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Dormancy within Staphylococcus epidermidis biofilms: a transcriptomic analysis by RNA-seq

ABSTRACT: We sequenced mRNA from three independent biological replicates of Staphylococcus epidermidis biofilms with different proportion of dormant cells.

ORGANISM(S): Staphylococcus epidermidis

PROVIDER: GSE60834 | GEO | 2014/08/28

SECONDARY ACCESSION(S): PRJNA259641

REPOSITORIES: GEO

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Dormancy within Staphylococcus epidermidis biofilms: a transcriptomic analysis by RNA-seq

Project description:We sequenced mRNA from three independent biological replicates of Staphylococcus epidermidis biofilms with different proportion of dormant cells. Whole trancriptome analysis of Staphylococcus epidermidis biofilms with prevented and induced dormancy.

2014-08-28 | E-GEOD-60834 | biostudies-arrayexpress

The mutual effect of Staphylococcus epidermidis and Staphylococcus aureus in dual species biofilms as revealed by RNA-Seq

Project description:We examined the differential gene expression of Staphylococcus epidermidis and Staphylococcus epidermidis in dual species biofilms. Therefore, we performed RNA-Seq on single and dual species biofilms and we compared the gene expression levels in dual species biofilms to those in single species biofilms.

2016-05-27 | GSE79575 | GEO

Transcriptomic analyses of Staphylococcus epidermidis in mixed-species biofilms with Candida albicans

2012-02-28 | GSE35438 | GEO

Transcriptomic analyses of Staphylococcus epidermidis in mixed-species biofilms with Candida albicans

Project description:To explain enhanced biofilm formation and increased dissemination of S. epidermidis in mixed-species biofilms, microarrays were used to explore differential gene expression of S. epidermidis in mixed-species biofilms. One sample from single species biofilm (S1) and mixed-species biofilm (SC2) were excluded from analyses for outliers. We observed upregulation (2.7%) and down regulation (6%) of S. epidermidis genes in mixed-species biofilms. Autolysis repressors lrgA and lrgB were down regulated 36-fold and 27-fold respectively and was associated with increased eDNA possibly due to enhanced autolysis in mixed-species biofilms. These data suggest that bacterial autolysis and release of eDNA in the biofilm matrix may be responsible for enhancement and dissemination of mixed-species biofilms of S. epidermidis and C. albicans. Staphylococcal gene expression in mixed-species biofilms with Candida and in single species biofilms of S. epidermidis were analyzed. The experiment was repeated thrice on 3 different days (3 biological replicates each for single species biofilms of S. epidermidis and mixed-species biofilms). Only 2 biological replicates were analyzed and one biological replicate was not analyzed (S1 and SC1 - raw data files are provided on the Series record). Single species biofilms of S. epidermidis (strain 1457) and C. albicans (strain 32354) and mixed-species biofilms were formed on 6-well tissue culture plates. Five ml of organism suspensions (O.D. 0.3, S. epidermidis 107 CFU/ml or C. albicans 105 CFU/ml) or 2.5 ml each for mixed-species biofilms for 24 hr. RNA was harvested from single species and mixed-species biofilms.

2012-02-28 | E-GEOD-35438 | biostudies-arrayexpress

Staphylococcus epidermidis biofilms transcriptome alterations upon incubation with whole human blood

Project description:The ability of S. epidermidis to withstand the high bactericidal activity of the hostM-bM-^@M-^Ys blood is crucial for its systemic dissemination. Hence, in order to identify genes and pathways involved in the bacteriumM-bM-^@M-^Ys survival in human blood, we have characterized the transcriptome of S. epidermidis biofilms upon contact with human blood. Our results showed that genes whose transcription was increased in blood included those involved in biosynthesis and metabolism of amino acids, small molecules, carboxylic and organic acids, and cellular ketones. One of the striking changes, observed after 4 hours of exposure to human blood, was the increase in the expression of genes involved in iron utilization, suggesting iron acquisition is an important component of S. epidermidis survival in human blood. Twenty-four hour S. epidermidis biofilms were incubated with either whole human blood or tryptic soy broth (TSB) during 2 or 4 hours at 37oC, 5% CO2 and slight agitation. RNA was then extracted and the transcriptomic libraries constructed. Differential gene expression calculations were performed using the transcriptome of biofilms at the start of the culture (T0h) as a control. This experiment was performed twice with blood collected from 6 healthy human donors under a protocol approved by the PartnerM-bM-^@M-^Ys Health Care System Institutional Review Board (Boston, MA, USA).

2014-08-29 | E-GEOD-52111 | biostudies-arrayexpress

Staphylococcus epidermidis biofilms transcriptome alterations upon incubation with whole human blood

Project description:The ability of S. epidermidis to withstand the high bactericidal activity of the host’s blood is crucial for its systemic dissemination. Hence, in order to identify genes and pathways involved in the bacterium’s survival in human blood, we have characterized the transcriptome of S. epidermidis biofilms upon contact with human blood. Our results showed that genes whose transcription was increased in blood included those involved in biosynthesis and metabolism of amino acids, small molecules, carboxylic and organic acids, and cellular ketones. One of the striking changes, observed after 4 hours of exposure to human blood, was the increase in the expression of genes involved in iron utilization, suggesting iron acquisition is an important component of S. epidermidis survival in human blood.

2014-08-29 | GSE52111 | GEO

Cells released from Staphylococcus epidermidis biofilms interact differently from biofilm or planktonic cells with murine host immune system.

Project description:S. epidermidis ability to form biofilms on indwelling medical devices and its association with the emergence of chronic infections is its main virulence factor. Nevertheless, it has been shown that the cells released from these biofilms are associated with the advent of serious acute infections with bacteraemia as one of the major clinical manifestations. Despite their clinical relevance, very little is known about the impact of biofilm-released cells in pathogenesis. Hence, herein, we characterized the murine immune response to the presence of cells released from S. epidermidis biofilms analysing spleen cells transcriptome by microarrays. These findings may help to explain the recurrent inflammatory symptoms presented by patients with colonization of indwelling medical devices.

2017-02-22 | GSE60992 | GEO

Staphylococcus aureus and Staphylococcus epidermidis transcriptomic response to sapienic acid

Project description:Staphylococcus aureus Newman and Staphylococcus epidermidis Tu3298, 20 minutes post challenge with sub-inhibitory concentration of sapienic acid vs equivalent concentration of ethanol. Challenge was added at mid logarithmic growth (OD600 0.5). Biological triplicates of samples were sequenced.

2016-07-31 | E-MTAB-4587 | biostudies-arrayexpress

Marker gene discovery for Staphylococcus epidermidis infection in zebrafish embryos (RNA-Seq)

Project description:We use the zebrafish embryo model to study the innate immune response against Staphylococcus epidermidis. Therefore, we injected S. epidermidis into the yolk at 2 hpf and took samples at 5 days post injection.

2013-04-01 | GSE42846 | GEO

Marker gene discovery for Staphylococcus epidermidis infection in zebrafish embryos (Agilent)

Project description:We use the zebrafish embryo model to study the innate immune response against Staphylococcus epidermidis. Therefore, we injected S. epidermidis (and three controls groups) into the yolk at 2 hpf and samples at mutiple timepoints. Gene expression profiles were obtained at 6, 30, 54, 78, 102 and 126 hpi by microarrays. The results show that the gram-positive bacterium S. epidermidis induces a late immune response with a strong response at 102 hpi.

2013-04-01 | GSE37227 | GEO

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