Enterococci, staphylococci
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA868571 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21102102_1.fastq.gz | Fastqsanger.gz | |||
| SRR21102102_2.fastq.gz | Fastqsanger.gz | |||
| SRR21102103_1.fastq.gz | Fastqsanger.gz | |||
| SRR21102103_2.fastq.gz | Fastqsanger.gz | |||
| SRR21102104_1.fastq.gz | Fastqsanger.gz |
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Project description:To survive during colonization or infection of the human body, microorganisms must defeat antimicrobial peptides, which represent a key component of innate host defense in phagocytes and on epithelia. However, is not known how the clinically important group of Gram-positive bacteria sense antimicrobial peptides to coordinate a directed defensive response. By determining the genome-wide gene regulatory response to human beta defensin 3 in the nosocomial pathogen Staphylococcus epidermidis, we discovered an antimicrobial peptide sensor system that controls major specific resistance mechanisms to antimicrobial peptides and is unrelated to the Gram-negative PhoP/PhoQ system. Keywords: Wild type control vs treated vs mutant
2008-02-26 | GSE7163 | GEO
Project description:To survive during colonization or infection of the human body, microorganisms must defeat antimicrobial peptides, which represent a key component of innate host defense in phagocytes and on epithelia. However, is not known how the clinically important group of Gram-positive bacteria sense antimicrobial peptides to coordinate a directed defensive response. By determining the genome-wide gene regulatory response to human beta defensin 3 in the nosocomial pathogen Staphylococcus epidermidis, we discovered an antimicrobial peptide sensor system that controls major specific resistance mechanisms to antimicrobial peptides and is unrelated to the Gram-negative PhoP/PhoQ system. Wild type untreated in triplicate is compared to wild type treated in triplicate along with three mutants in triplicate with and without treatment of human beta defensin 3, totalling 30 samples
2010-05-26 | E-GEOD-7163 | biostudies-arrayexpress
Project description:In order to understand the appropriate use of potentially beneficial Gram positive microbes through their introduction in the gut microbiome, it is necessary to understand the influence of individual bacteria on the host response system at a cellular level. In the present study we showed that lipopolysaccharide (LPS), flagellated Gram negative bacteria, potentially beneficial Gram positive bacteria and yeast interact differently with human intestinal enterocytes (IEC) with a custom-designed expression microarray evaluating 17 specific host-response pathways. Only, LPS and flagellated Gram negative bacteria induced inflammatory response, while a subset of Gram positive microbes had anti-inflammatory potential. The main outcome from the study was the differential regulation of the central MAPK signaling pathway by these Gram positive microbes versus commensal/pathogenic Gram negative bacteria. The microarray was efficient to highlight the impact of individual bacteria on IEC response, but q-RT-PCR validation demonstrated some underestimation for down regulated genes by the microarray. This Immune Array will allow us to better understand the mechanisms underlying pathogen-induced host immune responses, aid in the selection potentially probiotic microbes and perhaps select biomarkers for future clinical studies.
2011-12-31 | GSE31394 | GEO
Project description:The human C-type lectin Reg3a (HIP/PAP) is an antimicrobial peptide that kills Gram-positive bacteria. Reg3a preserves gut microbiota homeostasis, reinforces intestinal barrier function and thereby helps to fight induced colitis in mice. Transcriptomic data revealed an upregulation of numerous genes involved in the robustness of the intestinal barrier, and the biosynthesis pathway of mucin core 1 and 3 O-glycans.
2018-01-31 | GSE64932 | GEO
Project description:The gram- positive bacterial pathogen Clavibacter michiganensis subsp. michiganensis (Cmm) causes huge economic losses by infecting tomato plants worldwide. Cmm can be spread by contaminated seeds and transplants, penetrating the plant through natural openings or wounds and is transferred through the plant xylem. While in recent years significant progress has been made to elucidate plant responses to pathogenic gram-negative bacteria by gene expression studies, the molecular mechanisms that lead to disease symptoms caused by gram-positive bacteria like Cmm remain elusive. An indigenous virulent Cmm strain isolated from a farm crop of Pomodoro tomatoes in southern Greece was used for the infection of EKSTASIS F1 hybrid tomato seedlings. Here, we present the results of a deep RNA- sequencing (RNA-seq) analysis performed to characterize the dynamic expression profile of tomato genes upon Cmm infection.
2021-08-10 | GSE160971 | GEO
Project description:In order to understand the appropriate use of potentially beneficial Gram positive microbes through their introduction in the gut microbiome, it is necessary to understand the influence of individual bacteria on the host response system at a cellular level. In the present study we showed that lipopolysaccharide (LPS), flagellated Gram negative bacteria, potentially beneficial Gram positive bacteria and yeast interact differently with human intestinal enterocytes (IEC) with a custom-designed expression microarray evaluating 17 specific host-response pathways. Only, LPS and flagellated Gram negative bacteria induced inflammatory response, while a subset of Gram positive microbes had anti-inflammatory potential. The main outcome from the study was the differential regulation of the central MAPK signaling pathway by these Gram positive microbes versus commensal/pathogenic Gram negative bacteria. The microarray was efficient to highlight the impact of individual bacteria on IEC response, but q-RT-PCR validation demonstrated some underestimation for down regulated genes by the microarray. This Immune Array will allow us to better understand the mechanisms underlying pathogen-induced host immune responses, aid in the selection potentially probiotic microbes and perhaps select biomarkers for future clinical studies. In this study, human immune response was assessed by stimulating HT-29 intestinal epithelial cells (IEC) with different microorganisms (or LPS) individually. For each of the 12 different treatments, between 4 and 8 biological replicates were performed, analyzed with dye-swaps and hybridized against control or untreated cells. Genes that were showing a 1.3 mRNA transcript abundance fold change and a P-value below 0.05 were considered to be differentially expressed.
