Ontology highlight
ABSTRACT:
PROVIDER: PRJNA980458 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR24834172_1.fastq.gz | Fastqsanger.gz | |||
| SRR24834173_1.fastq.gz | Fastqsanger.gz |
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Project description:A popular strategy for enhancing the antibacterial properties of probiotic bacteria is to retrofit them with the ability to overproduce heterologous bacteriocins. This is often achieved from strong, non-native promoters. How the dysregulated overproduction of heterologous bacteriocins affects the fitness and antibacterial efficacy of the retrofitted probiotic bacteria is often overlooked. We conferred the prototypical probiotic Escherichia coli strain Nissle (EcN) the ability to produce different amounts of the bacteriocin microcin C (McC). Expression of the bacteriocin synthesis genes was driven from the native promoter (Pmcc-WT), or from promoters manipulated to be stronger (Pmcc-High) and weaker (Pmcc-Low) than the WT, in a plasmid-based system. Pmcc-Low and Pmcc-High retained their native regulation. A strain harbouring a non-functional promoter (Pmcc-Mut) produces no McC and was used as a control. Each strain was grown to early stationary phase, when production of McC starts, in Luria-Bertani broth at 37 degrees. The RNA was isolated and the effects of different levels of production of McC on the transcriptome of EcN was examined by RNA-Seq.
2023-06-30 | E-MTAB-13078 | biostudies-arrayexpress
Project description:Escherichia coli strains producing exogenous internal membrane proteins
2019-02-27 | GSE109819 | GEO
Project description:Whole genome sequencing of probiotic Escherichia coli strains
| PRJNA944444 | ENA
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
2008-01-22 | GSE8595 | GEO
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 (âpan-genomeâ) 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. Factorial design: Each of four test samples (G 1/2, G3/10, G 4/9, G5) are co-hybridized with two control strain samples (K-12 MG1655 and O157:H7 EDL933). Additional replicate co-hybridizations are included of the two control strain samples (O157:H7 EDL933 vs. K-12 MG1655).
2010-05-26 | E-GEOD-8595 | biostudies-arrayexpress
Project description:Proteomic Characterization of Bacteriocin-Producing Enterococcus faecium Strains from foodstuffs
2023-03-11 | PXD037241 | Pride
Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 ?fnr mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the FNR protein. WT strains were grown under aerobic and anaerobic growth conditions.
2013-06-20 | GSE41189 | GEO
Project description:The Escherichia coli strain Nissle 1917 (EcN) is used as a probiotic for the treatment of certain gastrointestinal diseases in several European and non-European countries. In vitro studies showed EcN to efficiently inhibit the production of Shiga toxin (Stx) by Stx producing E. coli (STEC) such as Enterohemorrhagic E. coli (EHEC). The occurrence of the latest EHEC serotype (O104:H4) responsible for the great outbreak in 2011 in Germany was due to the infection of an enteroaggregative E. coli by a Stx 2-encoding lambdoid phage turning this E. coli into a lysogenic and subsequently into a Stx producing strain. Since EHEC infected persons are not recommended to be treated with antibiotics, EcN might be an alternative medication. However, because a harmless E. coli strain might be converted into a Stx-producer after becoming host to a stx encoding prophage, we tested EcN for stx-phage genome integration. Our experiments revealed the resistance of EcN towards not only stx-phages but also against the lambda phage. This resistance was not based on the lack of or by mutated phage receptors. Rather the expression of certain genes (superinfection exclusion B (sieB) and a phage repressor (pr) gene) of a defective prophage of EcN was involved in the complete resistance of EcN to infection by the stx- and lambda phage. Obviously, EcN cannot be turned into a Stx producer. Furthermore, we observed EcN to inactivate phages and thereby to protect E. coli K-12 strains against infection by stx- as well as lambda-phages. Inactivation of lambda-phages was due to binding of lambda-phages to LamB of EcN whereas inactivation of stx-phages was caused by a thermostable protein of EcN. These properties together with its ability to inhibit Stx production make EcN a good candidate for the prevention of illness caused by EHEC and probably for the treatment of already infected people.
2018-06-14 | GSE109932 | GEO
Project description:Comparative genomic hybridization between Escherichia coli strains to determine core and pan genome content of clinical and environmental isolates
2012-08-30 | GSE39667 | GEO