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Genome-wide analysis of gene expression by B. subtilis biofilms grown in buffered or minimally buffered conditions,

ABSTRACT: Genome-wide analysis of gene expression by B. subtilis biofilms grown in buffered or minimally buffered conditions,

PROVIDER: PRJNA970277 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24465244.fastq.gz	Fastqsanger.gz
	SRR24465245.fastq.gz	Fastqsanger.gz
	SRR24465246.fastq.gz	Fastqsanger.gz
	SRR24465247.fastq.gz	Fastqsanger.gz
	SRR24465248.fastq.gz	Fastqsanger.gz

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Genome-wide analysis of gene expression by B. subtilis biofilms grown in buffered or minimally buffered conditions,

Project description:Analysis of B. subtilis biofilm metabolism at gene expression level. The hypothesis tested in the present study was that extracellular pH and environmental buffer influence the biofilm development. Results provide important information of the response of biofilms to changes in extracellular pH.

2023-05-12 | GSE231939 | GEO

Quantitative transcriptome analysis of C. albicans biofilms grown in high and low carbon dioxide conditions.

Project description:C. albicans is a dimorphic yeast which can switch from budding yeast and to hyphal forms and this property is essential for biofilm establishment and maturation. C. albicans undergoes this yeast-to-hyphal switch in response to high CO2. The purpose of this study is to use RNA-seq to investigate pathways whose genes are differentially expressed when C. albicans biofilms are grown in a physiologically relevant elevated (5%) CO2 environment compared to a low/atmospheric (0.03%) CO2 environment. We report that in C.albicans biofilms grown under 5% CO2 conditions, genes controlled by core biofilm regulatory transcription factors such as Brg1, Efg1, Ndt80, and Bcr1 are overall expressed at significantly higher levels compared to those grown in 0.03% CO2 conditions. We find that genes encoding glucose and amino acid transporters, as well as genes previously found to be involved in the response to Ketoconazole treatment, are significantly upregulated in 5% CO2 C. albicans biofilms. Overall, these data suggest a high CO2 environment enhances biofilm formation of C. albicans and may also increase antifungal tolerance of such biofilms.

2021-04-14 | GSE172004 | GEO

Evidence for proline utilisation by oral bacterial biofilms grown in saliva

Project description:Within the mouth bacteria are starved of saccharides as their main nutrient source between meals and it is unclear what drives their metabolism. Previously oral in vitro biofilms grown in saliva have shown proteolytic degradation of salivary proteins and increased extracellular proline. Although arginine and glucose have been shown before to have an effect on oral biofilm growth and activity, there is limited evidence for proline. Nuclear magnetic resonance (NMR) spectroscopy was used to identify extracellular metabolites produced by bacteria in oral biofilms grown on hydroxyapatite discs. Biofilms were inoculated with whole mouth saliva and then grown for 7 days using sterilised whole mouth saliva supplemented with proline, arginine and glucose as a growth-medium. Overall proline had a beneficial effect on biofilm growth – with significantly fewer dead bacteria present by biomass and surface area of the biofilms (p <0.05). Where arginine and glucose significantly increased and decreased pH, respectively, the pH of proline supplemented biofilms remained neutral at pH 7.3-7.5. SDS-polyacrylamide gel electrophoresis of the spent saliva from proline and arginine supplemented biofilms showed inhibition of salivary protein degradation of immature biofilms. NMR analysis of the spent saliva revealed that proline supplemented biofilms were metabolically similar to unsupplemented biofilms, but these biofilms actively metabolised proline to 5-aminopentanoate, butyrate and propionate, and actively utilised glycine. This study shows that in a nutrient limited environment, proline has a beneficial effect on in vitro oral biofilms grown from a saliva inoculum.

2020-07-23 | ST001433 | MetabolomicsWorkbench

Transcriptome Analysis of Candida albicans Biofilms Grown in the Presence of Arachidonic Acid and Fluconazole

Project description:Candida albicans is a commensal yeast within the human microbiota with significant medical importance because of its pathogenic potential. The yeast produces biofilms, which are highly resistant to available antifungals. High level of antifungal resistance by C. albicans biofilms has resulted in the need for alternative treatment. Polyunsaturated fatty acids such as arachidonic acid has been reported to increase the susceptibility of C. albicans biofilms to azole. However, the underlining mechanism is unknown. To unravel the mechanism behind this phenomenon, identification of differentially regulated genes in C. albicans biofilms grown in the presence of arachidonic acid, fluconazole, and the combination of both compounds was conducted using RNAseq.

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Transcriptome analysis of developing Bacillus subtilis biofilms

Project description:The objective of the study was to uncover the developmental dynamics in Bacillus subtilis biofilms on a transcriptome level. The experiment covered a developmental timeline over two months of biofilm growth.

2020-10-05 | GSE141305 | GEO

Garde2020 - metabolic oscillations in Bacillus subtilis biofilms

Project description:Ravindra Garde, Bashar Ibrahim & Stefan Schuster. Extending the minimal model of metabolic oscillations in Bacillus subtilis biofilms. Scientific Reports 10, 1 (2020). Biofilms are composed of microorganisms attached to a solid surface or floating on top of a liquid surface. They pose challenges in the field of medicine but can also have useful applications in industry. Regulation of biofilm growth is complex and still largely elusive. Oscillations are thought to be advantageous for biofilms to cope with nutrient starvation and chemical attacks. Recently, a minimal mathematical model has been employed to describe the oscillations in Bacillus subtilis biofilms. In this paper, we investigate four different modifications to that minimal model in order to better understand the oscillations in biofilms. Our first modification is towards making a gradient of metabolites from the center of the biofilm to the periphery. We find that it does not improve the model and is therefore, unnecessary. We then use realistic Michaelis-Menten kinetics to replace the highly simple mass-action kinetics for one of the reactions. Further, we use reversible reactions to mimic the diffusion in biofilms. As the final modification, we check the combined effect of using Michaelis-Menten kinetics and reversible reactions on the model behavior. We find that these two modifications alone or in combination improve the description of the biological scenario.

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Tobramycin Treatment of P. aeruginosa Biofilms Grown on CFBE41o- Cells

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Escherichia coli biofilms vs planktonic culture

Project description:Transcription profile of Escherichia coli cells in biofilms under static batch culture was compared to that of E. coli cells in planktonic cultures. Both E. coli biofilm and planktonic cultures were cultivated for 18 h in 10% Luria-Bertani broth at room temperature (20 degree Celsius). Biofilms were grown in static batch culture in petri dishes. Both planktonic culture and biofilms were homogenized and run through a separated protocol.

2013-12-30 | GSE24914 | GEO

Transcription profiling of P. aeruginosa biofilms treated with tobramycin grown on CFBE41o- cells

Project description:We grew Pseudomonas aeruginosa biofilms on CFBE41o- human airway cells in culture, and we treated these biofilms with tobramycin. Microarray analysis was performed to gain an understanding of the global transcriptional changes that occur during antibiotic treatment. Experiment Overall Design: We compared three untreated control samples with three tobramycin-treated samples. Biofilms were grown on CFBE41o- cells in culture for 9 hours in MEM/0.4% arginine. Replicate samples were then incubated in the presence or absence of 500 Î¼g/mL tobramycin for 30 minutes.

2008-06-18 | E-GEOD-9989 | biostudies-arrayexpress

Quantitative transcriptome analysis of C. albicans biofilms grown in high and low carbon dioxide conditions.

Project description:Quantitative transcriptome analysis of C. albicans biofilms grown in high and low carbon dioxide conditions.

| PRJNA721681 | ENA