2011-12-31 | E-GEOD-31394 | biostudies-arrayexpress
Project description:Guanidine DNA quadruplex (G4-DNA) structures convey a distinctive layer of epigenetic information that is critical for the regulation of key biological activities and processes as genome transcription regulation, replication and repair. Despite several works that have been published recently, the information regarding their role and possible use as therapeutic drug targets in bacteria is still scarce. Here, we tested the biological activity of a small G4-DNA ligand library based on the naphthalene diimide (NDI) pharmacophore, against both Gram-positive and Gram-negative bacteria. For the best compound identified, NDI-10, the action mechanism was further characterized. Gram-negative bacteria were more resistant altogether due to the presence of the outer membrane, although the activity of the G4-Ligand was generally bactericidal, while it was bacteriostatic for Gram-positive bacteria. This asymmetric activity could be related to the different prevalence of putative G4-DNA structures in each group, the influence that they can exert on the gene expression (which was found more severe for the Gram-negative bacteria) and the role of the G4 structures in these bacteria, that seems to be more related to promote transcription in Gram-positive bacteria and repress transcription in Gram-negative.
2022-12-10 | GSE178890 | GEO
Project description:Objective: Reg3g has been proposed to have a protective role against infection due to its bactericidal effect on Gram-positive bacteria, but evidence from in vivo studies is lacking. Therefore we generated a Reg3g-/- mouse, to determine its role in intestinal homeostasis and protection against experimental infection. Methods: Reg3g-/- mice were phenotyped using histological methods and a range of innate and immune markers. To investigate the antimicrobial role of Reg3g we experimentally infected mice with Gram-positive Listeria monocytogenes and Gram-negative Salmonella entertitidis and measured translocated bacteria, mucosal and systemic markers of infection. Results: Reg3g-/- mice display altered ileal mucus distribution and increased bacterial contact with the epithelium. , concomitant with This increased the inflammatory status in of the ileal mucosa and increased expression of Il-22, myeloperoxidase (MPO) and serum chemokines in serum. In response to infection, Reg3g-/- mice showed transcriptome changes and elevated levels of mucosal MPO in the ileum, but no increased bacterial translocation to the organs. Conclusions: Reg3g is equally distributed throughout the mucus of wild type (wt) mice and its absence results in an altered distribution of the ileal mucus. Reg3g deficiency also results resulted in increased bacterial contact with the epithelium and heightened inflammatory responses in the ileal mucosa. We propose that Reg3g binds pathogens suggesting it and contributes to mucus barrier function by ensnaring bacteria. Compared to wt mice, Reg3g-/- mice infected with S. enteritidis and L. monocytogenes show an increase of mucosal inflammatory markers indicating the protective, anti-microbial roles of Reg3g in defence against both Gram-positive and -negative bacteria.
2014-06-06 | GSE44409 | GEO
Project description:The race to combat antibiotic resistance and develop novel therapies has triggered studies on novel metal-based formulations. Silver remains a strong candidate since ancient times due to its multimodal and broad-spectrum activity against bacterial and fungal pathogens. N-heterocyclic carbene (NHC) complexes coordinate transition metals to generate a broad range of anticancer and/or antimicrobial agents with ongoing efforts being made to enhance lipophilicity and drug stability. The lead silver(I) acetate complex, 1,3-dibenzyl-4,5-diphenylimidazol-2-ylidene (NHC*) (SBC3) synthesised by the Tacke group has previously demonstrated promising growth and biofilm-inhibiting properties. As an extension of this, we examined the responses of two structurally different bacteria to SBC3 using label-free quantitative proteomic analysis. Multidrug resistant Pseudomonas aeruginosa (Gram-negative) and Staphylococcus aureus (Gram-positive) are associated with chronic wound infections and Cystic Fibrosis lung colonisation where co-infection often exacerbates disease. SBC3 increased the abundance of alginate biosynthesis, secretion system and drug detoxification proteins in P. aeruginosa whilst a multitude of pathways including anaerobic respiration, twitching motility, and ABC transport were decreased. This contrasted with affected pathways in S. aureus such as increased DNA replication/repair and cell redox homeostasis and decreased protein synthesis, lipoylation, glucose metabolism. Increased abundance of cell wall/membrane proteins were indicative of the structural damage induced by SBC3 to both cell types. These findings show the potential broad applications of SBC3 in treating Gram-positive and Gram-negative bacteria.
2023-03-11 | PXD038616 | Pride