Biofilm
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA591694 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10571035.fastq.gz | Fastqsanger.gz | |||
| SRR10571036.fastq.gz | Fastqsanger.gz |
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Project description:Stainless steel biofilm
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Project description:Previously, we performed DNA array-based transcriptomic analysis of Clostridium acetobutylicum biofilm adsorbed onto fibrous matrix in batch fermentation. Here, to further shed light on the transcriptomic modulation of maturing Clostridium acetobutylicum biofilm, we performed the DNA array-based transcriptomic analysis in repeated-batch fermentation. Significant time course changes in expression levels were observed for the genes involved in amino acid metabolism, oligopeptide ABC transporter, nitrogen fixation, and various other processes. Repeated-batch fermentation was carried out in 2-L stainless steel columns packed with 40 g of cotton towel ?cut into pieces?approximately 3 cm × 5 cm) containing 1.5 L of P2 medium. Medium circulation rate was maintained at 35 mL/min via a peristaltic pump and the temperature was controlled at 37°C. Fermentation broth was replaced with fresh P2 medium every 12 h. Samples were withdrawn at 6 h after the medium replacement at predetermined interval, except for the last 3 samples. The last 3 samples were withdrawn at 12 h, 15 h, and 17 h after the medium replacement, respectively, to study the transcriptomic response to the adverse condition at the end of fermentation. A total of 8 samples were withdrawn over a period of 7 days, and time course gene expression profiles were studied.
2015-09-09 | E-GEOD-72765 | biostudies-arrayexpress
Project description:Listeria monocytogenes (Lm) cells can attach to both cantaloupe surface and food contact surfaces and promote biofilm growth. This study was to understand the impact of cantaloupe juice on the physiology and transcriptome of Lm planktonic cells and biofilm cells grown on stainless steel coupons using confocal laser scanning microscopy (CLSM), Cryo-Scanning Electron Microscopy (Cryo-SEM) and RNA Seq technology. Lm showed a strong autoaggregation phenotype when grown in cantaloupe juice at room temperature. It is interesting to note that Lm formed significantly more biofilms on stainless steel (SS) coupons when grown in cantaloupe juice than in TSB. SEM images revealed a different attachment profile of Lm on SS coupons. In TSB, Lm cells were mainly found in scratches/groves of the metal surface, whereas, in cantaloupe juice they attached to the smooth surface as well. Interestingly, Lm planktonic and biofilm cells in cantaloupe juice showed an elongated cell shape which might be a stress-induced phenotype in cantaloupe juice. Cantaloupe juice induced a distinct transcriptional profile of biofilm and planktonic cells of Lm from TSB. Functional annotation indicated that the significantly differentially expressed genes (DEGs, Padj < 0.05, log2foldchange ≥ 1) from the comparison mainly participated in metabolism, signaling and stress response. Notably, certain pathways downregulated for planktonic cells were significantly upregulated for biofilm cells in cantaloupe juice compared to TSB, including ABC transporters, two-component system, quorum sensing, chemotaxis, and flagellar assembly. These data highlighted the interaction of Lm with food matrix (i.e., cantaloupe) and the role of food matrix on Lm survival and adaptation. These results provided the basis for future functional characterization of genes with potential roles in biofilm formation and persistence of Lm in cantaloupe juice, as well as for development of mitigation practices for Lm biofilms on produce and food contact surfaces.
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Project description:Pseudomonas aeruginosa is a pathogenic micro-organism responsible for many hospital-acquired infections. It is able to adhere to solid surfaces and develop an immobilised community or so-called biofilm. Many studies have been focusing on the use of specific materials to prevent the formation of these biofilms, but the reactivity of the bacteria in contact to surfaces remains unknown. In order to evaluate the impact of different materials on the physiology of Pseudomonas aeruginosa during the first stage of biofilm formation, i.e. adhesion, we investigated the total proteome of cells adhering to three materials: stainless steel, glass and polystyrene. Using tandem mass spectrometry performed at the PAPPSO proteomic platform, 930 proteins were identified, 70 of which were differentially expressed between the materials. Dysregulated proteins belonged to 19 PseudoCAP (Pseudomonas Community Annotation Project) functional classes, with a particular abundance of proteins involved in small molecule transport and membrane proteins. Notably, ten porins or porin precursors were under-produced in bacteria adhering to stainless steel when compared to those adhering to polystyrene and glass. Although adhesion to solid surfaces is an extracellular phenomenon, it involves not only extracellular proteins but also intracellular reactions, as observed with the dysregulation of 11 proteins involved in various metabolisms and five in protein translation. Overall, this work showed that during bacterial adhesion, P. aeruginosa senses the materials concerned and is able to modulate its physiology accordingly.
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Project description:Previously, we performed DNA array-based transcriptomic analysis of Clostridium acetobutylicum biofilm adsorbed onto fibrous matrix in batch fermentation. Here, to further shed light on the transcriptomic modulation of maturing Clostridium acetobutylicum biofilm, we performed the DNA array-based transcriptomic analysis in repeated-batch fermentation. Significant time course changes in expression levels were observed for the genes involved in amino acid metabolism, oligopeptide ABC transporter, nitrogen fixation, and various other processes.
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Project description:Microbial biofilms are omnipresent and implicated in a wide spectrum of areas ranging from bioremediation, food production and biomedical applications. To date little is understood about how biofilm communities develop and function on a molecular level, due to the complexity of these biological systems. Here we ap-ply a meta-proteomics approach to investigate the mechanism driving biofilm formation in a microbial model consortium of four bacterial soil isolates of Steno-trophomonas rhizophila, Xanthomonas retroflexus, Microbacterium oxydans and Paeni-bacillus amylolyticus. The protein abundances between community and the single species biofilms were compared to describe how different metabolic pathways were influenced by inter-species interactions. Our results indicate that community development is dependent on interactions between community members facilitat-ing surface attachment and cross-feeding on specific amino acids. Opposite regu-lation patterns of fermentation and nitrogen pathways in Paenibacillus amylolyticus and Xanthomonas retroflexus may, however, also indicate that competition for lim-ited resources affects community development. Overall our results demonstrate the multitude of pathways characterizing biofilm formation in mixed communities. In order to obtain full taxonomic resolution between closely related species and empower correct protein quantification, we developed a novel pipeline for removing peptide sequences shared between community members from the ref-erence proteomes used for spectral database searches. This pipeline can readily be applied to other microbial communities.
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