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New Microbes and New Infections May 2016Strain FF11(T) was isolated from the wound on a researcher's finger who had been bitten by a fish (Protopterus annectens) in Senegal. Analysis by matrix-assisted laser...
Strain FF11(T) was isolated from the wound on a researcher's finger who had been bitten by a fish (Protopterus annectens) in Senegal. Analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry did not provide any identification, but the 16S rRNA sequence exhibited 97.9% identity with Dermabacter hominis. Phenotypic and genomic analyses demonstrated that strain FF11(T) is Gram-positive, facultatively anaerobic, nonmotile and non-spore forming; it exhibited a genome of 2 222 902 bp encoding 2074 protein-coding and 50 RNA genes, with a 63.2% G+C content. We consequently proposed the creation of Dermabacter indicis strain FF11(T).
PubMed: 27081494
DOI: 10.1016/j.nmni.2016.02.007 -
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 -
Changes in gastric and lung microflora with acid suppression: acid suppression and bacterial growth.JAMA Pediatrics Oct 2014The use of acid suppression has been associated with an increased risk of upper and lower respiratory tract infections in the outpatient setting but the mechanism behind...
IMPORTANCE
The use of acid suppression has been associated with an increased risk of upper and lower respiratory tract infections in the outpatient setting but the mechanism behind this increased risk is unknown. We hypothesize that this infection risk results from gastric bacterial overgrowth with subsequent seeding of the lungs.
OBJECTIVES
To determine if acid-suppression use results in gastric bacterial overgrowth, if there are changes in lung microflora associated with the use of acid suppression, and if changes in lung microflora are related to full-column nonacid gastroesophageal reflux.
DESIGN, SETTING, AND PARTICIPANTS
A 5-year prospective cohort study at a tertiary care center where children ages 1 to 18 years were undergoing bronchoscopy and endoscopy for the evaluation of chronic cough. Acid-suppression use was assessed through questionnaires with confirmation using an electronic medical record review.
MAIN OUTCOMES AND MEASURES
Our primary outcome was to compare differences in concentration and prevalence of gastric and lung bacteria between patients who were and were not receiving acid-suppression therapy. We compared medians using the Wilcoxon signed rank test and determined prevalence ratios using asymptotic standard errors and 95% confidence intervals. We determined correlations between continuous variables using Pearson correlation coefficients and compared categorical variables using the Fisher exact test.
RESULTS
Forty-six percent of patients taking acid-suppression medication had gastric bacterial growth compared with 18% of untreated patients (P = .003). Staphylococcus (prevalence ratio, 12.75 [95% CI, 1.72-94.36]), Streptococcus (prevalence ratio, 6.91 [95% CI, 1.64-29.02]), Veillonella (prevalence ratio, 9.56 [95% CI, 1.26-72.67]), Dermabacter (prevalence ratio, 4.78 [95% CI, 1.09-21.02]), and Rothia (prevalence ratio, 6.38 [95% CI, 1.50-27.02]) were found more commonly in the gastric fluid of treated patients. The median bacterial concentration was higher in treated patients than in untreated patients (P = .001). There was no difference in the prevalence (P > .23) of different bacterial genera or the median concentration of total bacteria (P = .85) in the lungs between treated and untreated patients. There were significant positive correlations between proximal nonacid reflux burden and lung concentrations of Bacillus (r = 0.47, P = .005), Dermabacter (r = 0.37, P = .008), Lactobacillus (r = 0.45, P = .001), Peptostreptococcus (r = 0.37, P = .008), and Capnocytophagia (r = 0.37, P = .008).
CONCLUSIONS AND RELEVANCE
Acid-suppression use results in gastric bacterial overgrowth of genera including Staphylococcus and Streptococcus. Full-column nonacid reflux is associated with greater concentrations of bacteria in the lung. Additional studies are needed to determine if acid suppression-related microflora changes predict clinical infection risk; these results suggest that acid suppression use may need to be limited in patients at risk for infections.
Topics: Adolescent; Antacids; Bacterial Infections; Child; Child, Preschool; Female; Gastroesophageal Reflux; Humans; Hydrogen-Ion Concentration; Infant; Lung; Lung Diseases; Male; Prospective Studies; Stomach; Stomach Diseases
PubMed: 25133779
DOI: 10.1001/jamapediatrics.2014.696 -
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 -
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 -
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 -
Evidence-based Complementary and... 2017Several species are known for their uses in traditional medicine and consequently are studied for their phytochemical content and their biological activities. In the...
Several species are known for their uses in traditional medicine and consequently are studied for their phytochemical content and their biological activities. In the framework of a previous study conducted on eight extremophile plants from Tunisia, we highlighted that the crude methanolic extract of , a not investigated thistle, showed moderate but quite selective cytotoxic activity against the cancerous cell line J774 compared to the noncancerous cell line WI38 (IC = 11.53 g/ml on J774, IC = 29.89 g/ml on WI38, and selectivity index = 2.6). In the current study, the partitions of the leaves of were analyzed for their antiproliferative activity on the same cell lines. From the most active petroleum ether partition, we isolated four triterpenoids including lupeol, taraxasterol acetate, and a (1 : 1) mixture of 25-hydroperoxycycloart-23-en-3-ol and 24-hydroperoxycycloart-25-en-3-ol. These two cycloartane-type triterpenoids are mostly responsible for this cytotoxic activity. On the other hand, the antimicrobial potential of this plant was also evaluated against 36 microorganisms. The moderate antibacterial activity against 6 and 2 strains is mainly attributed to the butanol partition whose major compounds are glycosides of flavones.
