Ontology highlight
ABSTRACT:
PROVIDER: PRJNA679426 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13120350.fastq.gz | Fastqsanger.gz |
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Project description:Multispecies biofilms are the predominant form of bacterial growth in natural and human-associated environments. Although the pathways involved in monospecies biofilm have been well characterized, less is known about the metabolic pathways and emergent traits of a multispecies biofilm community. Here, we performed a transcriptome survey of the developmental stages of a 3-species biofilm community and combined it with quantitative imaging and growth experiments. We report the remodelling of central metabolism of two of the three species in this community. Specifically, we observed an increase in the expression of genes associated with glycolysis and pentose phosphate pathways in K. pneumoniae. Similarly, a decrease in the expression of the same pathways in P. protegens was observed along with an increase in expression of glyoxalate cycle genes when grown as a mixed species biofilm, suggesting reorganisation of metabolic pathways and metabolite sharing for the community biofilms. To test the possibility of cross-feeding for the community, planktonic growth experiments revealed that both the Pseudomonads grew well in TCA cycle intermediates, while K. pneumoniae grew poorly when given those carbon sources. Despite this poor growth in mono-culture, K. pneumoniae was still the dominant species in mixed species biofilms cultivated in TCA intermediates as the sole source of carbon. The biofilm growth data, combined with the transcriptomics data, suggests there is reorganisation of metabolism for the community members and may allow for cross-feeding that allows K. pneumoniae to dominate the community. We also demonstrated that sdsA1 of P. aeruginosa was induced upon exposure to the surfactant SDS and that this gene was essential in protecting mono and mixed species biofilms from surfactant stress. This also suggests that the community members can share defence mechanisms. Overall, this study describes a comprehensive transcriptomics level investigation of shared resources, metabolites and stress defence that may underpin the emergent properties of mixed species biofilm communities.
2022-10-07 | GSE214543 | GEO
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.
2023-09-18 | GSE243459 | GEO
Project description:Stainless steel biofilm
| PRJEB49170 | ENA
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.
2018-10-24 | PXD006881 | Pride
Project description:Anode-associated multi-species exoelectrogenic biofilms are essential to the function of bioelectrochemical systems (BESs). The investigation of electrode-associated biofilms is critical to advance understanding of the function of individual members within communities that thrive using an electrode as the terminal electron acceptor. This study focusses on the analysis of a model biofilm community consisting of Shewanella oneidensis, Geobacter sulfurreducens and Geobacter metallireducens. The conducted experiments revealed that the organisms can build a stable biofilm on an electrode surface that is rather resilient to changes in the redox potential of the anode surface. The community operated at maximum electron transfer rates with electrode potentials of 0.04 V versus normal hydrogen electrode. Current densities decreased gradually with lower potentials and reached half-maximal values at -0.08 V. A positive interaction of the individual strains could be observed in our experiments. At least S. oneidensis and G. sulfurreducens show an upregulation of their central metabolism as a response to cultivation under mixed-species conditions. Interestingly, G. sulfurreducens was detected in the planktonic phase of the bioelectrochemical reactors only in mixed-culture experiments but not when it was grown in the absence of the other two organisms. It is possible that G. sulfurreducens cells used flavins which were released by S. oneidensis cells as electron shuttles. This would allow the organism to broaden its environmental niche. To the best of our knowledge, this is the first study describing the dynamics of biofilm formation of a model exoelectrogenic community, the resilience of the biofilm, and the molecular responses towards mixed-species conditions.
2017-01-18 | GSE79750 | GEO
Project description:Biofilms undergo a life cycle where cells attach to a surface, grow and produce a structured community before dispersing to seed biofilms in new environments. Progression through this life cycle requires controlled temporal gene expression to maximise fitness at each stage. Previous studies have focused on the essential genome for the formation of a mature biofilm, but here we present an insight into the genes involved at different stages of biofilm formation. We used TraDIS-Xpress (a massively parallel transposon mutagenesis using transposon-located promoters to assay expression of all genes in the genome) to determine how gene essentiality and expression affects the fitness of E. coli growing as a biofilm on glass beads after 12, 24 and 48 hours. An E. coli transposon mutant library of approximately 800,000 unique mutants was grown on glass beads, and a planktonic sample was taken alongside this at each time point to compare gene essentiality and expression at each time point.
2021-06-09 | E-MTAB-9873 | biostudies-arrayexpress