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Items: 1 to 20 of 128

1.

High-throughput transposon mutagenesis in the family Enterobacteriaceae reveals core essential genes and rapid turnover of essentiality

(Submitter supplied) The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the gut commensal and model organism Escherichia coli, as well as several major human pathogens including Salmonella enterica and Klebsiella pneumoniae. Essential gene sets have been determined for several members of the Enterobacteriaceae, and the E. coli Keio single-gene deletion library is often regarded as a gold standard for gene essentiality studies. more...
Organism:
Klebsiella pneumoniae; Citrobacter rodentium; Salmonella enterica subsp. enterica serovar Enteritidis; Enterobacter cloacae; Escherichia coli; Salmonella enterica subsp. enterica serovar Typhimurium
Type:
Other
8 related Platforms
13 Samples
Download data: TXT, XLSX
Series
Accession:
GSE216013
ID:
200216013
2.

The transcriptional response to low temperature is weakly conserved across Enterobacteriales

(Submitter supplied) Bacteria respond to changes in their external environment like temperature by changing the transcription of their genes, but we know little about how these regulatory patterns evolve. We used RNA-seq to study the transcriptional response of a shift from 37°C to 15°C in wild-type Escherichia coli, Salmonella enterica, Citrobacter rodentium, Enterobacter cloacae, Klebsiella pneumoniae, and Serratia marcescens, as well as ∆rpoS strains of E. more...
Organism:
Serratia marcescens; Enterobacter cloacae; Escherichia coli; Klebsiella pneumoniae; Salmonella enterica; Citrobacter rodentium
Type:
Expression profiling by high throughput sequencing
6 related Platforms
64 Samples
Download data: TXT
Series
Accession:
GSE267531
ID:
200267531
3.

Drug efflux and lipid A modification by 4-L-aminoarabinose are key mechanisms of polymyxin B resistance in the sepsis pathogen Enterobacter bugandensis

(Submitter supplied) To investigate the mechanism of PmB resistance and heteroresistance in Enterobacter bugandensis by analysing the differential gene expression under PmB treatment.
Organism:
Enterobacter cloacae
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32875
12 Samples
Download data: CSV
Series
Accession:
GSE218614
ID:
200218614
4.

TnpB homologs exapted from transposons are RNA-guided transcription factors

(Submitter supplied) Transposon-encoded tnpB and iscB genes encode RNA-guided DNA nucleases that promote their own selfish spread through targeted DNA cleavage and homologous recombination. These widespread gene families were repeatedly domesticated over evolutionary timescales, leading to the emergence of diverse CRISPR-associated nucleases including Cas9 and Cas12. We set out to test the hypothesis that TnpB nucleases may have also been repurposed for novel, unexpected functions other than CRISPR-Cas. more...
Organism:
Escherichia coli; Enterobacter sp. BIDMC93; Enterobacter cloacae
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other
4 related Platforms
51 Samples
Download data: BED, BW, XLSX
Series
Accession:
GSE245749
ID:
200245749
5.

Aminoglycoside heteroresistance in Enterobacter cloacae is driven by the cell envelope stress response.

(Submitter supplied) Enterobacter cloacae is a Gram-negative nosocomial pathogen of the ESKAPE (Enterococcus, Staphylococcus, Klebsiella, Acinetobacter, Pseudomonas, and Enterobacter spp.) priority group with increasing multi-drug resistance via the acquisition of resistance plasmids. However, E. cloacae can also display forms of antibiotic refractoriness, such as heteroresistance and tolerance. Here, we report that E. cloacae displays transient heteroresistance to aminoglycosides, which is accompanied with the formation of small colony variants (SCVs) with increased minimum inhibitor concentration (MIC) of gentamicin and other aminoglycosides used in the clinic, but not other antibiotic classes. To explore the underlying mechanisms, we performed RNA sequencing of heteroresistant bacteria, which revealed global gene-expression changes and a signature of the CpxRA cell envelope stress response. Deletion of the cpxRA two-component system abrogated aminoglycoside heteroresistance and SCV formation, pointing to its indispensable role in these processes. The introduction of a constitutively active allele of cpxA led to high aminoglycoside MICs, consistent with cell envelope stress response driving these behaviours in E. cloacae. Cell envelope stress can be caused by environmental cues, including heavy metals. Indeed, bacterial exposure to copper increased gentamicin MIC in the wild-type, but not in the ΔcpxRA mutant. Moreover, copper exposure also elevated the gentamicin MICs of clinical isolates from bloodstream infections, suggesting that CpxRA- and copper-dependent aminoglycoside resistance is broadly conserved in E. cloacae strains. Altogether, we establish that E. cloacae relies on transcriptional reprogramming via the envelope stress response pathway for transient resistance to a major class of frontline antibiotic.
Organism:
Enterobacter cloacae subsp. cloacae ATCC 13047
Type:
Expression profiling by high throughput sequencing
Platform:
GPL33540
9 Samples
Download data: CSV
Series
Accession:
GSE236124
ID:
200236124
6.

