Commensal Klebsiella oxytoca
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB42167 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR6364690_1.fastq.gz | Fastqsanger.gz | |||
| ERR6364690_2.fastq.gz | Fastqsanger.gz | |||
| ERR6364700_1.fastq.gz | Fastqsanger.gz | |||
| ERR6364700_2.fastq.gz | Fastqsanger.gz | |||
| ERR6364710_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:These datasets describe the eliciting conditions for the leup operon in K. oxytoca and the metabolites of the pyr gene in K. oxytoca
File descriptions: 16495_KO1-3: ESI+ runs of the pyr KO K. oxytoca strain in M9+CAS+Gal KOx_WT1-3: ESI+ runs of K. oxytoca WT in M9+CAS+Gal
These files should be compared to each other.
KOxy_M9CASGAL_MSMS_Pyrazine files are targeted MS2 Qtof runs of compounds from Klebsiella oxytoca that have the pyrazine-like UV-Vis spectrum.
KoxNeu5Ac_1-3_AutoMSMS: ESI+ MS2 runs of WT K. oxytoca in M9+CAS+Neu5AC
KoxWT_1-3_AutoMSMS: ESI+ MS2 runs of WT K. oxytoca in M9+CAS
These files should be compared to each other.
| MSV000095925 | MassIVE
Project description:Klebsiella oxytoca from bloodstream infections
| PRJNA908117 | ENA
Project description:Purpose: Klebsiella oxytoca M5a1 (previously Klebsiella pneumonia M5a1) is a principle model organism for free-living biological nitrogen fixation. This strain has been used for decades in the characterisation of nitrogenase function and the genetic regulation of nitrogen fixation physiology. Currently it represents a key model for synthetic biology and biotechnology approaches. This project involves a multi-omics approach to modelling nitrogen physiology in Klebsiella oxytoca M5a1, in order to inform rational genetic engineering for improved nitrogen fixation activity. Here we studied the transition from nitrogen replete (high NH4Cl) to nitrogen starved (NH4Cl run-out) conditions, the latter of which induce nif gene expression and synthesis of the nitrogenase enzyme. We mapped RNA-sequencing (Illumina) reads to our assembled M5aI genome in order to compare the transcriptome between nitrogen replete and nitrogen fixing conditions using differential gene expression (DEG) analysis. Methods: Total RNA was extracted from fixed M5a1 cell samples after culturing in nitrogen replete (10 mM NH4Cl; one replicate) or nitrogen starved (3 hours after complete run-out of 0.5 mM NH4Cl; two replicates) growth medium (NFDM). cDNA libraries were prepared for Illumina (NextSeq 500) sequencing, with a read length of 75 nt and a depth of 100 million reads. Following processing and quality control, sequence reads were mapped to a M5a1 genomic template (GenBank WGS accession JAFHKG010000000; BioSample SAMN17288411) and gene count normalisation performed (RPKM). Differential gene expression analysis was performed using the DEseq2 package utilising settings of regularized logarithm (rlog) normalisation of read counts, Wald hypothesis testing and p-value adjustment using a False Discovery Rate threshold of 0.05. Log2 fold changes between conditions were calculated for differentially expressed genes (DEGs) with an adjusted p value of <0.05. Results: Across the three samples, between 22.0-25.1 million reads (81.4-87.7%) were mapped to the genome, including 56.7-68.5% mapped to annotated genes. More than 50% of genes (2694/5279 genes) were differentially expressed (adjusted p-value <0.05) in the nitrogen starved condition with respect to the nitrogen replate condition. 925 genes were upregulated and 1117 genes downregulated by more than 2-fold. Of these, 1515 differentially expressed genes correspond to annotated proteins in the KEGG functional orthology (KO) database. The 20 nitrogen fixation (nif) genes were ranked among the 200 genes with highest calculated expression values (RPKM) in the nitrogen starved condition. Conclusions: Our study provides a detailed insight into the global gene expression profile associated with diazotrophic (nitrogen fixing) growth, revealing a dominant role for nif and other nitrogen regulatory genes in the adaptation to nitrogen stress, in addition to a large array of secondary genes indirectly associated with shifts in metabolism and growth phenotype (e.g. metabolic enzymes, gene expression machinery, transporters).
2021-07-09 | GSE164668 | GEO
Project description:The rise of multi-drug resistance in bacterial pathogens imposes the need to study these organisms from new angles. A little explored outset is to scrutinize bacterial niche adaptations and interactions among pathogenic and commensal bacteria, because they can provide a better understanding of the fitness of pathogens in their human host. We have previously shown that co-culturing of the pathogen Staphylococcus aureus with co-resident Klebsiella oxytoca or Bacillus thuringiensis wound isolates resulted in reduced levels of virulence factor secretion, suggesting that the presence of these co-resident bacteria would modulate S. aureus virulence. In the present study, we performed an in-depth investigation of changes in S. aureus gene expression upon co-cultivation with K. oxytoca and B. thuringiensis under infection-mimicking conditions. To this end, we profiled the cellular proteomes of the co-existing bacteria with special focus on S. aureus. In parallel, we employed RNA sequencing to highlight global changes in staphylococcal behaviour. The results imply that co-colonizing bacteria from chronic wounds can pacify S. aureus, and this conclusion was verified in a Galleria mellonella infection model. Altogether, our findings show that the presence of K. oxytoca and B. thuringiensis leads to massive rearrangements in S. aureus physiology and substantial reduction in virulence.
2020-04-22 | PXD017208 | Pride