Bovine gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA258277 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1598922.fastq.gz | Fastqsanger.gz | |||
| SRR1598923.fastq.gz | Fastqsanger.gz | |||
| SRR1598854.fastq.gz | Fastqsanger.gz | |||
| SRR1598924.fastq.gz | Fastqsanger.gz | |||
| SRR1598855.fastq.gz | Fastqsanger.gz |
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Project description:Enterohemorrhagic Escherichia coli (EHEC) are transmitted from cattle to human by means of contaminated food products resulting from fecal contamination. Transcriptome analysis was performed to gain further insight into the metabolic pathways required for persistence and growth of EHEC in the bovine intestine. Understanding the physiology of EHEC in the gut of ruminants is critical to identifying the potential nutritional basis to limiting EHEC shedding. A global transcriptome analysis was performed to gain further insight into the metabolic pathways required for persistence and growth of EHEC in the bovine intestine. DNA microarrays were performed using RNA from EHEC O157:H7 EDL933 incubated in bovine small intestine content (BSIC) compared with cells incubated in M9-minimal media.
2013-08-01 | GSE49468 | GEO
Project description:Enterohemorrhagic Escherichia coli (EHEC) are transmitted from cattle to human by means of contaminated food products resulting from fecal contamination. Transcriptome analysis was performed to gain further insight into the metabolic pathways required for persistence and growth of EHEC in the bovine intestine. Understanding the physiology of EHEC in the gut of ruminants is critical to identifying the potential nutritional basis to limiting EHEC shedding. A global transcriptome analysis was performed to gain further insight into the metabolic pathways required for persistence and growth of EHEC in the bovine intestine. DNA microarrays were performed using RNA from EHEC O157:H7 EDL933 incubated in bovine small intestine content (BSIC) compared with cells incubated in M9-minimal media. Four biological replicates collected for bacterial cultures on separate days for each media and labelled following a dye-switch design : For each media two replicates labeled in Cy3 and two replicates in Cy5.
2013-08-01 | E-GEOD-49468 | biostudies-arrayexpress
Project description:Cattle shedding > 10e4 CFU of Escherichia coli O157 per g of feces are defined as super-shedders. RNA-sequencing was performed to identify the transcriptome of tissues, including duodenum, proximal jejunum, distal jejunum, distal jejunum, cecum, spiral colon and descending colon of super-shedder cattle in comparison with non-shedders. The total number of genes detected in gut tissues ranged from 16,846 ± 639 (cecum) to 18,137 ± 696 (distal jejunum), and immune functions were enriched for the transcriptomes of small intestinal tissues, reflecting their greater immune activity than large intestine. Totally 351 differentially expression genes were identified between super-shedders and non-shedders, including 101 up-regulated and 250 down-regulated in super-shedders. Differential gene expression analysis suggested increased T-cell responses and cholesterol absorption in distal jejunum and descending colon, and inhibited B-cell maturation in intestines of super-shedders. distal jejunum of super-shedders. Our findings suggested that host genetics and E. coli O157 activities are involved in super-shedding phenomenon.
2017-08-21 | GSE85277 | GEO
Project description:Unlike many other types of diarrheagenic bacteria that act primarily in the small intestine, O157:H7 expresses virulence primarily in the large intestine. In this study, microarray analysis is employed to examine the transcriptional response of O157:H7 to bile treatment, to gain insight into how bile affects virulence and whether bile might be temporally defending the small intestine against virulence by these bacteria. Keywords: Expression profiling of two different growth conditions
2012-07-31 | GSE20380 | GEO
Project description:Unlike many other types of diarrheagenic bacteria that act primarily in the small intestine, O157:H7 expresses virulence primarily in the large intestine. In this study, microarray analysis is employed to examine the transcriptional response of O157:H7 to bile treatment, to gain insight into how bile affects virulence and whether bile might be temporally defending the small intestine against virulence by these bacteria. Keywords: Expression profiling of two different growth conditions Two groups of three replicates were used: E.coli O157:H7 grown in Luria broth with or without 0.8% bile salts
2012-07-30 | E-GEOD-20380 | biostudies-arrayexpress
Project description:Escherichia coli O157:H7 strains have been classified into different genotypes based on the presence of specific shiga toxin-encoding bacteriophage insertion sites. Genotypes that are predominant in clinical isolates are named clinical genotypes and those that are isolated mostly from bovine sources are bovine-biased genotypes. To determine whether inherent differences in gene expression could possibly explain the variation in infectivity of these genotypes, we compared the expression patterns of O157:H7 strains isolated from cattle, which belonged to either clinical genotype 1 or bovine-biased genotype 5. Important virulence factors of O157, including locus of enterocyte effacement, enterohemolysin, and pO157 plasmid encoded genes, showed increased expression in clinical genotype. Genes essential for acid resistance such as gadA, gadB, and gadC and other stress fitness-associated genes were up-regulated in the bovine-biased genotype 5. Overall, these results suggest that clinical genotype 1 strains more commonly cause human illness because of an enhanced ability to express O157 virulence factors known to be important for disease pathogenesis. By contrast, strains of the bovine-biased genotype 5 appear to be more resistant to adverse environmental conditions, which enable them to survive well in bovines without causing disease.
