganisms may have an important potential relationship with eye discomfort and eye diseases of OP patients. PMMA, as an artificial eye material, demonstrated potential advantages in reducing the colonization of opportunistic pathogens.
Topics: Humans; Eye, Artificial; Lacrimal Apparatus; Polymethyl Methacrylate; Cross-Sectional Studies; RNA, Ribosomal, 16S; Anophthalmos; Bacteria; Microbiota
PubMed: 36960044
DOI: 10.3389/fcimb.2023.1117673 -
Archives of Pharmacal Research Jan 2023Dermabacter vaginalis is a human-derived bacterium isolated from vaginal fluid of a Korean female in 2016. Although several human-related species in Dermabacter genus...
Isolation, structure elucidation, total synthesis, and biosynthesis of dermazolium A, an antibacterial imidazolium metabolite of a vaginal bacterium Dermabacter vaginalis.
Dermabacter vaginalis is a human-derived bacterium isolated from vaginal fluid of a Korean female in 2016. Although several human-related species in Dermabacter genus have been reported there are few studies on their bioactive metabolites. Dermazolium A (1), a rare imidazolium metabolite, was isolated from D. vaginalis along with five known metabolites (2-6) and their chemical structures were determined by NMR, HRMS, and MS/MS data analysis. Feeding experiments using predicted precursors and biomimetic total synthesis of 1 corroborated its structure and led to suggestion of biosynthetic pathway of 1. Antibacterial tests on the isolated compounds showed that 1 is a mild antibacterial agent with MIC values of 41 µg/mL against methicillin-resistant Staphylococcus aureus (MRSA) USA300, Lacticaseibacillus paracasei subsp. paracasei KCTC 3510 and Brevibacterium epidermidis KCTC 3090.
Topics: Female; Humans; Methicillin-Resistant Staphylococcus aureus; Tandem Mass Spectrometry; Anti-Bacterial Agents; Actinobacteria; Bacteria; Microbial Sensitivity Tests
PubMed: 36642761
DOI: 10.1007/s12272-022-01424-z -
Frontiers in Microbiology 2022Antimicrobial chemicals are used as preservatives in cosmetics, pharmaceuticals, and food to prevent the growth of bacteria and fungi in the products. Unintentional...
Antimicrobial chemicals are used as preservatives in cosmetics, pharmaceuticals, and food to prevent the growth of bacteria and fungi in the products. Unintentional exposure in humans to such chemicals is well documented, but whether they also interfere with human oral microbiome composition is largely unexplored. In this study, we explored whether the oral bacterial composition is affected by exposure to antibacterial and environmental chemicals. Gingival fluid, urine, and interview data were collected from 477 adults (18-47 years) from the RHINESSA study in Bergen, Norway. Urine biomarkers of triclosan, triclocarban, parabens, benzophenone-3, bisphenols, and 2,4- and 2,5-dichlorophenols (DCPs) were quantified (by mass spectrometry). Microbiome analysis was based on 16S amplicon sequencing. Diversity and differential abundance analyses were performed to identify how microbial communities may change when comparing groups of different chemical exposure. We identified that high urine levels (>75th percentile) of propyl parabens were associated with a lower abundance of bacteria genera , and , as compared with low propylparaben levels (<25 percentile). High exposure to ethylparaben was associated with a higher abundance of . High urine levels of bisphenol A were associated with a lower abundance of and exposure to another environmental chemical, 2,4-DCP, was associated with a lower abundance of , and . High exposure to antibacterial and environmental chemicals was associated with an altered composition of gingiva bacteria; mostly commensal bacteria in the oral cavity. Our results highlight a need for a better understanding of how antimicrobial chemical exposure influences the human microbiome.
PubMed: 35572708
DOI: 10.3389/fmicb.2022.790496 -
Frontiers in Cellular and Infection... 2022Chronic infections play an important role in the progress of lung disease in patients suffering from cystic fibrosis (CF). Recent studies indicate that polymicrobial...
