Vibrio parahaemolyticus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1077923 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR28407117_1.fastq.gz | Fastqsanger.gz | |||
| SRR28407117_2.fastq.gz | Fastqsanger.gz | |||
| SRR28407118_1.fastq.gz | Fastqsanger.gz | |||
| SRR28407118_2.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Vibrio parahaemolyticus is the causative agent of food-borne gastroenteritis disease. Once consumed, human acid gastric fluid is perhaps one of the most important environmental stresses imposed on the bacterium. Herein, for the first time, we investigated Vibrio parahaemolyticus CHN25 response to artificial gastric fluid (AGF) stress by transcriptomic analysis. The bacterium at logarithmic growth phase (LGP) displayed lower survival rates than that at stationary growth phase (SGP) under a sub-lethal acid condition (pH 4.9). Transcriptome data revealed that 11.6% of the expressed genes in Vibrio parahaemolyticus CHN25 was up-regulated in LGP cells after exposed to AGF (pH 4.9) for 30 min, including those involved in sugar transport, nitrogen metabolism, energy production and protein biosynthesis, whereas 14.0% of the genes was down-regulated, such as ABC transporter and flagellar biosynthesis genes. In contrast, the AGF stress only elicited 3.4% of the genes from SGP cells, the majority of which were attenuated in expression. Moreover, the number of expressed regulator genes was also substantially reduced in SGP cells. Comparison of transcriptome profiles further revealed forty-one growth-phase independent genes in the AGF stress, however, half of which displayed distinct expression features between the two growth phases. Vibrio parahaemolyticus seemed to have evolved a number of molecular strategies for coping with the acid stress. The data here will facilitate future studies for environmental stresses and pathogenicity of the leading food-borne pathogen worldwide.
2015-06-30 | GSE63167 | GEO
Project description:Vibrio parahaemolyticus is the causative agent of food-borne gastroenteritis disease. Once consumed, human acid gastric fluid is perhaps one of the most important environmental stresses imposed on the bacterium. Herein, for the first time, we investigated Vibrio parahaemolyticus CHN25 response to artificial gastric fluid (AGF) stress by transcriptomic analysis. The bacterium at logarithmic growth phase (LGP) displayed lower survival rates than that at stationary growth phase (SGP) under a sub-lethal acid condition (pH 4.9). Transcriptome data revealed that 11.6% of the expressed genes in Vibrio parahaemolyticus CHN25 was up-regulated in LGP cells after exposed to AGF (pH 4.9) for 30 min, including those involved in sugar transport, nitrogen metabolism, energy production and protein biosynthesis, whereas 14.0% of the genes was down-regulated, such as ABC transporter and flagellar biosynthesis genes. In contrast, the AGF stress only elicited 3.4% of the genes from SGP cells, the majority of which were attenuated in expression. Moreover, the number of expressed regulator genes was also substantially reduced in SGP cells. Comparison of transcriptome profiles further revealed forty-one growth-phase independent genes in the AGF stress, however, half of which displayed distinct expression features between the two growth phases. Vibrio parahaemolyticus seemed to have evolved a number of molecular strategies for coping with the acid stress. The data here will facilitate future studies for environmental stresses and pathogenicity of the leading food-borne pathogen worldwide. When V.parahemolyticus CHN25 grown to log phase and stationary phase at 37°C in TSB-3% NaCl, different cultures were subsequently exposed to artificial gastric fluid at 37°C for 30 min. Two independent experiments were performed at each phase for microarray expreriments.
