Ontology highlight
ABSTRACT:
PROVIDER: PRJNA763811 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:YerA41 is a myoviridae bacteriophage that was originally isolated due its ability to infect Yersinia ruckeri bacteria, the causative agent of enteric redmouth disease of salmonid fish. Several attempts to determine its genomic DNA sequence using traditional and next generation sequencing technologies failed, indicating that the phage genome is modified such way that it is an unsuitable template for PCR amplification and sequencing. To determine the YerA41 genome sequence we isolated RNA from phage-infected Y. ruckeri cells at different time points post-infection, and sequenced it. The host-genome specific reads were substracted and de novo assembly was performed on the unaligned reads.
2020-03-04 | GSE146319 | GEO
Project description:Bile acids are steroid compounds from the digestive tracts of vertebrates that enter agricultural environments in unusual high amounts with manure. Bacteria degrading bile acids can readily be isolated from soils and waters including agricultural areas. Under laboratory conditions, these bacteria transiently release steroid compounds as degradation intermediates into the environment. These compounds include androstadienediones (ADDs), which are C19-steroids with potential hormonal effects. Experiments with Caenorhabditis elegans showed that ADDs derived from bacterial bile acid degradation had effects on its tactile response, reproduction rate, and developmental speed. Additional experiments with a deletion mutant as well as transcriptomic analyses revealed that these effects might be conveyed by the putative testosterone receptor NHR-69. Soil microcosms showed that the natural microflora of agricultural soil is readily induced for bile acid degradation accompanied by the transient release of steroid intermediates. Establishment of a model system with a Pseudomonas strain and C. elegans in sand microcosms indicated transient release of ADDs during the course of bile acid degradation and negative effects on the reproduction rate of the nematode. This proof-of-principle study points at bacterial degradation of manure-derived bile acids as a potential and so-far overlooked risk for invertebrates in agricultural soils.
2019-02-08 | GSE126214 | 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: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:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:Bacteria isolated from soil Genome sequencing and assembly
| PRJNA623261 | ENA
Project description:Non-alcoholic fatty liver disease (NAFLD) is rapidly becoming the most common liver disease worldwide, yet the pathogenesis of NAFLD is only partially understood. Here, we investigated the role of the gut bacteria in NAFLD by stimulating the gut bacteria via feeding mice the fermentable dietary fiber guar gum and suppressing the gut bacteria via chronic oral administration of antibiotics. Guar gum feeding profoundly altered the gut microbiota composition, in parallel with reduced diet-induced obesity and improved glucose tolerance. Strikingly, despite reducing adipose tissue mass and inflammation, guar gum enhanced hepatic inflammation and fibrosis, concurrent with markedly elevated plasma and hepatic bile acid levels. Consistent with a role of elevated bile acids in the liver phenotype, treatment of mice with taurocholic acid stimulated hepatic inflammation and fibrosis. In contrast to guar gum, chronic oral administration of antibiotics effectively suppressed the gut bacteria, decreased portal secondary bile acid levels, and attenuated hepatic inflammation and fibrosis. Neither guar gum or antibiotics influenced plasma lipopolysaccharide levels. In conclusion, our data indicate a causal link between changes in gut microbiota and hepatic inflammation and fibrosis in a mouse model of NAFLD, possibly via alterations in bile acids.
2017-06-06 | GSE76087 | GEO
Project description:Purpose：Bifidobacteria are common inhabitants of the human gastrointestinal tract. In order to colonize in the gut, it is important to adapt to the physiological concentrations of bile salts. The global response to bile in B. longum BBMN68, isolated from a healthy centenarian in the Bama County of the Guangxi Zhuang Autonomous Region in China, has been investigated through RNA-seq transcriptomics sequencing in our previous work. However, a long-term bile salts treatment is more suitable to simulate the human gastrointestinal tract environment. The goals of this study are to invstigated the global response to a long-term treatment of bile salts in B. longum BBMN68. Methods: Samples from BBMN68 cultured with or without 0.75 g liter-1 ox-bile for 24 hours were sequenced on an Illumina Hiseq platform. Three independent biological replicates were produced including 6 samples in total. Results: Raw data were firstly processed through in-house perl scripts to generate clean data, and then clean date were mapped to the reference genome, getting about 11-13 million total mapped reads per sample.
2018-05-04 | GSE113993 | GEO
Project description:Obstruction of bile flow results in bacterial proliferation and mucosal injury in the small intestine that can lead to the translocation of bacteria across the epithelial barrier and systemic infection. These adverse effects of biliary obstruction can be inhibited by administration of bile acids. Here we show that the farnesoid X receptor (FXR), a nuclear receptor for bile acids, induces genes involved in enteroprotection and inhibits bacterial overgrowth and mucosal injury in ileum caused by bile duct ligation. Mice lacking FXR have increased ileal levels of bacteria and a compromised epithelial barrier. These findings reveal a central role for FXR in protecting the distal small intestine from bacterial invasion and suggest that FXR agonists may prevent epithelial deterioration and bacterial translocation in patients with impaired bile flow. In this report we have examined the role of FXR in the ileum. We demonstrate that it plays a crucial role in preventing bacterial overgrowth and maintaining the integrity of the intestinal epithelium
2012-07-19 | GSE39507 | GEO