Ontology highlight
ABSTRACT:
PROVIDER: PRJNA613764 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| JAATGY01.dat.gz | Other | |||
| JAATGY01.fasta.gz | Fasta.gz | |||
| JAATGY01.master.dat | Other | |||
| JAATGZ01.dat.gz | Other |
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Project description:<p>The gut microbiota is increasingly recognized for playing a critical role in human health and disease, especially in conferring resistance to both virulent pathogens such as Salmonella, which infects 1.2 million people in the United States every year [1], and opportunistic pathogens like Candida, which causes an estimated 46,000 cases of invasive candidiasis each year in the United States [2]. The dynamics of pathogen-microbiome interactions and the metabolites involved in this process remain largely unknown. </p><p>We use gnotobiotic mice infected with the virulent pathogen Salmonella enterica serovar Typhimurium or the opportunistic pathogen Candida albicans in combination with metagenomics and discovery metabolomics to identify changes in the community and metabolome during infection. To isolate the role of the microbiota in response to pathogens, we compared mice monocolonized with the pathogen, uninfected mice 'humanized' with a synthetic human microbiome, or infected humanized mice. We observe that changes in the community and in biosynthetic gene cluster potential occur within 3 days for the virulent Salmonella enterica serovar Typhimurium, but there are minimal changes with a poorly colonizing Candida albicans. In addition, the metabolome shifts depending on infection status, including changes in glutathione metabolites in response to Salmonella infection. The LC-MS metabolomic fingerprint of the cecum differed between mice monocolonized with either pathogen and humanized infected mice. Specifically, we identified an increase in glutathione disulfide, glutathione cysteine disulfide, inosine 5'-monophosphate, and hydroxybutyrylcarnitine in mice infected with Salmonella in contrast to uninfected mice and mice monocolonized with Salmonella. These metabolites potentially play a role in pathogen-induced oxidative stress. These results provide insight into how the microbiota community members interact with each other and with pathogens on a metabolic level.</p><p><br></p><p>Ref:</p><p>[1] Scallan E, Hoekstra RM, Angulo FJ, Tauxe RV, Widdowson MA, Roy SL, Jones JL, and Griffin PM. Foodborne Illness Acquired in the United States—Major Pathogens. Emerg Infect Dis 2011;17:7-15. doi.org/10.3201/eid1701.P11101</p><p>[2] Centers for Disease Control and Prevention, Antibiotic Resistance Threats in the United States, 2013</p>
2019-09-20 | MTBLS753 | MetaboLights
Project description:Raghunathan2009 - Genome-scale metabolic
network of Salmonella typhimurium (iRR1083)
This model is described in the article:
Constraint-based analysis of
metabolic capacity of Salmonella typhimurium during
host-pathogen interaction.
Raghunathan A, Reed J, Shin S,
Palsson B, Daefler S.
BMC Syst Biol 2009; 3: 38
Abstract:
BACKGROUND: Infections with Salmonella cause significant
morbidity and mortality worldwide. Replication of Salmonella
typhimurium inside its host cell is a model system for studying
the pathogenesis of intracellular bacterial infections.
Genome-scale modeling of bacterial metabolic networks provides
a powerful tool to identify and analyze pathways required for
successful intracellular replication during host-pathogen
interaction. RESULTS: We have developed and validated a
genome-scale metabolic network of Salmonella typhimurium LT2
(iRR1083). This model accounts for 1,083 genes that encode
proteins catalyzing 1,087 unique metabolic and transport
reactions in the bacterium. We employed flux balance analysis
and in silico gene essentiality analysis to investigate growth
under a wide range of conditions that mimic in vitro and host
cell environments. Gene expression profiling of S. typhimurium
isolated from macrophage cell lines was used to constrain the
model to predict metabolic pathways that are likely to be
operational during infection. CONCLUSION: Our analysis suggests
that there is a robust minimal set of metabolic pathways that
is required for successful replication of Salmonella inside the
host cell. This model also serves as platform for the
integration of high-throughput data. Its computational power
allows identification of networked metabolic pathways and
generation of hypotheses about metabolism during infection,
which might be used for the rational design of novel
antibiotics or vaccine strains.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180058.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
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 | MODEL1507180058 | BioModels
Project description:In this study, we have defined the NsrR regulon in Salmonella enterica sv. Typhimurium 14028s using a transcriptional microarray. Wild-type and nsrR mutant S. Typhimurium were grown aerobically to early log-phase (OD600~0.5) at 37C in LB medium. Total RNA was isolated from three independent cultures of both strains and interrogated on a PCR product array representing almost all ORFs.
