Delftia acidovorans SPH-1
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA17413 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR253103.fastq.gz | Fastqsanger.gz | |||
| SRR9434330.fastq.gz | Fastqsanger.gz | |||
| SRR9434340.fastq.gz | Fastqsanger.gz | |||
| SRR9434321.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Isolated from soil enriched with acetamide
| PRJNA17425 | ENA
Project description:Protein expression and fatty acid profiles of biofilm cells of chlorhexidine-tolerant Delftia acidovorans (MIC = 15 µg/ml) and its chlorhexidine-susceptible mutant (MIC = 1 µg/ml) were investigated. The chlorhexidine-susceptible mutant (MT51) was derived from the parental strain (WT15) using Tn5 transposon mutagenesis. The disrupted gene was identified as tolQ, a component of the tolQRAB gene cluster known to be involved in outer membrane stability. Proteomic responses of biofilm cells were compared by differential in-gel electrophoresis following exposure to chlorhexidine at sub-MIC (10 µg/ml) and above-MIC (30 µg/ml) concentrations. Numerous changes in protein abundance were observed in biofilm cells following chlorhexidine exposure, suggesting that molecular changes occurred during adaptation to chlorhexidine. Forty proteins showing significant differences (≥1.5-fold; P < 0.05) were identified by mass spectrometry and were associated with various functions, including amino acid and lipid biosynthesis, protein translation, energy metabolism, and stress-related functions (e.g., GroEL, aspartyl/glutamyl-tRNA amidotransferase, elongation factor Tu, Clp protease, and hydroxymyristoyl-ACP dehydratase). Several proteins involved in fatty acid synthesis were affected by chlorhexidine, in agreement with fatty acid analysis, wherein chlorhexidine-induced shifts in the fatty acid profile were observed in the chlorhexidine-tolerant cells, primarily the cyclic fatty acids. Transmission electron microscopy revealed more prominent changes in the cell envelope of chlorhexidine-susceptible MT51 cells. This study suggests that multiple mechanisms involving both the cell envelope (and likely TolQ) and panmetabolic regulation play roles in chlorhexidine tolerance in D. acidovorans. IMPORTANCE Delftia acidovorans has been associated with a number of serious infections, including bacteremia, empyema, bacterial endocarditis, and ocular and urinary tract infections. It has also been linked with a variety of surface-associated nosocomial infections. Biofilm-forming antimicrobial-resistant D. acidovorans strains have also been isolated, including ones displaying resistance to the common broad-spectrum agent chlorhexidine. The mechanisms of chlorhexidine resistance in D. acidovorans are not known; hence, a chlorhexidine-susceptible mutant of the tolerant wild-type strain was obtained using transposon mutagenesis, and the proteome and ultrastructural changes of both strains were compared under chlorhexidine challenge.
| S-EPMC4863599 | biostudies-literature
Project description:A novel phosphodiesterase (PdeA) was purified from Delftia acidovorans, the gene encoding the enzyme was cloned and expressed in Escherichia coli, and the recombinant enzyme was purified to apparent homogeneity and characterized. PdeA is an 85-kDa trimer that exhibits maximal activity at 65 degrees C and pH 10 even though it was isolated from a mesophilic bacterium. Although PdeA exhibited both mono- and diesterase activity, it was most active on the phosphodiester bis(p-nitrophenyl)phosphate with a K(m) of 2.9 +/- 0.1 mM and a k(cat) of 879 +/- 73 min(-1). The enzyme showed sequence similarity to cyclic AMP (cAMP) phosphodiesterase and cyclic nucleotide phosphodiesterases and exhibited activity on cAMP in vivo when the gene was expressed in E. coli. The IS1071 transposon insertion sequence was found downstream of pdeA.
| S-EPMC152426 | biostudies-literature
Project description:Polycyclic aromatic hydrocarbons (PAH) are ubiquitous environmental pollutants and microbial biodegradation is an important means of remediation of PAH-contaminated soil. Delftia acidovorans Cs1-4 (formerly Delftia sp. Cs1-4) was isolated by using phenanthrene as the sole carbon source from PAH contaminated soil in Wisconsin. Its full genome sequence was determined to gain insights into a mechanisms underlying biodegradation of PAH. Three genomic libraries were constructed and sequenced: an Illumina GAii shotgun library (916,416,493 reads), a 454 Titanium standard library (770,171 reads) and one paired-end 454 library (average insert size of 8 kb, 508,092 reads). The initial assembly contained 40 contigs in two scaffolds. The 454 Titanium standard data and the 454 paired end data were assembled together and the consensus sequences were computationally shredded into 2 kb overlapping shreds. Illumina sequencing data was assembled, and the consensus sequence was computationally shredded into 1.5 kb overlapping shreds. Gaps between contigs were closed by editing in Consed, by PCR and by Bubble PCR primer walks. A total of 182 additional reactions were needed to close gaps and to raise the quality of the finished sequence. The final assembly is based on 253.3 Mb of 454 draft data (averaging 38.4 X coverage) and 590.2 Mb of Illumina draft data (averaging 89.4 X coverage). The genome of strain Cs1-4 consists of a single circular chromosome of 6,685,842 bp (66.7 %G+C) containing 6,028 predicted genes; 5,931 of these genes were protein-encoding and 4,425 gene products were assigned to a putative function. Genes encoding phenanthrene degradation were localized to a 232 kb genomic island (termed the phn island), which contained near its 3' end a bacteriophage P4-like integrase, an enzyme often associated with chromosomal integration of mobile genetic elements. Other biodegradation pathways reconstructed from the genome sequence included: benzoate (by the acetyl-CoA pathway), styrene, nicotinic acid (by the maleamate pathway) and the pesticides Dicamba and Fenitrothion. Determination of the complete genome sequence of D. acidovorans Cs1-4 has provided new insights the microbial mechanisms of PAH biodegradation that may shape the process in the environment.
