GEO DataSets

(Submitter supplied) Plant pathogenic bacteria encounter a drastic increase in apoplastic pH during the early stages of plant immunity. The effects of alkalization on pathogen-host interactions have not been comprehensively characterized. Here we used a global transcriptomic approach to assess the impact of environmental alkalization on Pseudomonas syringae pv. tomato DC3000 in vitro. In addition to the Type 3 Secretion System (T3SS), we found expression of genes encoding other virulence factors such as iron uptake, and coronatine biosynthesis to be strongly affected by environmental alkalization. more...

Organism:

Pseudomonas syringae pv. tomato str. DC3000

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34917

18 Samples

Download data: TXT

(Submitter supplied) Every protein progresses through a natural lifecycle from birth to maturation to death; this process is coordinated by the protein homeostasis system. Environmental or physiological conditions trigger pathways that maintain the homeostasis of the proteome. An open question is how these pathways are modulated to respond to the many stresses that an organism encounters during its lifetime. To address this question, we tested how the fitness landscape changes in response to environmental and genetic perturbations using directed and massively parallel transposon mutagenesis in Caulobacter crescentus. more...

Organism:

Caulobacter vibrioides

Type:

Other

Platform:

GPL24555

217 Samples

Download data: TAB

(Submitter supplied) Acinetobacter baumannii is an ESKAPE pathogen that rapidly develops resistance to antibiotics and persists for extended periods in the host or on abiotic surfaces. Survival in environmental stress such as phosphate scarcity, represents a clinically significant challenge for nosocomial pathogens. In the face of phosphate starvation, certain bacteria encode adaptive strategies, including the substitution of glycerophospholipids with phosphorus-free lipids. more...

Organism:

Acinetobacter baumannii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34857

6 Samples

Download data: XLS

(Submitter supplied) Different genetic engineering strategies have been proposed to obtain E. coli strains that selectively consume xylose. In this study, a previously reported strategy for obtaining a xylose-selective strain in E. coli K12 was applied to E. coli BL21 (DE3). While this approach resulted in the expected xylose-selective phenotype, a low xylose consumption rate was recorded when the strain was grown on a mixture of xylose and glucose. more...

Organism:

Escherichia coli BL21(DE3)

Type:

Expression profiling by array

Platform:

GPL34929

2 Samples

Download data: CSV, DOCX, TXT

(Submitter supplied) Antibiotic use can lead to expansion of multi-drug resistant pathobionts within the gut microbiome that can cause life-threatening infections. Selective alternatives to conventional antibiotics are in dire need. Here, we describe a Klebsiella PhageBank that enables the rapid design of antimicrobial bacteriophage cocktails to treat multi-drug resistant Klebsiella pneumoniae. Using a transposon library in carbapenem-resistant K. more...

Organism:

Klebsiella pneumoniae

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34705

4 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Lactiplantibacillus plantarum; Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30015 GPL33401 GPL34033

30 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) A challenging task to reveal health and disease-associated microbiome signatures is to disentangle regulatory networks of microbes among themselves and with their host. Using the integrated Drosophila-commensal-pathogen model system, we here reported that Drosophila and commensal bacterium L. plantarum cooperated to compete with the opportunistic pathogen S. marcescens. At first, we found that Drosophila larvae and L. more...

Organism:

Serratia marcescens; Lactiplantibacillus plantarum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33401 GPL30015 GPL34033

6 Samples

Download data: MTX, TSV

(Submitter supplied) A challenging task to reveal health and disease-associated microbiome signatures is to disentangle regulatory networks of microbes among themselves and with their host. Using the integrated Drosophila-commensal-pathogen model system, we here reported that Drosophila and commensal bacterium L. plantarum cooperated to compete with the opportunistic pathogen S. marcescens. At first, we found that Drosophila larvae and L. more...

Organism:

Lactiplantibacillus plantarum; Serratia marcescens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL30015 GPL34033 GPL33401

24 Samples

Download data: TXT

(Submitter supplied) In nature, organisms experience combinations of stressors. However, laboratory studies use batch cultures, which simplify reality and focus on population-level responses to individual stressors. In recent years, bacterial stress responses have been examined with single-cell resolution using microfluidics. Here, we use a microfluidic approach to simultaneously provide a physical stressor (shear flow) and a chemical stressor (H2O2) to the human pathogen Pseudomonas aeruginosa. more...

Organism:

Pseudomonas aeruginosa PA14

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28328

4 Samples

Download data: TXT

(Submitter supplied) LF82, an adherent invasive Escherichia coli (AIEC) pathobiont, is associated with Crohn’s disease, an inflammatory bowel disease of unknown etiology. No genetic features have been identified that distinguish AIEC strains, such as LF82, from “commensal” or pathogenic E. coli. We investigated an extremely rare single nucleotide polymorphism (SNP) within the highly conserved rpoD gene, encoding sigma70 [primary sigma factor, RNA polymerase (RNAP)]. more...

