Differential expression analysis of a Vibrio parahaemolyticus ∆luxO mutant compared to wild-type in mouse intestinal mucus
Ontology highlight
ABSTRACT:
ORGANISM(S): Vibrio parahaemolyticus RIMD 2210633
PROVIDER: GSE93547 | GEO | 2017/01/13
SECONDARY ACCESSION(S): PRJNA361081
REPOSITORIES: GEO
Similar Datasets
Project description:Vibrio parahaemolyticus is the leading bacterial cause for seafood-related gastroenteritis worldwide. As an intestinal pathogen, V. parahaemolyticus competes with other commensal bacteria for the same pool of nutrients. The major source of nutrition for intestinal bacteria is intestinal mucus. We wanted to determine the expression profile of wild-type V. parahaemolyticus in mouse intestinal mucus and then perform a differential expression analysis in a ∆rpoN deletion mutant.
2020-02-14 | GSE95555 | GEO
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:Vibrio parahaemolyticus an emerging pathogen that is a causative agent of foodborne gastroenteritis when raw or undercooked seafood is consumed. Previous microarray data using a Vibrio parahaemolyticus RIMD2210633 chip has shown the master quorum-sensing regulator OpaR controls virulence, type III and type VI secretion systems, and flagellar and capsule production genes. In a parallel study, RNA-Seq was used to comparatively study the transcriptome changes of wild type Vibrio parahaemolyticus BB22 and a ΔopaR strain directly. Differences in mRNA expression were analyzed using next generation Illumina sequencing and bioinformatics techniques to align and count reads. A comparison with the previous microarray data showed good correlation between the shared genes. The RNA-Seq offered an insight into control of genes specific to the Vibrio parahaemolyticus BB22 strain as well as a new look at the sRNAs that are expressed. Eleven transcriptional regulators with greater than 4 fold regulation in the previous microarray study and 2 fold regulation in the RNA-Seq analysis, were chosen to validate the data using qRT-PCR and further characterized with electrophoretic mobility shift assays (EMSAs) to determine if they are direct targets of OpaR. The transcription factors chosen play key roles in virulence, surface motility, cell to cell interactions, and cell surface characteristics. One small RNA was identified in the RNA-Seq data to be quorum-sensing controlled and unidentified by other programs. The RNA-Seq data has aided in understanding and elucidating the hierarchy of quorum-sensing control of OpaR in Vibrio parahaemolyticus. The wild type Vibrio parahaemolyticus BB22 strain LM5312 and an opaR deletion strain LM5674 were analyzed for mRNA expression using RNA-Seq.
2013-12-31 | E-GEOD-53639 | biostudies-arrayexpress
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 an emerging pathogen that is a causative agent of foodborne gastroenteritis when raw or undercooked seafood is consumed. Previous microarray data using a Vibrio parahaemolyticus RIMD2210633 chip has shown the master quorum-sensing regulator OpaR controls virulence, type III and type VI secretion systems, and flagellar and capsule production genes. In a parallel study, RNA-Seq was used to comparatively study the transcriptome changes of wild type Vibrio parahaemolyticus BB22 and a ΔopaR strain directly. Differences in mRNA expression were analyzed using next generation Illumina sequencing and bioinformatics techniques to align and count reads. A comparison with the previous microarray data showed good correlation between the shared genes. The RNA-Seq offered an insight into control of genes specific to the Vibrio parahaemolyticus BB22 strain as well as a new look at the sRNAs that are expressed. Eleven transcriptional regulators with greater than 4 fold regulation in the previous microarray study and 2 fold regulation in the RNA-Seq analysis, were chosen to validate the data using qRT-PCR and further characterized with electrophoretic mobility shift assays (EMSAs) to determine if they are direct targets of OpaR. The transcription factors chosen play key roles in virulence, surface motility, cell to cell interactions, and cell surface characteristics. One small RNA was identified in the RNA-Seq data to be quorum-sensing controlled and unidentified by other programs. The RNA-Seq data has aided in understanding and elucidating the hierarchy of quorum-sensing control of OpaR in Vibrio parahaemolyticus.
2013-12-31 | GSE53639 | 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:Antibiotic use is a risk factor for development of inflammatory bowel diseases (IBDs). IBDs are characterized by a damaged mucus layer, which does not properly separate the host intestinal epithelium from the microbiota. Here, we hypothesized that antibiotics might affect the integrity of the mucus barrier. By systematically determining the effects of different antibiotics on mucus layer penetrability we found that oral antibiotic treatment led to breakdown of the mucus barrier and penetration of bacteria into the mucus layer. Using fecal microbiota transplant, RNA sequencing followed by machine learning and ex vivo mucus secretion measurements, we determined that antibiotic treatment induces ER stress and inhibits colonic mucus secretion in a microbiota-independent manner. This mucus secretion flaw led to penetration of bacteria into the colonic mucus layer, translocation of microbial antigens into circulation and exacerbation of ulcerations in a mouse model of IBD. Thus, antibiotic use might predispose to development of intestinal inflammation by impeding mucus production.
2024-03-19 | GSE260592 | GEO
Project description:Naturally bacteria are commonly forced to remain in stationary phase. There is no increase in cell mass, however, cell division keep on. Vibrio (V.) parahaemolyticus is an aquatic bacterium capable of causing foodborne gastroenteritis outbreaks all over the world. So far, little is known about whole genomic expression of V. parahaemolyticus in the early stationary phase compared with the phase of exponential growth. Since under starvation cell sizes decrease and endogenous metabolism reduces, genes are considered to be highly repressed in the stationary phase. However, our data shows in total 172 induced genes, while 61 genes were repressed in the early stationary phase compared with exponential phase. In fatty acid and phospholipid metabolism functional category only induced genes were found, whereas in three other metabolic functional groups appeared no significant up-regulated genes (adjusted P-value<0.05). Genes in two metabolic functional categories remained stable in the early stationary phase. DAVID analyses were carried out exploring the gene regulation. In total, ten functional categories showed a total up-regulation in early stationary phase, while only three metabolic functional categories showed a down-regulation and four categories showed stably in early stationary phase. Early stationary phase gene expression was detected in total bacterial RNA of V. parahaemolyticus. Two phases (exponential phase and early stationary phase) were used in 8 biological replicates. Gene expression in exponential phase was used for normalization.
2015-01-31 | E-GEOD-65448 | 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: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