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Transcriptome of floating aggregate biofilms in Pseudomonas aeruginosa

ABSTRACT: Pseudomonas aeruginosa is a critical priority pathogen, whose proclivity to establish chronic infections and to resist antibiotic treatment is intimately linked to its ability to form biofilms at the infection site. Recent developments in our understanding of these biofilms has pointed to the fact that the surface-bound biofilms recapitulated by in vitro models do not sufficiently capture the type of biofilms that occur in infection sites, such as the CF lung. This study aimed to develop a straightforward and medium throughput model for free floating biofilms, alongside a protocol that permits fractionating of the biofilm into its constituent parts. The RNA-seq investigation takes the cells fraction at three timepoints in biofilm development (and one point in a planktonic culture for comparison), to ask what genes are driving the development of these free floating aggregate biofilms.

ORGANISM(S): Pseudomonas aeruginosa

PROVIDER: GSE301018 | GEO | 2025/06/27

REPOSITORIES: GEO

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Project description:Streptococcus pneumoniae is a Gram positive bacterium that causes severe invasive infection such as pneumonia, septicemia, meningitis and otitis media especially in children, the elderly and immune-compromised patients. Pneumococcal colonization and disease is often associated with biofilm formation. Bacteria in biofilms exhibit elevated resistance both to antibiotics and to host defense systems, which often results in persistent and difficult-to-treat infections. Therefore, the ongoing treat to human health posed by pneumococcal biofilms has prompted extensive research aimed to identify alternative targets and new antimicrobial agents that are effective against bacteria biofilms. The effective anti-biofilm strategies should include inhibition of microbial adhesion to the surface and of colonization, interference with the signal molecules modulating biofilm development and the disaggregation of the biofilm matrix. In this study, we examine the effect of DAM inhibitor small molecule pyrimidine-diones on streptococcus pneumoniae D-39 strain growth (planktonic and biofilm) and evaluate the changes in global gene expression using c-DNA microarray. The microarray analysis was performed on total RNA extracted from biofilms grown in 24-well microtiter plate with 7µm/ml pyrimidine-diones small molecule and control biofilms (biofilms grown without pyrimidine-diones small molecule). To validate the results of microarray, real-time RT-PCR was performed on 12 differentially expressed genes from six different functional groups. cDNA-microarray analysis detected a total of 259 genes that were significantly differentially expressed in biofilm growth with pyrimidine-diones small molecule. 204 genes were significantly down expressed and 55 genes were significantly up expressed in biofilms grown with 7µm/ml pyrimidine-diones small molecule. Among the 204 down expressed genes, 45 were hypothetical protein encoding gene and 159 were functional protein encoding genes. Of 55 up-regulated genes 21 were hypothetical genes and 34 were functional protein encoding genes. The functional annotation showed that gene involve in fatty acid metabolism, cell division, cell cycles, DNA metabolism, cell assembly were significantly down regulated and galactose metabolism related gene were up-expressed in biofilm grown with pyrimidine-diones small molecule.

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Transcriptome of floating aggregate biofilms in Pseudomonas aeruginosa

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