PubMed: 28785293
DOI: 10.1155/2017/7247016 -
Annals of Medicine and Surgery (2012) Dec 2018Strains of the genus is a recently established species, recognized as relatively rare opportunistic human pathogen, and is infrequently isolated from clinical...
INTRODUCTION
Strains of the genus is a recently established species, recognized as relatively rare opportunistic human pathogen, and is infrequently isolated from clinical specimens, including blood cultures, abscesses, wounds, bone, eye, and skin.
PRESENTATION OF CASE
We present a 78-year old female with chronic symmetrical peripheral gangrene and hand infection. The patient underwent surgical debridement with amputation on gangrene with infection of both fingers. At 2 weeks postoperatively, pus discharge was newly observed and the patient underwent reoperation. In the subsequent reinfection, unknown organism has been repeatedly identified, may be the most likely causative agent. On the basis of phenotypic and genotypic distinctness and DNA-DNA hybridization results, new strain should be placed in the genus as representing a novel species, for which the name sp. nov. is proposed.
DISCUSSION
We judged the novel species as the causative bacteria. Because of, a novel species called was repeatedly identified more than common bacteria. It can be considered as a postoperative nosocomial infection or opportunistic infection. It is not clear how the infection of occurred.
CONCLUSION
This is the first reported case of a human infection. We were able to treat patients without any complications by operative treatment and administering appropriate antimicrobial agents according to antibiotics susceptibility test.
PubMed: 30402221
DOI: 10.1016/j.amsu.2018.10.008 -
Frontiers in Microbiology 2018Two strains, VM2412 and VR2415, were isolated from the feces of an Andean condor () living in Seoul Grand Park, Gyeonggi-do, South Korea. Cells of both strains were...
Two strains, VM2412 and VR2415, were isolated from the feces of an Andean condor () living in Seoul Grand Park, Gyeonggi-do, South Korea. Cells of both strains were observed to be Gram-stain positive, non-motile, aerobic, catalase positive and oxidase negative. Growth was found to occur at 10-30°C, showing optimum growth at 30°C. The strains could tolerate up to 15% (w/v) NaCl concentration and grow at pH 6-9. The strains shared 99.3% 16S rRNA gene sequence similarity to each other but were identified as two distinct species based on 89.0-89.2% ANIb, 90.3% ANIm, 89.7% OrthoANI and 38.0% dDDH values calculated using whole genome sequences. Among species with validly published names, DCY80 shared high 16S rRNA gene sequence similarities with strains VM2412 (98.7%) and VR2415 (98.4%) and close genetic relatedness with strains VM2412 (83.3-83.5% ANIb, 87.0% ANIm, 84.3% OrthoANI and 27.8% dDDH) and VR2415 (82.8-83.2% ANIb, 86.7% ANIm, 83.9% OrthoANI and 27.2% dDDH). The major fatty acid of the two strains was identified as anteiso-C and the polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol, presumptively phosphatidylethanolamine and three unidentified glycolipids. Strain VR2415 also produced an unidentified phospholipid. The cell walls of the two strains contained -diaminopimelic acid as diagnostic diamino acid and the whole cell sugars were ribose, glucose, and galactose. The strains contained MK-7 as their predominant menaquinone. The genomes of strains VM2412, VR2415, and DCY80 were sequenced in this study. The genomic G+C contents of strains VM2412 and VR2415 were determined to be 70.8 and 70.4 mol%, respectively. A genome-based phylogenetic tree constructed using an up-to-date bacterial core gene set (UBCG) showed that the strains formed a clade with members of the genus , supporting their taxonomic classification into the genus . Based on phenotypic and genotypic analyses in this study, strains VM2412 and VR2415 are considered to represent two novel species of the genus and the names sp. nov. and sp. nov. are proposed for strains VM2412 (=KCTC 39996 = JCM 32142) and VR2415 (=KCTC 39997 = JCM 32143), respectively.
PubMed: 30131788
DOI: 10.3389/fmicb.2018.01809 -
Revista Argentina de Microbiologia 2016Dermabacter hominis species is constituted by Gram positive facultative anaerobic coryneform rods being part of the resident microbiota human skin, and exceptionally...
Dermabacter hominis species is constituted by Gram positive facultative anaerobic coryneform rods being part of the resident microbiota human skin, and exceptionally associated to infections in immunocompromised or severely debilitated patients. An immunocompetent young adult woman with a neck sebaceous cyst infected by D. hominis as unique etiologic agent is presented. Phenotypic identification of the causative agent was achieved through simple tests, based on the originally scheme proposed by Funke and Bernard, and feasible to be performed in a hospital Microbiology Laboratory. Phenotypic characteristics as coccoid morphology, the acrid/spermatic odor, esculin hydrolysis, the production of pyrrolidonyl-arylamidase, lysine and ornithine decarboxylase, are key tests to identify D. hominis. The matrix-asisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) confirmed the phenotypic identification.
Topics: Abscess; Actinomycetales Infections; Bacterial Proteins; Bacterial Typing Techniques; Drainage; Drug Resistance, Multiple, Bacterial; Epidermal Cyst; Female; Humans; Immunocompetence; Micrococcaceae; Middle Aged
PubMed: 27773466
DOI: 10.1016/j.ram.2016.09.003