2015-06-30 | E-GEOD-63167 | biostudies-arrayexpress
Project description:Vibrio parahaemolyticus is a Gram-negative marine bacterium. A limited population of the organisms causes acute gastroenteritis in humans. Almost all of the clinical V. parahaemolyticus isolates exhibit a beta-type hemolysis on Wagatsuma agar, known as the Kanagawa phenomenon (KP). KP is induced by the thermostable direct hemolysin (TDH) produced by the organism, and has been considered a crucial marker to distinguish pathogenic strains from non-pathogenic ones. Since 1996, so-called “pandemic clones”, the majority of which belong to serotype O3:K6, have caused worldwide outbreaks of gastroenteritis. In this study, we used a DNA microarray constructed based on the genome sequence of a pandemic V. parahaemolyticus strain RIMD2210633 to examin the genomic composition of 22 strains of V. parahaemolyticus, including both pathogenic (pandemic as well as non-pandemic) and non-pathogenic strains. Over 85% of the RIMD2210633 genes were conserved in all the strains tested. Many of variably present genes formed gene clusters on the genome of RIMD2210633 and were probably acquired through lateral gene transfer. At least 70 genes over 10 loci were specifically present in the pandemic strains when compared with any of the non-pandemic strains, suggesting that the difference between pandemic and non-pandemic strains is not due to a simple genetic event. Only the genes in the 80-kb pathogenicity island (Vp-PAI) on chromosome II, including two tdh genes and a set of genes for the Type III secretion system, were detected only in the KP-positive pathogenic strains. These results strongly suggest that acquisition of this Vp-PAI was crucial for the emergence of V. parahaemolyticus strains that are pathogenic for humans. Keywords: comparative genomic hybridization, CGH
2008-03-31 | GSE10020 | GEO
Project description:We investigated antibacterial activities of benzyl isothiocyanate (BITC) against V. parahaemolyticus by transcriptomic analysis and morphological verification. Treatment with 1/8MIC BITC resulted in 234 up-regulated genes and 273 down-regulated genes. In V. parahaemolyticus, we selected six genes that were significantly down-regulated from the transcriptome results and verified them using quantitative Real-time Polymerase Chain Reaction (qRT-PCR). The verification experiments indicated that the relative expressions of the six virulence genes VP0820, VP0548, VP2233, VPA2362, fliA and fliG were only 31.0%, 31.1%, 55.8%, 57.0%, 75.3%, and 79.9% of the control group, respectively. Among them, VP2233, fliA and fliG are related to flagella, and VP2362 can regulate a protein related to biofilm formation. From the morphological aspect, we verified that under the action of 1/8 MIC BITC, the swimming diffusion diameter of V. parahaemolyticus was significantly reduced by 14.9%, and biofilm formation was significantly inhibited. These results indicate that 1/8 MIC BITC can reduce the pathogenicity of V. parahaemolyticus by inhibiting virulence gene expression related to flagella and biofilm, which is helpful for further understanding of bacteriostatic mechanism of BITC on V. parahaemolyticus and other food-borne pathogens.
2020-06-18 | GSE152671 | GEO
Project description:Vibrio (V.) parahaemolyticus is the leading cause of seafood borne gastro-intestinal infections in humans worldwide. It is widely found in marine environments and is isolated frequently from seawater, estuarine waters, sediments and raw or insufficiently cooked seafood. Within the food chain, V. parahaemolyticus encounters different temperature conditions that might alter the metabolism and pathogenicity of the bacterium. In this study, we performed gene expression profiling of V. parahaemolyticus RIMD 2210633 after exposure to 4°C, 15°C, 20°C, 37°C and 42°C to describe the cold and heat shock response. Analysis of transcriptomics data resulted in differential expression of 19 genes at 20°C, 193 genes at 4°C, 625 genes at 42°C and 639 genes at 15°C. Thus the highest portion of significantly expressed genes was observed at 15°C and 42°C with 13.3% and 13%, respectively. Genes of many functional categories were highly regulated even at lower temperatures. Our results showed that virulence associated genes (tdh1, tdh2, toxR, toxS, vopC, T6SS1, T6SS2) remained largely unaffected by heat or cold stresses. Along with folding and temperature shock depending systems, an overall temperature depended regulation of expression could be shown. Particularly the energy metabolism was affected most by changed temperatures. Whole-genome gene expression studies of food related pathogens such as V. parahaemolyticus reveal how these pathogens react to stress impacts for prediction of its behaviour under conditions like storage and transport.
