Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB12663 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR351055_1.fastq.gz | Fastqsanger.gz | |||
| DRR351055_2.fastq.gz | Fastqsanger.gz | |||
| DRR351056_1.fastq.gz | Fastqsanger.gz | |||
| DRR351056_2.fastq.gz | Fastqsanger.gz | |||
| DRR351057_1.fastq.gz | Fastqsanger.gz |
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Project description:Background: Based on 32 Escherichia coli and Shigella genome sequences, we have developed an E. coli pan-genome microarray. Publicly available genomes were annotated in a consistent manor to define all currently known genes potentially present in the species. The chip design was evaluated by hybridization of DNA from two sequenced E. coli strains, K-12 MG1655 (a commensal) and O157:H7 EDL933 (an enterotoxigenic E. coli). A dual channel and single channel analysis approach was compared for the comparative genomic hybridization experiments. Moreover, the microarray was used to characterize four unsequenced probiotic E. coli strains, currently marketed for beneficial effects on the human gut flora. Results: Based on the genomes included in this study, we were able to group together 2,041 genes that were present in all 32 genomes. Furthermore, we predict that the size of the E. coli core genome will approach ~1,560 essential genes, considerably less than previous estimates. Although any individual E. coli genome contains between 4,000 and 5,000 genes, we identified more than twice as many (11,872) distinct gene groups in the total gene pool (“pan-genome”) examined for microarray design. Benchmarking of the design based on sequenced control strain samples demonstrated a high sensitivity and relatively low false positive rate. Moreover, the array was highly sufficient to investigate the gene content of apathogenic isolates, despite the strong bias towards pathogenic E. coli strains that have been sequenced so far. Our analysis of four probiotic E. coli strains demonstrate that they share a gene pool very similar to the E. coli K-12 strains but also show significant similarity with enteropathogenic strains. Nonetheless, virulence genes were largely absent. Strain-specific genes found in probiotic E. coli but absent in E. coli K12 were most frequently phage-related genes, transposases and other genes related to mobile DNA, and metabolic enzymes or factors that may offer colonization fitness, which together with their asymptomatic nature may explain their nature. Conclusion: This high-density microarray provides an excellent tool for characterizing either DNA content or gene expression from unknown E. coli strains. Keywords: Comparative genomic hybridizations
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Project description:A genome reduced E. coli strain MDS42ΔgalK::Ptet-gfp-kan were applied for the comparative transcriptome analysis. Genome-wide transcriptional changes under high osmotic prresure, high temperature condition and starvation were evaluated.
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Project description:Counting DNA reads using whole genome sequencing is providing new insight into DNA double-strand break repair (DSBR) in the model organism Escherichia coli. We describe the application of RecA chromatin immunoprecipitation coupled to genomic DNA sequencing (RecA-ChIP-seq) and marker frequency analysis (MFA) to analyse the genomic consequences of DSBR.
2019-01-03 | GSE117541 | GEO
Project description:Counting DNA reads using whole genome sequencing is providing new insight into DNA double-strand break repair (DSBR) in the model organism Escherichia coli. We describe the application of RecA chromatin immunoprecipitation coupled to genomic DNA sequencing (RecA-ChIP-seq) and marker frequency analysis (MFA) to analyse the genomic consequences of DSBR.
2019-01-03 | GSE117952 | GEO
Project description:Transcriptome analysis of genome reduced E. coli
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Project description:The purpose of this study is to determine whether the presence of pathogenic Escherichia coli in colon is associated with psychiatric disorders.
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Project description:Despite the characterization of many aetiologic genetic changes. The specific causative factors in the development of sporadic colorectal cancer remain unclear. This study was performed to detect the possible role of Enteropathogenic Escherichia coli (EPEC) in developing colorectal carcinoma.
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Project description:We describe the design and evaluate the use of a high density oligonuclotide microarray covering seven sequenced E. coli genomes in addition to several sequenced E. coli plasmids, bacteriophages, pathogenicity islands and virulence genes. Its utility is demonstrated for comparative genomic profiling of two unsequenced strains, O175:H16 D1 and O157:H7 3538 as well as two well-known control strains, K-12 W3110 and O157:H7 EDL933. By using fluorescently labelled genomic DNA to query the microarrays and subsequently analyse common virulence genes and phage elements, and perform whole genome comparisons, we observed that O175:H16 D1 is a K-12 like strain and confirmed that its phi3538 phage element originated from the E. coli 3538 strain with which it shares a substantial proportion of phage elements. Moreover, a number of genes involved in DNA transfer and recombination was identified in both new strains providing a likely explanation for their capability to transfer phi3538 between them. Analyses of control samples demonstrated that results using our custom designed microarray were representative of the true biology, e.g. by confirming the presence of all known chromosomal phage elements as well as 98.8 and 97.7 percent of queried chromosomal genes for the two control strains. Finally, we demonstrate that use of spatial information, in terms of the physical chromosomal locations of probes, improves the analysis. Keywords: Genomic DNA hybridizations
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Project description:Cinnamaldehyde is a natural antimicrobial and has been found to be effective against many foodborne pathogens including Escherichia coli O157:H7. Although its antimicrobial effects have been well investigated, limited information is available on its effects at the molecular level. Sublethal treatment at 200 mg/l cinnamaldehyde inhibited growth of E. coli O157:H7 at 37oC and for ≤ 2 h caused cell elongation, but from 2 to 4 h growth resumed and cells reverted to normal length. To understand this transient behaviour, genome-wide transcriptional analysis of E. coli O157:H7 was performed at 2 and 4 h exposure to cinnamaldehyde. Drastically different gene expression profiles were obtained at 2 and 4 h. At 2 h exposure, cinnamaldehyde induced overexpression of many oxidative stress-related genes, reduced DNA replication, and synthesis of protein, O-antigen and fimbriae. At 4 h, many cinnamaldehyde-induced repressive effects on E. coli O157:H7 gene expressions were reversed and oxidatve stress genes were nolonger differentially expressed.
2012-09-08 | GSE40693 | GEO
Project description:Escherichia coli, the common inhabitant of the mammalian intestine, exhibits considerable intraspecies genomic variation, which has been suggested to reflect adaptation to different ecological niches. Also, regulatory trade-offs, e.g., between catabolic versatility and stress protection, are thought to result in significant physiological differences between strains. For these reasons, the relevance of experimental observations made for “domesticated” E. coli strains with regard to the behaviour of this species in its natural environments is often questioned and frequently doubts are raised on the status of E. coli as a defined species. We therefore investigated the variability of important eco-physiological functions such as carbon substrate uptake and breakdown capabilities as well as stress defence mechanisms in the genomes of commensal and pathogenic E. coli strains. Furthermore, eco-physiological properties of environmental strains were compared to standard laboratory strain K-12 MG1655. Catabolic, stress protection, and carbon- and energy source transport operons showed a very low intraspecies variability in 57 commensal and pathogenic E. coli. Environmental isolates adapted to glucose-limited growth in a similar way as E. coli MG1655, namely by increasing their catabolic flexibility and by inducing high affinity substrate uptake systems. Our results indicate that the major eco-physiological properties are highly conserved in the natural population of E. coli. This questions the proposed dominant role of horizontal gene transfer for niche adaptation. Keywords: comparative genomic hybridisation
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