Organism:

Escherichia coli LF82

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34117

6 Samples

Download data: CSV, TXT

(Submitter supplied) Biofilm lifestyle is critical for bacterial pathogens to colonize and protect themselves from host immunity and antimicrobial chemicals in plants and animals. The formation and regulation mechanism of phytobacterial biofilm are still obscure. Here, we found that Ralstonia solanacearum Resistance to ultraviolet C (RuvC) is highly abundant in biofilm and positively regulates pathogenicity by governing systemic movement in tomato xylem. more...

Organism:

Ralstonia solanacearum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL34644

6 Samples

Download data: TXT

(Submitter supplied) To investigate how cell elongation impacts extracellular electron transfer (EET) of electroactive microorganisms (EAMs), the division of model EAM Shewanella oneidensis MR-1 was engineered by reducing the formation of cell divisome. Specially, by blocking the translation of division proteins via anti-sense RNAs or expressing division inhibitors, the cellular length and output power density were all increased. more...

Organism:

Shewanella oneidensis MR-1

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33796

12 Samples

Download data: XLSX

(Submitter supplied) RNA molecules can populate an ensemble of alternative structural conformations, but the true extent of the RNA secondary structure folding space of a living cell has never been explored. We here generated the first transcriptome-wide maps of RNA secondary structure ensembles in Escherichia coli, both at physiological temperature and upon cold-shock. Our analysis revealed hundreds of novel putative conserved RNA switches.

Organism:

Escherichia coli

Type:

Other

Platforms:

GPL33919 GPL33918

10 Samples

Download data: WIG

(Submitter supplied) The long-term resistance to desiccation on abiotic surfaces is a key determinant of the adaptive success of Acinetobacter baumannii as a healthcare-associated bacterial pathogen. Here, the cellular and molecular mechanisms enabling A. baumannii to resist desiccation and persist on abiotic surfaces were investigated. Experiments were set up to mimic the A. baumannii response to air-drying that would occur when bacterial cells contaminate fomites in hospitals. more...

Organism:

Acinetobacter baumannii ACICU; Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33972 GPL33973

12 Samples

Download data: TXT

(Submitter supplied) Since the molecular mechanisms behind adaptation and the bacterial stress response toward antimicrobial photodynamic therapy (aPDT) are not entirely clear yet, the aim of the present study was to investigate the transcriptomic stress response in Escherichia coli after sublethal treatment with aPDT using RNA sequencing (RNA-Seq). Planktonic cultures of stationary phase E. coli were treated with aPDT using a sublethal dose of the photosensitizer SAPYR. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

20 Samples

Download data: TSV

(Submitter supplied) To get insights in the electrogenic anaerobic lifestyle of P. putida KT2440 cultivated in a bioelectrochemical system (BES), we employed whole genome microarray expression profile.

Organism:

Pseudomonas putida KT2440

Type:

Expression profiling by array

Platform:

GPL31933

12 Samples

Download data: TXT, XLSX

(Submitter supplied) The non-typhoidal Salmonella enterica serotype Heidelberg is a major foodborne pathogen primarily transmitted to humans through contaminated poultry products. Current control measures emphasize novel approaches to mitigate Salmonella Heidelberg colonization in poultry and the contamination of poultry products, thereby reducing its transmission to humans. This study highlight that commensal E. coli 47-1826 can potentially be used to control of S. more...

Organism:

Salmonella enterica subsp. enterica serovar Heidelberg; Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34890 GPL34889 GPL16085

9 Samples

Download data: TXT

(Submitter supplied) L-rhamnose, a naturally abundant sugar, plays diverse biological roles in bacteria, influencing biofilm formation and pathogenesis. This study investigates the global impact of L-rhamnose on the transcriptome and biofilm formation of PHL628 E. coli under various experimental conditions. We compared growth in planktonic and biofilm states in rich (LB) and minimal (M9) media at 28 °C and 37 °C, with varying concentrations of L-rhamnose or D-glucose as a control. more...

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25368

48 Samples

Download data: TXT

(Submitter supplied) SdiA is a LuxR-type protein found in some Enterobacteriaceae. SdiA encoding bacteria do not encode a luxI homolog and rely on foreign bacteria for the production of N-acyl homoserine lactones (AHLs), SdiA's ligand. The regulon of Salmonella SdiA is largely unknown. In this study, we measured the sdiA dependent transcriptional changes of two serovars of Salmonella, Typhimurium and Typhi, exposed to synthetic AHLs. more...

Organism:

Salmonella enterica subsp. enterica serovar Typhi; Salmonella enterica subsp. enterica serovar Typhimurium

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL34830 GPL23683

24 Samples

Download data: CSV

(Submitter supplied) To elucidate the target genes of ArgR in Aeromonas veronii, we engineered an Aeromonas veronii strain that expresses the ArgR protein fused to a 3× FLAG tag, and FLAG antibodies were employed for the immunoprecipitation of DNA-protein complexes.

Organism:

Aeromonas veronii

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL34901

2 Samples

Download data: XLS