Genomic and Transcriptional Characterisation of Carbapenem and Colistin Resistance Mechanisms in Klebsiella pneumoniae

(Submitter supplied) The transcriptional, epigenomic, and genomic profiles of K. pneumoniae isolates were characterised to identify novel colistin and carbapenem resistance mechanisms. The genomic DNA and total RNA of the isolates were isolated and sequenced on PacBio.
Organism:
Enterobacter cloacae; Klebsiella pneumoniae; Enterobacter bugandensis; Enterobacter cloacae complex sp. R_G8; Acinetobacter baumannii; Enterobacter asburiae
Type:
Expression profiling by high throughput sequencing; Other
12 related Platforms
22 Samples
Download data: CSV, DIFF, GFF, PDF
Series
Accession:
GSE217148
ID:
200217148
7.

Molecular Epidemiology of Enterobacterales Resistant to Antibiotics of Last Resort in Pregnant Women in Labour at a Tertiary Hospital

(Submitter supplied) This study aims to determine the epidemiology of Enterobacteriaceae resistant to antibiotics of last resort in pregnant women in labour at a tertiary hospital, Pretoria, South Africa. Rectal swabs shall be used to screen for colonisation with CRE and colistin-resistant Enterobacteriales in pregnant women during labour. Carbapenem and colistin-resistant Enterobacterales can cause the following infections: bacteraemia; nosocomial pneumonia; urinary tract infections, and intra-abdominal infections. more...
Organism:
Enterobacter cloacae; Klebsiella pneumoniae; Enterobacter roggenkampii
Type:
Methylation profiling by high throughput sequencing; Other
Platforms:
GPL32493 GPL27625 GPL32492
5 Samples
Download data: GFF, XLSX
Series
Accession:
GSE208573
ID:
200208573
8.

Cefazolin and Imipenem Enhance AmpC Expression and Resistance in NagZ-dependent manner in Enterobacter cloacae complex

(Submitter supplied) Background: Enterobacter cloacae complex (ECC) is a common opportunistic pathogen and is responsible for causing various infections in humans. Owing to its inducible chromosomal AmpC β-lactamase (AmpC), ECC is inherently resistant to the 1st- and 2nd- generation cephalosporins. However, whether β-lactams antibiotics enhance ECC resistance remains unclear. Results: In this study, we found that subinhibitory concentrations (SICs) of cefazolin (CFZ) and imipenem (IMP) can advance the expression of AmpC and enhance its resistance towards β-lactams through NagZ in Enterobacter cloacae (EC). more...
Organism:
Enterobacter cloacae complex
Type:
Expression profiling by high throughput sequencing
Platform:
GPL32411
6 Samples
Download data: TXT
Series
Accession:
GSE207144
ID:
200207144
9.

Transcriptional reprogramming of the endophytic bacterium Enterobacter sp. SA187 upon Arabidopsis colonization

(Submitter supplied) Enterobacter sp. SA187 is a plant growth-promoting bacterium (PGPB) that promotes growth of the crop plant alfalfa under saline irrigation and desert farming conditions. SA187 also enhances salt tolerance of the model plant Arabidopsis thaliana under in vitro conditions. In the present study, we used a transcriptomic approach to elucidate the mechanisms underlying plant growth promotion by SA187 under salt stress. more...
Organism:
Enterobacter sp. SA187
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26001
6 Samples
Download data: XLSX
Series
Accession:
GSE124591
ID:
200124591
10.

