Ontology highlight
ABSTRACT:
PROVIDER: PRJNA941886 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23720769_1.fastq.gz | Fastqsanger.gz | |||
| SRR23720769_2.fastq.gz | Fastqsanger.gz |
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Project description:<p>Traveler's diarrhea (TD) is caused by enterotoxigenic Escherichia coli (ETEC), other pathogenic gram-negative pathogens, norovirus and some parasites. Nevertheless, standard diagnostic methods fail to identify pathogens in more than 30% of TD patients, so it is predicted that new pathogens or groups of pathogens may be causative agents of disease. A comprehensive metagenomic study of the fecal microbiomes from 23 TD patients and seven healthy travelers was performed, all of which tested negative for the known etiologic agents of TD in standard tests. Metagenomic reads were assembled and the resulting contigs were subjected to semi-manual binning to assemble independent genomes from metagenomic pools. Taxonomic and functional annotations were conducted to assist identification of putative pathogens. We extracted 560 draft genomes, 320 of which were complete enough to be enough characterized as cellular genomes and 160 of which were bacteriophage genomes. We made predictions of the etiology of disease in individual subjects based on the properties and features of the recovered cellular genomes. Three subtypes of samples were observed. First were four patients with low diversity metagenomes that were predominated by one or more pathogenic E. coli strains. Annotation allowed prediction of pathogenic type in most cases. Second, five patients were co-infected with E. coli and other members of the Enterobacteriaceae, including antibiotic resistant Enterobacter, Klebsiella, and Citrobacter. Finally, several samples contained genomes that represented dark matter. In one of these samples we identified a TM7 genome that phylogenetically clustered with a strain isolated from wastewater and carries genes encoding potential virulence factors. We also observed a very high proportion of bacteriophage reads in some samples. The relative abundance of phage was significantly higher in healthy travelers when compared to TD patients. Our results highlight that assembly-based analysis revealed that diarrhea is often polymicrobial and includes members of the Enterobacteriaceae not normally associated with TD and have implicated a new member of the TM7 phylum as a potential player in diarrheal disease. </p>
| phs001352 | dbGaP
Project description:Escherichia coli Genome sequencing and assembly 55
| PRJNA276371 | ENA
Project description:Reed2003 - Genome-scale metabolic network of
Escherichia coli (iJR904)
This model is described in the article:
An expanded genome-scale
model of Escherichia coli K-12 (iJR904 GSM/GPR).
Reed JL, Vo TD, Schilling CH,
Palsson BO.
Genome Biol. 2003; 4(9): R54
Abstract:
BACKGROUND: Diverse datasets, including genomic,
transcriptomic, proteomic and metabolomic data, are becoming
readily available for specific organisms. There is currently a
need to integrate these datasets within an in silico modeling
framework. Constraint-based models of Escherichia coli K-12
MG1655 have been developed and used to study the bacterium's
metabolism and phenotypic behavior. The most comprehensive E.
coli model to date (E. coli iJE660a GSM) accounts for 660 genes
and includes 627 unique biochemical reactions. RESULTS: An
expanded genome-scale metabolic model of E. coli (iJR904
GSM/GPR) has been reconstructed which includes 904 genes and
931 unique biochemical reactions. The reactions in the expanded
model are both elementally and charge balanced. Network gap
analysis led to putative assignments for 55 open reading frames
(ORFs). Gene to protein to reaction associations (GPR) are now
directly included in the model. Comparisons between predictions
made by iJR904 and iJE660a models show that they are generally
similar but differ under certain circumstances. Analysis of
genome-scale proton balancing shows how the flux of protons
into and out of the medium is important for maximizing cellular
growth. CONCLUSIONS: E. coli iJR904 has improved capabilities
over iJE660a. iJR904 is a more complete and chemically accurate
description of E. coli metabolism than iJE660a. Perhaps most
importantly, iJR904 can be used for analyzing and integrating
the diverse datasets. iJR904 will help to outline the
genotype-phenotype relationship for E. coli K-12, as it can
account for genomic, transcriptomic, proteomic and fluxomic
data simultaneously.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180060.
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BioModels Database:
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quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180060 | BioModels
Project description:An oligonucleotide tiling array technology is utilized to measure the entire Escherichia coli transcriptome and its transcriptional changes after induction of the adaptive response by the alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG). Keywords: Gene expression during the adaptive response in Escherichia coli Escherichia coli K-12 MG1655 single colony in five parallells was grown to mid-log phase and exposed to the ada-response inducer MNNG. Total RNA was extracted from induced and uninduced cells and cDNA was prepared, fragmented and labelled prior to hybridizing to arrays. The Escherichia coli genome was split in two; sequences encoding proteins, tRNAs or rRNAs with a known function on either strand, and sequences without such annotation. A selective tiling approach was used to ensure sufficient coverage of unnanotated genomic regions due to the limited number of array probes.
2010-05-06 | E-GEOD-13830 | biostudies-arrayexpress
Project description:We employed the orthogonally detectable red, green, and blue fluorescent proteins in a single vector system, dubbed RGB-S reporter, to enable simultaneous, independent and real-time analysis of the stress response in E. coli to physiological stress, genotoxicity, and cytotoxicity.
2023-05-29 | GSE211360 | GEO
Project description:Primary objectives: The study investigates whether a Escherichia coli Nissle-suspenison has a (preventive) antidiarrheal effect in patients with tumors who are treated with chemotherapeutic schemes which are associated with increased occurances of diarrhea. Diarrhea caused by treatment are thought to be reduced in intensity and/or frequency by the treatment with Escherichia coli Nissle-Suspension.
Primary endpoints: Common toxicity criteria (CTC) for diarrhea
| 2534265 | ecrin-mdr-crc