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699 results for “Biofilms”
Social evolution of shared biofilm matrix components
<p>Biofilm formation is an important and ubiquitous mode of growth among bacteria. Central to the evolutionary advantage of biofilm formation is cell-cell and cell-surface adhesion achieved by a variety of factors, some of which are diffusible compounds that may operate as classical public goods – factors that are costly to produce but may benefit other cells. An outstanding question is how diffusible matrix production, in general, can be stable over evolutionary timescales. In this work, using Vibrio cholerae as a model, we show that shared diffusible biofilm matrix proteins are indeed susceptible to cheater exploitation, and that the evolutionary stability of producing these matrix components fundamentally depends on biofilm spatial structure, intrinsic sharing mechanisms of these components, and flow conditions in the environment. We further show that exploitation of diffusible adhesion proteins is localized within a well-defined spatial range around cell clusters that produce them. Based on this exploitation range and the spatial distribution of cell clusters, we construct a model of costly diffusible matrix production and relate these length scales to the relatedness coefficient in social evolution theory. Our results show that production of diffusible biofilm matrix components is evolutionarily stable under conditions consistent with natural biofilm habitats and host environments. We expect the mechanisms revealed in this study to be relevant to other secreted factors that operate as cooperative public goods in bacterial communities, and the concept of exploitation range and the associated analysis tools to be generally applicable.</p>
Diversity, adaptation and metabolic potential of the microbiome in biofilms from a high-temperature hot spring
<p>Hot spring microbiomes have garnered significant research attention from exploring the diversity of prokaryotic communities to genes and functional potentials. While cyanobacteria-rich biofilms, characterized by warm temperatures, have been extensively studied, there is limited investigation into high-temperature streamer biofilm communities (SBC) devoid of photosynthetic ability. Here, we studied the biofilm of a Dusun Tua (DT) hot spring with a temperature of 75°C and a pH of 7.6. This grey-tan colored biofilm appeared at sites where water had slowed down following the deposition of plants and inorganic debris along the hot spring after a flood event. Amplicon sequencing of V3-V4 regions of 16S rRNA showed that dominant phyla included the Aquificota, Chloroflexota, and Desulfobacterota together with other abundant amplicon sequence variants from the Bacteroidota, Deinococcota, Hydrothermae and Armatimonadota. These microbial populations appeared to be distinct from other reported SBCs from Yellowstone National Park in the USA and Rehai Hot Springs in China. Additional shotgun sequencing of the DT biofilm revealed functional insights which were compared to counterparts obtained from low-temperature biofilms to identify possible thermophilic traits. GC content of tRNA and amino acid preferences were found to be clear indicators of thermophilicity. However, other signatures such as reverse gyrase, heat shock proteins, and average GC content of the genome may not be reliable indicators. The genome-centric analyses revealed that DT biofilm members were primarily chemo-organoheterotrophic, chemolithoautotrophic, and chemolithoheterotrophic. We speculate that the biofilm could utilize plant litter as carbon sources, but the efficiency of this process is estimated to be low due to rapid water flux that would rapidly remove dissolved organic carbon. The results of this study enhance current understanding of microbial diversity, thermal adaptation and metabolic processes related to carbon, nitrogen, sulfur and other metabolisms for hot springs in tropical climates with high allochthonous plant litter inputs.</p>
Raw and analyzed data for manuscript "In vitro eradication of Candida albicans biofilm through cold atmospheric plasma: Unravelling the interdependence of exposure and voltage in the antifungal mode of action."
<p><strong><span>Raw and analysed data for the manuscript, to be submitted to Journal of Infection and Public Health.</span></strong></p> <p> </p> <p><strong><span>Abstract:</span></strong></p> <p><strong><span>Introduction:</span></strong><span> Since <em>Candida spp</em>.</span> <span>is the fourth leading cause of healthcare-associated infections globally, the need for novel antifungal agents is increasing among scientists. This study investigates the potential of cold atmospheric plasma for <em>C. albicans</em> biofilm treatment. <strong>Methods:</strong> Our research focused on <em>in vitro</em> <em>C. albicans</em> biofilm response to varying parameters of plasma application, specifically the impact of treatment duration and input voltage. Evaluation of plasma influence on <em>C. albicans</em> was assessed with viability, membrane integrity, and oxidative stress measurements, along with observations of biofilm chemical composition and hyphae growth after plasma treatment. <strong>Results and Discussion:</strong> The higher plasma input voltage and increased exposure tme resulted in lower <em>C. albicans</em> cell viability, with complete reductions observed after 5 min plasma treatment duration across all input voltages tested. The effect of plasma treatment was further confirmed with a microscopic examination after BacLight<sup>® </sup>staining.</span> <span>Low (8 V) CAP exposure could potentially lead to a phenomenon known as hormesis, which was observed in <em>C. albicans</em> 24 h growth measurements. Additionally, intracellular oxidative stress assessment further proved that with prolonged treatment times, the intensity of oxidative stress, increased. Plasma treatment also affected the hyphae, which exhibited signs of contraction and compression. The chemical characteristics revealed that increasing plasma voltage and exposure time also have a distinguished impact on lipids, proteins, and carbohydrates, typical constituents of fungi biofilms. <strong>Conclusion:</strong> This study underscores the potential of plasma as a promising approach in combating <em>Candida spp</em>. biofilms, shedding light on the intricate dynamics of its impact on biofilm viability, morphology and composition.</span></p>