2009-04-24 | GSE15783 | GEO
Project description:Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a notorious foodborne pathogen capable of causing severe gastrointestinal infections in humans. The bovine rectoanal junction (RAJ) has been identified as a primary reservoir of STEC O157:H7, playing a critical role in its transmission to humans through contaminated food sources. Despite the relevance of this host-pathogen interaction, the molecular mechanisms behind the adaptation of STEC O157:H7 in the bovine RAJ and its subsequent infection of human colonic epithelial cells remain largely unexplored. This study aimed to unravel the intricate dynamics of STEC O157:H7 in two distinct host environments: bovine RAJ squamous epithelial (RSE) cells and human colonic epithelial cells. Comparative transcriptomics analysis was employed to investigate the differential gene expression profiles of STEC O157:H7 during its interaction with these cell types. The bacterial cells were cultured under controlled conditions to simulate the microenvironments of both bovine RAJ and human colonic epithelial cells. Using high-throughput RNA sequencing, we identified key bacterial genes and regulatory pathways that are significantly modulated in response to each specific host environment. Our findings reveal distinct expression patterns of virulence factors, adhesion proteins, and stress response genes in STEC O157:H7 grown in bovine RAJ cells as opposed to human colonic epithelial cells. Additionally, the comparative analysis highlights the potential role of certain genes in host adaptation and tissue-specific pathogenicity. Furthermore, this study sheds light on the potential factors contributing to the survival and persistence of STEC O157:H7 in the bovine reservoir and its ability to colonize and cause disease in humans.
2023-11-09 | GSE240423 | GEO
Project description:Escherichia coli O157:H7 strains have been classified into different genotypes based on the presence of specific shiga toxin-encoding bacteriophage insertion sites. Genotypes that are predominant in clinical isolates are named clinical genotypes and those that are isolated mostly from bovine sources are bovine-biased genotypes. To determine whether inherent differences in gene expression could possibly explain the variation in infectivity of these genotypes, we compared the expression patterns of O157:H7 strains isolated from cattle, which belonged to either clinical genotype 1 or bovine-biased genotype 5. Important virulence factors of O157, including locus of enterocyte effacement, enterohemolysin, and pO157 plasmid encoded genes, showed increased expression in clinical genotype. Genes essential for acid resistance such as gadA, gadB, and gadC and other stress fitness-associated genes were up-regulated in the bovine-biased genotype 5. Overall, these results suggest that clinical genotype 1 strains more commonly cause human illness because of an enhanced ability to express O157 virulence factors known to be important for disease pathogenesis. By contrast, strains of the bovine-biased genotype 5 appear to be more resistant to adverse environmental conditions, which enable them to survive well in bovines without causing disease. The results are based on O157:H7 clinical and bovine-biased genotype cultures grown in DMEM medium to exponential phase. Four strains were selected from each genotype and strains were considered as biological replicates. A double loop microarray design was used for comparing the samples. Differences in transcript levels were determined using a mixed model ANOVA in R/MAANOVA which tested for significant differences due to strain (clinical or bovine-biased) using the following linear model: array+dye+sample (biological replicate)+strain+error. We incorporated the dye-swaps among the biological replicates.
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Project description:Super shedders of Escherichia coli O157:H7 have a unique fecal bacterial community structure
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