The TyrR regulon of Enterobacter ludwigii UW5

(Submitter supplied) The TyrR transcription factor controls the expression of genes for the uptake and biosynthesis of aromatic amino acids in Escherichia coli. In the plant-associated and clinically significant proteobacterium Enterobacter ludwigii UW5, the TyrR orthologue was previously shown to regulate genes that encode enzymes for synthesis of the plant hormone indole-3-acetic acid and gluconeogenesis, indicating a broader function for the transcription factor. more...
Organism:
Enterobacter ludwigii
Type:
Expression profiling by high throughput sequencing
Platform:
GPL29272
8 Samples
Download data: TXT, XLSX
Series
Accession:
GSE122440
ID:
200122440
11.

Detection of carbohydrate-active enzyme genes in the rumen of young lambs

(Submitter supplied) In this study, we studied the fibrolytic potential of the rumen microbiota in the rumen of 6 lambs separated from their dams from 12h of age and artificially fed with milk replacer (MR) and starter feed from d8, in absence (3 lambs) or presence (3 lambs) of a combination of the live yeast Saccharomyces cerevisiae CNCM I-1077 and selected yeast metabolites. The fibrolytic potential of the rumen microbiota of the lambs at 56 days of age was analyzed with a DNA microarray (FibroChip) targeting genes coding for 8 glycoside hydrolase (GH) families.
Organism:
Bacteroides fragilis; Xylanibacter ruminicola; Ruminococcus albus; Enterococcus faecium; Clostridium acetobutylicum; Acetivibrio thermocellus; Clostridium beijerinckii; Levilactobacillus brevis; Microbiota; Bacteroides ovatus; Fibrobacter intestinalis; Bacteroides sp.; Epidinium caudatum; Polyplastron multivesiculatum; Butyrivibrio hungatei; Epidinium ecaudatum; Bacteroides xylanisolvens; Cellulosilyticum ruminicola; Ruminococcus champanellensis; Orpinomyces sp.; Butyrivibrio fibrisolvens; Ruminococcus flavefaciens; Piromyces communis; Pseudobacteroides cellulosolvens; Eudiplodinium maggii; Segatella bryantii; Acetivibrio clariflavus; uncultured Neocallimastigales; Selenomonas ruminantium; Lactococcus lactis; Clostridioides difficile; Ruminiclostridium cellulolyticum; Limosilactobacillus fermentum; Cellulomonas flavigena; Neocallimastix patriciarum; Bifidobacterium animalis; Agathobacter rectalis; Enterobacter sp.; Orpinomyces joyonii; Piromyces rhizinflatus; Piromyces sp. 'equi'; Pseudobutyrivibrio xylanivorans; Bifidobacterium longum; Bacteroides thetaiotaomicron; Fibrobacter succinogenes; Clostridium cellulovorans; Bifidobacterium adolescentis; Cellulomonas fimi; Neocallimastix frontalis; [Eubacterium] cellulosolvens; Lachnospira eligens; Ruminococcus sp.; Piromyces sp.; Roseburia intestinalis; Roseburia hominis
Type:
Genome variation profiling by array
Platform:
GPL25777
6 Samples
Download data: TXT
Series
Accession:
GSE122256
ID:
200122256
12.

Colistin heteroresistance in Enterobacter cloacae is regualted by PhoPQ-dependent 4-amino-4-deoxy-L arabinose addition to lipid A

(Submitter supplied) We report the transcriptional expression from wild type, ΔphoPQ, and ΔpmrAB to understand their contribution to colistin resistance.
Organism:
Enterobacter cloacae subsp. cloacae ATCC 13047
Type:
Expression profiling by high throughput sequencing
Platform:
GPL26251
3 Samples
Download data: XLS
Series
Accession:
GSE127802
ID:
200127802
13.

iac gene expression in the indole-3-acetic acid-degrading soil bacterium Enterobacter soli LF7 

(Submitter supplied) We show for soil bacterium Enterobacter soli LF7 (synonym Enterobacter asburiae LF7a) that possession of a iac (indole 3-acetic acid catabolic) gene cluster is causatively linked to the ability to utilize the plant hormone indole 3-acetic acid (IAA) as a carbon and energy source. Genome-wide transcriptional profiling by mRNA sequencing revealed that these iac genes chromosomally arranged as iacHABICDEFG and coding for the transformation of IAA to catechol, were the most highly induced (>29-fold) among the relatively few (<1%) differentially expressed genes in response to IAA. more...
Organism:
Enterobacter soli
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24961
12 Samples
Download data: TXT
Series
Accession:
GSE114050
ID:
200114050
14.