2014-08-27 | GSE60815 | GEO
Project description:Vibrio (V.) parahaemolyticus is the leading cause of seafood borne gastro-intestinal infections in humans worldwide. It is widely found in marine environments and is isolated frequently from seawater, estuarine waters, sediments and raw or insufficiently cooked seafood. Within the food chain, V. parahaemolyticus encounters different temperature conditions that might alter the metabolism and pathogenicity of the bacterium. In this study, we performed gene expression profiling of V. parahaemolyticus RIMD 2210633 after exposure to 4°C, 15°C, 20°C, 37°C and 42°C to describe the cold and heat shock response. Analysis of transcriptomics data resulted in differential expression of 19 genes at 20°C, 193 genes at 4°C, 625 genes at 42°C and 639 genes at 15°C. Thus the highest portion of significantly expressed genes was observed at 15°C and 42°C with 13.3% and 13%, respectively. Genes of many functional categories were highly regulated even at lower temperatures. Our results showed that virulence associated genes (tdh1, tdh2, toxR, toxS, vopC, T6SS1, T6SS2) remained largely unaffected by heat or cold stresses. Along with folding and temperature shock depending systems, an overall temperature depended regulation of expression could be shown. Particularly the energy metabolism was affected most by changed temperatures. Whole-genome gene expression studies of food related pathogens such as V. parahaemolyticus reveal how these pathogens react to stress impacts for prediction of its behaviour under conditions like storage and transport. Temperature induced gene expression was detected in total bacterial RNA of V. parahaemolyticus. Five different temperatures (4°C, 15°C, 20°C, 37°C, 42°C) were used in at least 3 biological replicates (4 replicates for 37°C). Gene expression at 37°C was used for normalization.
2014-08-27 | E-GEOD-60815 | biostudies-arrayexpress
Project description:Vibrio parahaemolyticus is a Gram-negative marine bacterium. A limited population of the organisms causes acute gastroenteritis in humans. Almost all of the clinical V. parahaemolyticus isolates exhibit a beta-type hemolysis on Wagatsuma agar, known as the Kanagawa phenomenon (KP). KP is induced by the thermostable direct hemolysin (TDH) produced by the organism, and has been considered a crucial marker to distinguish pathogenic strains from non-pathogenic ones. Since 1996, so-called âpandemic clonesâ, the majority of which belong to serotype O3:K6, have caused worldwide outbreaks of gastroenteritis. In this study, we used a DNA microarray constructed based on the genome sequence of a pandemic V. parahaemolyticus strain RIMD2210633 to examin the genomic composition of 22 strains of V. parahaemolyticus, including both pathogenic (pandemic as well as non-pandemic) and non-pathogenic strains. Over 85% of the RIMD2210633 genes were conserved in all the strains tested. Many of variably present genes formed gene clusters on the genome of RIMD2210633 and were probably acquired through lateral gene transfer. At least 70 genes over 10 loci were specifically present in the pandemic strains when compared with any of the non-pandemic strains, suggesting that the difference between pandemic and non-pandemic strains is not due to a simple genetic event. Only the genes in the 80-kb pathogenicity island (Vp-PAI) on chromosome II, including two tdh genes and a set of genes for the Type III secretion system, were detected only in the KP-positive pathogenic strains. These results strongly suggest that acquisition of this Vp-PAI was crucial for the emergence of V. parahaemolyticus strains that are pathogenic for humans. Keywords: comparative genomic hybridization, CGH Total 66 test samples were analyzed. Genomic DNA from each test strain and a reference strain (RIMD2210633) were labeled with Cy3 and Cy5, respectively, and were cohybridized on a single array. Labeling and hybridization were performed three times independently.
2010-05-25 | E-GEOD-10020 | biostudies-arrayexpress
Project description:Vibrio parahaemolyticus is a Gram-negative marine bacterium. Strain RIMD 2210633, the wild type strain of the organism, causes acute gastroenteritis in humans. Human intestinal factor bile often affects the global gene regulation in some species of enteropathogenic bacteria. To determine the genes in V. parahaemolyticus that respond to bile, we investigated the differences in the transcriptomes of the wild type strain and the vtrA-null strain grown in Luria-Bertani medium cultivated with or without 0.04% crude bile. The vtrA gene encodes the previously identified T3SS2 regulator. Our goal is to demonstrate bile regulon controlled by VtrA in V. parahaemolyticus.
2010-10-10 | GSE21666 | GEO
Project description:Compare the secreted proteins of a wild-type Vibrio parahaemolyticus strain with those of a mutant in hcp2, rendering the T6SS2 inactive
2023-02-05 | PXD037864 | Pride
Project description:Vibrio parahaemolyticus clinical isolates
| PRJNA304021 | ENA