Biofilms of non-tuberculous mycobacteria display distinct expression patterns and form an extracellular matrix
Ontology highlight
ABSTRACT:
ORGANISM(S): Mycobacteroides chelonae
PROVIDER: GSE144514 | GEO | 2020/08/24
REPOSITORIES: GEO
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Project description:Mycobacterium chelonae is an environmental, non-tuberculous mycobacterial species, capable of causing infections in humans. Biofilm formation is a key strategy used by M. chelonae in colonising niches in the environment and in the host. We studied a water-air interface (pellicle) biofilm of M. chelonae using a wide array of approaches to outline the molecular structure and composition of the biofilm. Scanning electron micrographs showed that M. chelonae biofilms produced an extracellular matrix. Using a combination of biochemical analysis, Raman spectroscopy, and fluorescence microscopy, we showed the matrix to consist of proteins, carbohydrates, lipids and eDNA. Glucose was the predominant sugar present in the biofilm matrix, and its relative abundance decreased in late (established) biofilms. RNA-seq analysis of the biofilms showed upregulation of genes involved in redox metabolism. Additionally, genes involved in mycolic acid, other lipid and glyoxylate metabolism were also upregulated in the early biofilms.
| S-EPMC7421604 | biostudies-literature
Project description:Biofilms of non-tuberculous mycobacteria display distinct expression patterns and form an extracellular matrix
| PRJNA603891 | ENA
Project description:Comparison of transcriptional differences (RNA-seq) between biofilm and planktonic cultures of Mycobacterium abscessus
2021-04-28 | GSE165352 | GEO
Project description:Comparison of biofilm versus planktonic mode of growth in Staphylococcus aureus
2014-01-18 | E-MEXP-3924 | biostudies-arrayexpress
Project description:Transcriptional profiling of Candida albicans cells grown under planktonic and biofilm-inducing conditions, comparing SN76 and sfl1Δ/sfl1Δ strains. Goal was to study the effect of SFL1 deletion on the transcriptomic profile of C. albicans planktonic and biofilm cells under acidic conditions, in order to reveal the function of the Sfl1 transcription factor in C. albicans biofilm development.
2023-03-03 | GSE206208 | GEO
Project description:Biofilm formation is an important virulence trait of the pathogenic yeast Candida albicans. Large-scale genetics strategies aimed at identifying genes involved in biofilm development are hampered by lack of a complete sexual cycle in this diploid yeast in addition to the tedious generation of homozygous gene-deletion mutants. Gene overexpression is an attractive alternative strategy for large-scale phenotypic analyses and gene-function studies. We combined gene overexpression, strain barcoding and microarray profiling to screen a library of 531 C. albicans conditional overexpression strains (~10% of the genome) for genes affecting i) planktonic cell fitness and ii) biofilm development in mixed-population experiments. We found 5 genes whose overexpression affects planktonic strain fitness, including RAD53, RAD51, PIN4, orf19.2781, all encoding (or predicted to encode) regulators of DNA-damage response or cell-cycle progression and SFL2, involved in filamentous growth. We identified 16 and 4 genes (out of 531) whose overexpression respectively increases and decreases strain occupancy within the multi-strain biofilm. Strikingly, strains with increased abundance in the multi-strain biofilm were significantly enriched for genes encoding cell wall proteins (10 genes), including the glycosylphosphatidylinositol (GPI)-anchored proteins Pga15, Pga19, Pga22, Pga59, Pga32 and Pga41. Data validation experiments using either individually- or competitively-grown overexpression and/or the respective knock-out strains revealed that the identified genes differently contribute to biofilm formation during specific stages of biofilm development, including increased or decreased substrate adherence (IHD1, PGA32, PGA37, PGA15, PGA22, PGA59 and PGA19) or biofilm biomass growth and cohesion (PGA15, PGA59 and PGA22). In line with the hypothesis that cell wall genes contribute to biofilm development, we show that strains overexpressing PGA15 or PGA22 display altered cell wall structures. Our study reveals that cell wall proteins are important actors during C. albicans biofilm formation and illustrates the powerful use of signature tagging in conjunction with gene overexpression for the identification of genes involved in processes pertaining to C. albicans virulence. A total of 8 samples are included in this study. For fitness profiling of planktonic cells, 2 biological replicates were analyzed (samples Pool_Fitness_planktonic_rep1 and Pool_Fitness_planktonic_rep2). For quantification of strain abundance during biofilm formation, 6 biological replicates were analyzed (Pool_Biofilm_rep1, Pool_Biofilm_rep2, Pool_Biofilm_rep3, Pool_Biofilm_rep4, Pool_Biofilm_rep5, Pool_Biofilm_rep6). Genomic DNA was purified and used as template to PCR-amplify barcodes, which were then used as probes for microarray hybridization. This experiment was done twice independently. For quantification of strain abundance during multi-strain biofilm formation, strain pools were grown in minimal GHAUM medium with or without doxycycline, each inoculum was then diluted to an OD600 of 1 in fresh minimal GHAUM medium with or without doxycycline and left at room temperature for 30 min, to allow further overexpression. Plastic slides (ThermanoxM-bM-^DM-"; Nunc) were immersed in the inoculum for 30 min at room temperature to allow adhesion of cells to the plastic substrate. The plastic slides were then transferred to the glass vessel of a 40-mL incubation chamber. This vessel has two glass tubes inserted to drive the entry of medium and air, while used medium is evacuated through a third tube. The flow of medium is controlled by a recirculation pump (IsmatecM-BM-.) set at 0.6 mL.min-1 and pushed by pressured air supplied at 105 Pa, conditions minimizing planktonic phase growth and promoting biofilm formation. The chambers with the plastic substrate were incubated at 37C and biofilms were grown for 40h followed by genomic DNA extraction, barcode amplification and differential labeling (dox-treated samples with Cy5, untreated samples with Cy3) and hybridization to barcode microarrays.
2014-03-31 | E-GEOD-48647 | biostudies-arrayexpress
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
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. Two condition experiments: E. coli biofilm vs E. coli planktonic cultures. Two biological replicates with independently grown and harvested biofilms or planktonic cultures. Each biological replicate has two technical replicates of hybridization on microarray slides. Each slide has three built-in replicates for each probe.
2013-12-30 | E-GEOD-24914 | biostudies-arrayexpress
Project description:Background. During infection, pneumococci exist mainly in sessile biofilms rather than in planktonic form, except during sepsis. However, relatively little is known about how biofilms contribute to pneumococcal pathogenesis. Methods. We performed a biofilm assay and mouse infection experiments on opaque and transparent variants of a clinical serotype 19F strain. Results. After 4 days incubation, scanning electron microscopy revealed that opaque biofilm bacteria produced an extracellular matrix, whereas the transparent variant did not. The opaque biofilm-derived bacteria translocated from the nasopharynx to the lungs and brain of mice, and showed 100-fold greater in vitro adherence to A549 cells. Microarray analysis of planktonic and sessile bacteria from transparent and opaque variants showed differential gene expression in two operons: the lic operon, involved in choline uptake, and in the two-component system, ciaRH. Mutants of these genes did not form an extracellular matrix, could not translocate from the nasopharynx to the lungs or the brain, and adhered poorly to A549 cells. Conclusions. We conclude that only the opaque phenotype is able to form extracellular matrix, and that the lic operon and ciaRH contribute to this process. We propose that during infection, extracellular matrix formation enhances the ability of pneumococci to cause invasive disease. Data is also available from http://bugs.sgul.ac.uk/E-BUGS-117
2011-04-20 | E-BUGS-117 | biostudies-arrayexpress
Project description:Extracellular polymeric substances (EPS) produced by bacteria form a matrix for the complex three-dimensional architecture of biofilms. The EPS matrix of a biofilm is primarily composed of polysaccharides, proteins and extracellular DNA (eDNA). In addition to supporting the community structure, the EPS matrix protects bacterial biofilms from the environment. Specifically, the EPS matrix reduces the penetration of antimicrobial agents into the biofilm, thereby reducing their efficiency. Strategies for disrupting the formation of the EPS matrix can therefore lead to a more efficient use of antimicrobial agents. Here, we examine the biofilm-disrupting activity of vitamin C (sodium ascorbate). Quantitative proteomics analysis of vitamin C treated biofilms show that exposure to vitamin C inhibits quorum sensing and other regulatory mechanisms underpinning biofilm development. This results in inhibition of the EPS biosynthesis, and depletion of the polysaccharide component of the matrix. Once the EPS content is reduced beyond a critical point, bacterial cells get fully exposed to the medium, thereby experiencing a planktonic-like state. At this stage, the cells are more susceptible to killing, either by vitamin C-induced oxidative stress as reported here, or by other antibacterial compounds or treatments.
2017-12-19 | PXD007533 | Pride