Chronic infections play an important role in the progress of lung disease in patients suffering from cystic fibrosis (CF). Recent studies indicate that polymicrobial microbiome profiles in the airway are associated with less inflammation. Thus, the hypothesis was raised that certain commensal bacteria might protect the host from inflammation. We therefore performed a screening study with commensals isolated from CF airway microbiome samples to identify potential beneficial commensals. We isolated more than 80 aerobic or facultative anaerobic commensal strains, including strains from genera , , , , , and . Through a screening experiment of co-infection in human epithelial cell lines, we identified multiple commensal strains, especially strains belonging to , that reduced triggered inflammatory responses. The results were confirmed by co-infection experiments in precision cut lung slices (PCLS) from mice. The underlying mechanisms of the complex host-pathogen-commensal crosstalk were investigated from both the host and the bacterial sides with a focus on . Transcriptome changes in the host in response to co-infection and mono-infection were evaluated, and the results indicated that several signalling pathways mediating inflammatory responses were downregulated by co-infection with compared to mono-infection, such as neutrophil extracellular trap formation. The genomic differences among strains with and without protective effects were investigated by whole genome sequencing, revealing genes only present in the strains showing protective effects. In summary, through both and studies, we could identify a variety of commensal strains that may reduce host inflammatory responses induced by infection. These findings support the hypothesis that CF airway commensals may protect the host from inflammation.
Topics: Animals; Cystic Fibrosis; Humans; Inflammation; Lung; Mice; Microbiota; Pseudomonas Infections; Pseudomonas aeruginosa
PubMed: 35174108
DOI: 10.3389/fcimb.2022.824101 -
The Journal of Oral Implantology Aug 2021The reuse of healing abutments (HAs) has become common practice in implant dentistry for economic concerns and the aim of this in vitro study was to assess the effect of...
The reuse of healing abutments (HAs) has become common practice in implant dentistry for economic concerns and the aim of this in vitro study was to assess the effect of sodium hypochlorite (NaOCl) in decontamination of HAs. A total of 122 HAs (used and sterilized [n = 107]; new [n = 15]) were procured from 3 centers, of which 3 samples were discarded due to perforation in the sterilization pouch. For sterility assessment, the used HAs (n = 80) were cultured in Brain Heart Infusion Broth (BHI) and potato dextrose agar (PDA); bacterial isolates were identified in 7 samples. Also, 24 used HAs were stained with phloxine B, photographed, and compared to new HAs (n = 5). A scanning electron microscope (SEM) assessed the differences between 2 sets of HAs, after which the 7 contaminated HAs along with 24 used HAs from staining experiment (total: 31) were subsequently treated with sodium hypochlorite (NaOCl) and SEM images were observed. About 8.75% of HAs tested positive in bacterial culture; Streptococcus sanguis, Dermabacter hominis, Staphylococcus haemolyticus, and Aspergillus species were isolated. Phloxine B staining was positive for used and sterilized HAs compared to controls. The SEM images revealed deposits in the used HAs and although treatment with NaOCl eliminated the contamination of cultured HAs, the SEM showed visible debris in the HA thread region. This in vitro study concluded that SEM images showed debris in used HAs at screw-hole and thread regions even though they tested negative in bacterial culture. The treatment with NaOCl of used HAs showed no bacterial contamination but the debris was observed in SEM images. Future studies on the chemical composition, biological implications, and clinical influence is warranted before considering reuse of HAs.
Topics: Actinobacteria; Decontamination; Dental Abutments; Sodium Hypochlorite; Surface Properties
PubMed: 32780861
DOI: 10.1563/aaid-joi-D-19-00273 -
Diagnostic Microbiology and Infectious... Oct 2020We investigated the clinical relevance of Dermabacter hominis isolated from samples of 108 patients. Polymicrobial growth was evident in 88% of specimens. Isolation of...
We investigated the clinical relevance of Dermabacter hominis isolated from samples of 108 patients. Polymicrobial growth was evident in 88% of specimens. Isolation of D. hominis was of definitive or possible significance in only 14% of patients. Vancomycin remains the drug of choice given a penicillin resistance rate of 84%.
Topics: Actinobacteria; Actinomycetales; Actinomycetales Infections; Adult; Aged; Aged, 80 and over; Anti-Bacterial Agents; Bacterial Typing Techniques; DNA, Bacterial; Drug Resistance, Bacterial; Female; Humans; Male; Middle Aged; Penicillins; Retrospective Studies; Vancomycin
PubMed: 32683204
DOI: 10.1016/j.diagmicrobio.2020.115118 -
Revista Do Instituto de Medicina... 2020Myiasis represents a group of neglected tropical diseases caused by the infestation of vertebrate tissues by dipterous larvae. We herein report an imported case of...
Myiasis represents a group of neglected tropical diseases caused by the infestation of vertebrate tissues by dipterous larvae. We herein report an imported case of foruncular myasis caused by Dermatobia hominis in Mexico City. The species was confirmed by DNA sequencing and phylogenetic reconstruction analysis.
Topics: Actinobacteria; Adult; Animals; Diptera; Humans; Larva; Mexico; Myiasis; Phylogeny; Sequence Analysis, DNA; Skin Diseases, Parasitic; Travel
PubMed: 32667394
DOI: 10.1590/s1678-9946202062047