Escherichia coli strain:MS7163
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA427051 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR6706193.fastq.gz | Fastqsanger.gz | |||
| SRR6706194.fastq.gz | Fastqsanger.gz | |||
| SRR6706195.fastq.gz | Fastqsanger.gz | |||
| SRR6706196.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Two lineages of enterohemorrhagic (EHEC) Escherichia coli O157:H7 (EDL933, Stx1+ and Stx2+) and 86-24 (Stx2+) were investigated in regards to biofilm formation on an abiotic surface. Strikingly, EDL933 strain formed a robust biofilm while 86-24 strain formed no biofilm on either a polystyrene plate or a polyethylene tube. To identify the genetic mechanisms of different biofilm formation in two EHEC strains, DNA microarrays were first performed and phenotypic assays were followed. In the comparison of the EDL933 strain versus 86-24 strain, genes (csgBAC and csgDEFG) involved in curli biosynthesis were significantly induced while genes (trpLEDCB and mtr) involved in indole signaling were repressed. Additionally, a dozen of phage genes were differentially present between two strains. Curli assays using a Congo red plate and scanning electron microscopy corroborate the microarray data as the EDL 933 strain produces a large amount of curli, while 86-24 forms much less curli. Also, the indole production in the EDL933 was 2-times lower than that of 86-24. It was known that curli formation positively regulates and indole negatively regulates biofilm formation of EHEC. Hence, it appears that less curli formation and high indole production in the 86-24 strain are majorly responsible for no biofilm formation.
2011-01-19 | GSE19953 | GEO
Project description:Pathogenic biofilms have been associated with persistent infections due to their high resistance to antimicrobial agents. To identify non-toxic biofilm inhibitors for enterohemorrhagic Escherichia coli O157:H7, indole-3-acetaldehyde was used and reduced E. coli O157:H7 biofilm formation. Global transcriptome analyses revealed that indole-3-acetaldehyde most repressed two curli operons, csgBAC and csgDEFG, and induced tryptophanase (tnaAB) in E. coli O157:H7 biofilm cells. Electron microscopy showed that indole-3-acetaldehyde reduced curli production in E. coli O157:H7. Together, this study shows that Actinomycetales are an important resource of biofilm inhibitors as well as antibiotics.
2012-07-05 | GSE30424 | GEO
Project description:Two lineages of enterohemorrhagic (EHEC) Escherichia coli O157:H7 (EDL933, Stx1+ and Stx2+) and 86-24 (Stx2+) were investigated in regards to biofilm formation on an abiotic surface. Strikingly, EDL933 strain formed a robust biofilm while 86-24 strain formed no biofilm on either a polystyrene plate or a polyethylene tube. To identify the genetic mechanisms of different biofilm formation in two EHEC strains, DNA microarrays were first performed and phenotypic assays were followed. In the comparison of the EDL933 strain versus 86-24 strain, genes (csgBAC and csgDEFG) involved in curli biosynthesis were significantly induced while genes (trpLEDCB and mtr) involved in indole signaling were repressed. Additionally, a dozen of phage genes were differentially present between two strains. Curli assays using a Congo red plate and scanning electron microscopy corroborate the microarray data as the EDL 933 strain produces a large amount of curli, while 86-24 forms much less curli. Also, the indole production in the EDL933 was 2-times lower than that of 86-24. It was known that curli formation positively regulates and indole negatively regulates biofilm formation of EHEC. Hence, it appears that less curli formation and high indole production in the 86-24 strain are majorly responsible for no biofilm formation. For the microarray experiments, E. coli O157:H7 EDL933 and 86-24 were inoculated in 25 ml of LB in 250 ml shake flasks with overnight cultures that were diluted 1:100. Cells were shaken at 250 rpm and 37°C for an absorbance of 4.0 at 600 nm. Cells were immediately chilled with dry ice and 95% ethanol (to prevent RNA degradation) for 30 sec before centrifugation in 50 ml centrifuge tubes at 13,000 g for 2 min; cell pellets were frozen immediately with dry ice and stored -80°C. RNA was isolated using Qiagen RNeasy mini Kit (Valencia, CA, USA). RNA quality was assessed by Agilent 2100 bioanalyser using the RNA 6000 Nano Chip (Agilent Technologies, Amstelveen, The Netherlands), and quantity was determined by ND-1000 Spectrophotometer (NanoDrop Technologies, Inc., DE, USA).