| S-EPMC4572682 | biostudies-literature
Project description:Delftia acidovorans strain HK171, isolated from tomato roots, exhibited nematicidal activity against Meloidogyne incognita Here, we present the genome sequence of D. acidovorans strain HK171, which consists of one circular chromosome of 6,430,384 bp, with 66.9% G+C content.
| S-EPMC5334598 | biostudies-literature
Project description:Delftia acidovorans (D. acidovorans) is a Gram-negative bacteria and an uncommon cause of human infections. This retrospective cohort study investigated clinical and microbiological characteristics and outcomes of patients with D. acidovorans infections. We included patients with culture-confirmed D. acidovorans infections attending Rigshospitalet, during 2002-2020. Fifty-nine patients with a median interquartile ranges (IQR) age of 47 (15-67) years were included. Thirty-five (59%) were males, and 57 (97%) had at least one comorbidity, including 25 (42%) with solid or hematologic malignancies. Eight (14%) were admitted to ICU, and 15 (25%) died within 365 days after infection. Persistent infection was found in 4 (6.8%) patients, and 41 (70%) had polymicrobial cultures, mainly with Pseudomonas spp. and Stenotrophomonas maltophilia. More than 85% of the D. acidovorans isolates were susceptible to meropenem or ceftazidime. Although, 88% and 62% of the isolates were resistant to gentamicin and colistin, respectively. D. acidovorans infections mainly affect patients with preexisting comorbidities, including malignancies. In the first year, all-cause mortality is considerable, polymicrobial cultures are common, and meropenem or cephalosporins with antipseudomonal activity could be the antibiotics of choice. IMPORTANCE Delftia acidovorans (D. acidovorans) is a Gram-negative bacteria that can cause infection in immunocompetent and immunocompromised individuals. The current knowledge comes mainly from case reports and case series. In this retrospective cohort study, we found that D. acidovorans infections mainly affect male patients with preexisting comorbidities, including malignancies. Persistent infections were not common, and most of the patients had polymicrobial cultures, mainly with Pseudomonas spp. and Stenotrophomonas maltophilia. More than 85% of the D. acidovorans isolates were susceptible to meropenem or ceftazidime. In contrast, 88% and 62% of the isolates were resistant to gentamicin and colistin, respectively.
| S-EPMC9431703 | biostudies-literature
Project description:Delftia acidovorans strain D4B is an aerobic bacterium within the Betaproteobacteria lineage that was isolated from soil. The genome size is 6.26 Mbp, with a G+C content of 67%. The genome encodes enzymes potentially involved in the degradation of fluorinated compounds.
| S-EPMC8567785 | biostudies-literature
Project description:Delftia acidovorans PCA12 genome sequence
| PRJEB333 | ENA
Project description:Herein, we report the genome sequence of Delftia acidovorans strain RAY209, a plant growth-promoting rhizobacterium that is used in commercial inoculants for canola and soybean. The genome of RAY209 has a consensus of 6,528,879 bp and an estimated 5,721 coding sequences.
| S-EPMC5668544 | biostudies-literature
Project description:Per- and Polyfluorinated alkyl substances (PFAS) are a broad class of synthetic compounds that have fluorine substituted for hydrogen in several or all locations and are globally categorized as PFCs (perfluorochemicals; commonly called fluorinated chemicals). These compounds have unique chemical and physical properties that enable their use in non-stick surfaces, fire-fighting efforts, and as slick coatings. However, recent concerns over the health effects of such compounds, specifically perfluorooctanoic acid and perfluorooctane sulfonic acid (PFOA, PFOS; PFOA/S), have led to increased attention and research by the global community into degradation methods. In this study, soil samples from PFAS-contamination sites were cultured and screened for microbes with PFOA/S degradation potential, which led to the identification of Delftia acidovorans. It was found that D. acidovorans isolated from PFAS-contaminated soils was capable of growth in minimal media with PFOA as a sole carbon resource, and an observable fluoride concentration increase was observed when cells were exposed to PFOA. This suggests potential activity of a dehalogenase enzyme that may be of use in PFOA or PFAS microbial remediation efforts. Several associated haloacid dehalogenases have been identified in the D. acidovorans genome and have been engineered for expression in Escherichia coli for rapid production and purification. These enzymes have shown potential for enzymatic defluorination, a significant step in biological degradation and removal of PFOA/S from the environment. We hypothesize that bioremediation of PFAS using naturally occurring microbial degradation pathways may represent a novel approach to remove PFAS contamination.
| S-EPMC8857417 | biostudies-literature