2012-11-21 | GSE32585 | GEO
Project description:Transcriptional profiling of Salmonella Typhimurium strains SL1344 in exponential and stationary phase cultures
2017-03-29 | GSE97161 | GEO
Project description:Transcriptional profiling of Salmonella Typhimurium strains SL1344 (pSfR27) and SL1344 (pSfR27) delta sfh to identify 'Sfh-dependent' transcripts
2009-12-05 | GSE19230 | GEO
Project description:Transcriptional profiling of Salmonella enterica serovar Typhimurium SL1344 cells comparing wildtype with ΔfabR mutant. Salmonella strains were cultured under free-living TSB conditions (TSB 1/20, 200 rpm, 25 °C) for 6h (ca. 2 x 108 cells/ml).
2014-12-31 | GSE52880 | GEO
Project description:We used ChIP-seq to map binding of the CRISPR surveillance complex, Cascade, in a Salmonella enterica serovar Typhimurium strain lacking the gene encoding the endonuclease Cas3. We performed ChIP-seq in strains with wild-type and mutant sequences upstream of the two CRISPR arrays, and in strains with wild-type and mutant nusE genes to determine the impact of Nus factor antitermination on CRISPR array function.
2018-10-13 | E-MTAB-7242 | biostudies-arrayexpress
Project description:Many non-typhoidal serovars of Salmonella such as Salmonella enterica serovar Typhimurium (S. Typhimurium) are the leading cause of food-borne gastroenteritis, resulting in millions of infections each year and sometimes death. Salmonella enterica serovar Typhimurium is the most common non-typhoidal Salmonella strain isolated from patients around the world and is used as a mouse model to study bacterial pathogenesis and host-microbe interactions. Furthermore, S. Typhimurium is an important pathogen in livestock animals including chickens and cattle. S. Typhimurium utilises a multitude of virulence factors to reach and invade host cells and for its intracellular survival. However, little is known about the mechanism of protein synthesis of these virulence factors at the codon level. Here, we performed RNA-seq and ribosome profiling. Ribosome profiling allows the global mapping of translating ribosomes on the transcriptome and therefore provides direct measure of protein synthesis.
2023-04-01 | E-MTAB-8808 | biostudies-arrayexpress
Project description:SrfJ is an effector of the type III secretion systems of the Gram-negative intracellular pathogen Salmonella enterica serovar Typhimurium. To study the effects of this effector on global gene expression in host cells, we have infected murine RAW264.7 macrophages with two strains of Salmonella enterica serovar Typhimurium. The comparison between cells infected with the wild-type strain and cells infected with a srfJ mutant revealed a number of genes that are differentially expressed when SrfJ is present.
2023-05-17 | GSE215053 | GEO
Project description:RNA from in vitro grown Salmonella typhimurium is compared with RNA extracted from Salmonella typhimurium from infected chick caecums using a common DNA reference. Keywords: Disease state analysis, infected versus uninfected, common reference Five replicates from infected chick caecal contents compared to a common reference. Three replicates from in vitro grown Salmonella compared to a common reference. The common reference was genomic DNA and always occupies the Cy3 channel (channel 2).
2010-05-26 | E-GEOD-10337 | biostudies-arrayexpress