2011-01-19 | E-GEOD-19953 | biostudies-arrayexpress
Project description:In most ecosystems, bacteria primarily exist as structured surface-associated biofilms that can be highly tolerant to antibiotics and thus represent an important health issue. Here we explored drug repurposing as a strategy to identify new antibiofilm compounds, screening over 1000 compounds from the Prestwick Chemical Library of approved drugs for specific activities that prevent biofilm formation by Escherichia coli. Most growth-inhibiting compounds, which include known antibacterial but also antiviral and other drugs, had also reduced biofilm formation. However, we also identified several drugs that were biofilm-inhibitory at doses where only weak or no effect on planktonic growth could be observed. Activities of the most specific antibiofilm compounds were further characterized using gene expression analysis, proteomics and microscopy. We observed that most of these drugs acted by repressing genes responsible for production of curli, major component of E. coli biofilm matrix. This repression apparently occurred through induction of several different stress responses, including DNA and cell-wall damage, and homeostasis of divalent cations, demonstrating that biofilm formation can be inhibited through a variety of molecular mechanisms. One tested drug, tyloxapol, inhibited biofilm formation independent of curli expression or growth, by suppressing bacterial attachment at the surface.
2020-08-14 | PXD020710 | Pride
Project description:Leafy green vegetables, such as lettuce, have been increasingly implicated in outbreaks of foodborne illnesses due to contamination by Escherichia coli O157:H7. While E. coli can survive in soils, colonize plants, and survive on produce, very little is known about the interaction of E. coli with the roots of growing lettuce plants. In these studies a combination of microarray analyses and microbial genetics were used to gain a comprehensive understanding of bacterial genes involved in the colonization and growth of E. coli K12 on lettuce roots using a hydroponic assay system. Here we report that after three days of interaction with lettuce roots, 193 and 131 genes were significantly up-regulated and down-regulated at least 1.5 fold, respectively. Forty-five out of the 193 up-regulated genes (23%) were involved in protein synthesis and were highly induced. Genes involved in stress response, attachment and biofilm formation were up-regulated in E. coli when they interacted with lettuce roots under conditions of hydroponic growth. In particular crl, a gene regulating the cryptic csgA gene for curli production, was significantly up regulated. The crl, csgA and fliN mutants had a reduced capacity to attach to roots as determined by bacterial counts and by confocal laser scanning microscopy. Our microarray data showed that E. coli K12 increased the synthesis of proteins indicated that a dramatic change was induced in the physiology of the microorganism. This study indicates that E. coli K12 can efficiently colonize lettuce roots by using attachment and biofilm modulation genes and can readily adapt to the rhizosphere of lettuce plants. Further studies are needed to better characterize this interaction in pathogenic strains of this species. Escherichia coli MG1655 strains were grown in the lettuce rhizosphere for three days. Transcriptional profiling of E. coli was compared between cells grown with and without rhizosphere . Three biological replicates of each treatment were prepared, and six microarray slides were used.
2011-11-17 | E-GEOD-33735 | biostudies-arrayexpress
Project description:The experiment design involves RNA-seq of Hfq bound RNA co-immunoprecipitation in the uropathogenic Escherichia coli (UPEC) strain UTI89.