The FibroChip, a functional DNA microarray to monitor cellulolysis and hemicellulolysis activities of rumen microbiota

(Submitter supplied) Ruminants are the most efficient herbivorous animals to transform plant biomass into edible products, principally thanks to the rumen microbiota that produces a large array of enzymes responsible for the hydrolysis of plant cell wall polysaccharides. Several biotic and abiotic factors influence the efficiency of fiber degradation, which can ultimately impact the animal productivity and health. To provide more insight on mechanisms involved in the modulation of fibrolytic activity, a functional DNA microarray targeting genes coding for key enzymes involved in cellulose and hemicellulose degradation by rumen microbiota was designed. more...
Organism:
Butyrivibrio fibrisolvens; Selenomonas ruminantium; Lactococcus lactis; Clostridioides difficile; Ruminiclostridium cellulolyticum; Cellulomonas flavigena; Neocallimastix patriciarum; Bifidobacterium animalis; Agathobacter rectalis; Enterobacter sp.; Escherichia coli K-12; Pseudobutyrivibrio xylanivorans; Bifidobacterium longum; uncultured Neocallimastigales; Bacteroides fragilis; Ruminococcus albus; Enterococcus faecium; Acetivibrio thermocellus; Clostridium beijerinckii; Levilactobacillus brevis; Fibrobacter intestinalis; Epidinium caudatum; Polyplastron multivesiculatum; Orpinomyces joyonii; Piromyces rhizinflatus; Piromyces sp. 'equi'; Epidinium ecaudatum; Bacteroides xylanisolvens; Cellulosilyticum ruminicola; Ruminococcus champanellensis; Ruminococcus flavefaciens; Limosilactobacillus fermentum; Piromyces communis; Pseudobacteroides cellulosolvens; Eudiplodinium maggii; Fibrobacter succinogenes subsp. succinogenes S85; Segatella bryantii; Acetivibrio clariflavus; Bacteroides thetaiotaomicron; Fibrobacter succinogenes; Xylanibacter ruminicola; Clostridium acetobutylicum; Clostridium cellulovorans; Bifidobacterium adolescentis; Cellulomonas fimi; Neocallimastix frontalis; Bacteroides ovatus; [Eubacterium] cellulosolvens; Bacteroides sp.; Lachnospira eligens; Ruminococcus sp.; Piromyces sp.; Roseburia intestinalis; Butyrivibrio hungatei; Roseburia hominis; bovine gut metagenome; Bacteroides xylanisolvens XB1A; Orpinomyces sp.
Type:
Expression profiling by array; Other
Platform:
GPL24327
14 Samples
Download data: TXT
Series
Accession:
GSE107550
ID:
200107550
15.

NextSeq 550 (Enterobacter sp. BIDMC93)

Organism:
Enterobacter sp. BIDMC93
1 Series
9 Samples
Download data
Platform
Accession:
GPL34278
ID:
100034278
16.

NextSeq 550 (Enterobacter cloacae)

Organism:
Enterobacter cloacae
1 Series
9 Samples
Download data
Platform
Accession:
GPL34277
ID:
100034277
17.

Illumina NovaSeq 6000 (Enterobacter cloacae subsp. cloacae ATCC 13047)

Organism:
Enterobacter cloacae subsp. cloacae ATCC 13047
1 Series
9 Samples
Download data
Platform
Accession:
GPL33540
ID:
100033540
18.

Illumina NextSeq 500 (Enterobacter cloacae)

Organism:
Enterobacter cloacae
2 Series
20 Samples
Download data
Platform
Accession:
GPL32875
ID:
100032875
19.

Illumina MiSeq (Enterobacter cloacae complex sp. R_G8)

Organism:
Enterobacter cloacae complex sp. R_G8
1 Series
1 Sample
Download data
Platform
Accession:
GPL32818
ID:
100032818
20.

Illumina MiSeq (Enterobacter bugandensis)

Organism:
Enterobacter bugandensis
1 Series
1 Sample
Download data
Platform
Accession:
GPL32817
ID:
100032817
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