Ontology highlight
ABSTRACT:
PROVIDER: PRJNA922041 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Total microRNA from rectal tissues of E. coli O157 super-shedders and non-shedders were sequenced using Illumina Hiseq 2000 system. For comparative analysis, differentially expressed microRNAs were identified with edgeR. Two of differentially expressed genes were identified, and one of up-regulated microRNA in super-shedders potentially targets genes related to innate and adaptive immune functions. The findings indicated that microRNA could play a role in super-shedding phenomenon.
2016-12-31 | GSE74627 | GEO
Project description:Total RNA from rectal tissues of E. coli O157 super-shedders and non-shedders were sequenced using Illumina Hiseq 2000 system. For comparative analysis, differentially expressed genes were identified with edgeR. Fifteen of differentially expressed genes were related to innate and adaptive immune functions and were down-regulated in super-shedders, which could be one of reasons for super-shedding phenomenon.
2016-03-20 | GSE67099 | GEO
Project description:The current study aimed to investigate whether bovine non-coding RNA play a role in regulating E. coli O157 shedding through studying miRNAomes of the whole gastrointestinal tract including duodenum, proximal jejunum, distal jejunum, cecum, spiral colon, descending colon and rectum. The number of miRNAs detected in each intestinal region ranged from 390 ± 13 to 413 ± 49. Compared between SS and NS, the number of differentially expressed (DE) miRNAs ranged from one to eight, and through the whole gut, seven miRNAs were up-regulated and seven were down-regulated in SS. The distal jejunum and rectum were the regions where the most DE miRNAs were identified (8 and 7, respectively). Functional analysis indicated that the bta-miR-378b, bta-miR-2284j and bta-miR-2284d which were down-regulated in both distal jejunum and rectum of SS, the bta-miR-2887 which was down-regulated in rectum of SS, as well as the bta-miR-211 and bta-miR-29d-3p which were up-regulated in rectum of SS were potentially regulatory to host immune functions, including hematological system development and immune cell trafficking. Our findings suggest that the alternation of miRNA expression in the gut of SS may lead to differential regulation in immune functions involved in E. coli O157 super-shedding in cattle.
2018-12-01 | GSE96973 | GEO
Project description:The current study aimed to investigate whether bovine non-coding RNA play a role in regulating E. coli O157 shedding through studying miRNAomes of the whole gastrointestinal tract including duodenum, proximal jejunum, distal jejunum, cecum, spiral colon, descending colon and rectum. The number of miRNAs detected in each intestinal region ranged from 390 ± 13 to 413 ± 49. Compared between SS and NS, the number of differentially expressed (DE) miRNAs ranged from one to eight, and through the whole gut, seven miRNAs were up-regulated and seven were down-regulated in SS. The distal jejunum and rectum were the regions where the most DE miRNAs were identified (8 and 7, respectively). Functional analysis indicated that the bta-miR-378b, bta-miR-2284j and bta-miR-2284d which were down-regulated in both distal jejunum and rectum of SS, the bta-miR-2887 which was down-regulated in rectum of SS, as well as the bta-miR-211 and bta-miR-29d-3p which were up-regulated in rectum of SS were potentially regulatory to host immune functions, including hematological system development and immune cell trafficking. Our findings suggest that the alternation of miRNA expression in the gut of SS may lead to differential regulation in immune functions involved in E. coli O157 super-shedding in cattle.
2018-10-30 | GSE121916 | GEO
Project description:Transcriptome analysis of rectal tissues of E. coli O157 super-shedding and E. coli O157 negative cattle
| PRJNA278944 | ENA
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:Changes in bacterial community composition of Escherichia coli O157:H7 super-shedding cattle occur in the lower intestine
| PRJNA258277 | ENA
Project description:Multiple infection sources for enterohemorrhagic Escherichia coli O157:H7 are known, including food of animal origin and produce. The ecology of this pathogen outside its human host is largely unknown. One third of its annotated genes still are hypothetical. To identify genetic determinants expressed under environmental factors, we applied strand-specific RNA-sequencing of strain E. coli EDL933 under 11 different biotic and abiotic conditions: LB medium at pH4, pH7, pH9, or at 15°C; LB with nitrite or trimethoprim-sulfamethoxazole; LB-agar surface, M9 minimal medium, spinach leaf juice, surface of living radish sprouts, and cattle feces. Of 5379 annotated genes, only 144 are transcriptionally completely inactive under all conditions. Of 1,771 hypothetical genes, 1,672 exhibit significant transcriptional signals under at least one condition. The pathogenicity island LEE showed highest transcriptional activity in LB medium, minimal medium, and after treatment with antibiotics. Unique sets of genes, including many hypothetical genes, are highly up regulated on radish sprouts, cattle feces, or in the presence of antibiotics. For instance, azoR is biotechnologically important, but its environmental function has been elusive. This gene is highly active on radish sprouts. Further, we observed induction of the shiga-toxin carrying phages by antibiotics and confirmed active biofilm related genes on radish sprouts, in cattle feces, and on agar plates. Thus, environmental transcriptomics uncovers hitherto unknown gene functions and regulatory patterns of Escherichia coli O157:H7.
2014-07-20 | GSE48199 | GEO