2016-05-31 | E-MTAB-3498 | biostudies-arrayexpress
Project description:Novel genes associated with capsule production in uropathogenic Escherichia coli
| PRJNA385892 | ENA
Project description:Pathogenic biofilms have been associated with persistent infections due to high resistance to antimicrobial agents while commensal biofilms often fortify host immune system. Hence, controlling biofilm formation of both pathogenic bacteria and commensal bacteria is important in bacteria-related diseases. We investigated the effect of plant flavonoids on biofilm formation of both enterohemorrhagic Escherichia coli O157:H7 and three commensal E. coli K-12 strains. Phloretin abundant in apples markedly reduced E. coli O157:H7 biofilm formation without affecting the growth of planktonic cells while phloretin did not harm commensal E. coli K-12 biofilms. Also, phloretin reduced E. coli O157:H7 attachment to human colon epithelial cells. Global transcriptome analyses revealed that phloretin repressed toxin genes (hlyE and stx2), autoinducer-2 importer genes (lsrACDBF), a curli gene (csgA), and a dozens of prophage genes in E. coli O157:H7 cells. Electron microscopy confirmed that phroretin reduced the curli production in E. coli O157:H7. In addition, phloretin suppressed TNF-α-induced inflammatory response in vitro using human colonic epithelial cells. Moreover, in the trinitrobenzene sulfonic acid (TNBS)-induced rat colitis model, phloretin significantly ameliorated colon inflammation and body weight loss. Taken together, our results suggest that phloretin may act as an inhibitor of E. coli O157:H7 biofilm formation as well as anti-inflammatory agent on inflammatory bowel diseases while leaving beneficial commensal E. coli biofilm intact.
2011-11-22 | GSE28144 | GEO
Project description:Intercellular signal indole and its derivative hydroxyindoles inhibit Escherichia coli biofilm and diminish Pseudomonas aeruginosa virulence. However, indole and bacterial indole derivatives were unstable in microbial community due to the widespread of diverse oxygenases that could quickly degrade them. Hence, we sought to identify novel non-toxic, stable, and potent indole derivatives from plant sources for inhibiting biofilm formation of E. coli O157:H7 and P. aeruginosa PAO1. Here, plant auxin 3-indolylacetonitrile (IAN) was found to inhibit biofilm formation of both E. coli O157:H7 and P. aeruginosa without affecting its growth. IAN inhibited biofilms more effectively than indole for both E. coli and P. aeruginosa. Additionally, IAN decreased the production of virulence factor pyocyanin in P. aeruginosa. DNA microarray analysis indicated that IAN repressed genes involved in curli formation and glycerol metabolism, while IAN induced indole-related genes and prophage genes in E. coli. It appears that IAN inhibits biofilm formation of E. coli by reducing curli formation and inducing indole production. Furthermore, unlike bacterial indole derivatives, plant-originated IAN was stable in the presence of either E. coli or P. aeruginosa.
2010-12-31 | GSE19842 | GEO
Project description:Intercellular signal indole and its derivative hydroxyindoles inhibit Escherichia coli biofilm and diminish Pseudomonas aeruginosa virulence. However, indole and bacterial indole derivatives were unstable in microbial community due to the widespread of diverse oxygenases that could quickly degrade them. Hence, we sought to identify novel non-toxic, stable, and potent indole derivatives from plant sources for inhibiting biofilm formation of E. coli O157:H7 and P. aeruginosa PAO1. Here, plant auxin 3-indolylacetonitrile (IAN) was found to inhibit biofilm formation of both E. coli O157:H7 and P. aeruginosa without affecting its growth. IAN inhibited biofilms more effectively than indole for both E. coli and P. aeruginosa. Additionally, IAN decreased the production of virulence factor pyocyanin in P. aeruginosa. DNA microarray analysis indicated that IAN repressed genes involved in curli formation and glycerol metabolism, while IAN induced indole-related genes and prophage genes in E. coli. It appears that IAN inhibits biofilm formation of E. coli by reducing curli formation and inducing indole production. Furthermore, unlike bacterial indole derivatives, plant-originated IAN was stable in the presence of either E. coli or P. aeruginosa.
2011-02-20 | GSE21508 | GEO