Demo dataset for code to quantify the 3D biofilm biovolume in images
<p>This dataset contains the raw and analyzed images that can be used as a test/demo dataset for running the code to compute the 3D biofilm biovolume. The code is stored on this Gitlab repository: https://github.com/knutdrescher/biofilm-3D-biovolume </p>
Data set "Correlation of in vitro biofilm formation capacity with persistence of antibiotic-resistant Escherichia coli on fresh leafy produce"
<p>This repository contains the metadata and raw data for the analysis of an <em>in vitro </em>screening of 174 antibiotic-resistance E. coli strains isolated from various sources to evaluate their ability and strength to form biofilms.</p> <p>This repository contains the raw data to characterise a subset of eleven <em>E. coli </em>strains in their population dynamics and persistance on lamb's lettuce (<em>Valerianella locusta</em>) leaves.</p> <p>Raw images (czi format) of live/dead stain of selected strains in <em>V. locusta </em>leaves are provided.</p> <p>Data analysis and image processing scripts can be found in the GitHub repository associated to the manuscript.</p>
Dataset for manuscript entitled "The effects of a synthetic and biological surfactant on the community composition and metabolic activity of a freshwater biofilm"
<p>The following datasets were used for the 16s rRNA analysis in the manuscript entitled " The effects of a synthetic and biological surfactant on the community composition and metabolic activity of a freshwater biofilm". BZ2 files were obtained from next generation sequencing with the Illumina Mi-Seq. Mothur was used to analyze the BZ2 files, creating the listed excel documents.</p>
Data for Rhamnolipids mediate the effects of a gastropod grazer in regards to carbon-nitrogen stoichiometry of intertidal microbial biofilms
<p>Data for the manuscript: <strong>Rhamnolipids mediate the effects of a gastropod grazer in regards to carbon-nitrogen stoichiometry of intertidal microbial biofilms. </strong></p>
Data from: eDNA-stimulated cell dispersion from Caulobacter crescentus biofilms upon oxygen limitation is dependent on a toxin-antitoxin system
<p><span>In their natural environment, most bacteria preferentially live as complex surface-attached multicellular colonies called biofilms. Biofilms begin with a few cells adhering to a surface, where they multiply to form a mature colony. When conditions deteriorate, cells can leave the biofilm. This dispersion is thought to be an important process that modifies the overall biofilm architecture and that promotes colonization of new environments. In <em>Caulobacter crescentus</em> biofilms, extracellular DNA (eDNA) is released upon cell death and prevents newborn cells from joining the established biofilm. Thus, eDNA promotes the dispersal of newborn cells and the subsequent colonization of new environments. These observations suggest that eDNA is a cue for sensing detrimental environmental conditions in the biofilm. Here we show that </span><span>the toxin-antitoxin system (TAS) <em>ParDE<sub>4</sub></em> stimulates cell death in areas of a biofilm with decreased O<sub>2</sub> availability. In conditions where O<sub>2</sub> availability is low, eDNA concentration is correlated with cell death. Cell dispersal away from biofilms is decreased when <em>parDE<sub>4</sub></em> is deleted, probably due to the lower local eDNA concentration. Expression of <em>parDE<sub>4</sub></em> is positively regulated by O<sub>2</sub> and the expression of this operon is decreased in biofilms where O<sub>2</sub> availability is low. Thus, a programmed cell death mechanism using an O<sub>2</sub>-regulated TAS stimulates dispersal away from areas of a biofilm with decreased O<sub>2</sub> availability and favors colonization of a new, more hospitable environment. </span></p>
Disturbing the spatial structure of biofilms affects the expression of agr regulated virulence factors in Staphylococcus aureus
<p><em>Staphylococcus aureus</em> uses quorum sensing and nutrient availability to control the expression of <em>agr</em>-regulated virulence factors. Quorum sensing is mediated by autoinducing peptide (AIP), which at high concentration, reduces expression of surface attachment proteins (<em>coa</em>, <em>fnbpA</em>), and increases expression of exotoxins (<em>lukS</em>) and proteases (<em>splA</em>). Nutrient availability can be sensed through the <em>saeS</em>/<em>saeR</em> system. Low nutrients increase expression of <em>saeR</em>, which augments expression of <em>coa</em> and <em>fnbpA</em> distinct from AIP. The formation of spatial structure, such as biofilms, can alter quorum sensing and nutrient acquisition. In natural environments, biofilms encounter forces that may alter their spatial structure. This may impact quorum sensing and/or nutrient acquisition, and thus affect the expression of <em>agr</em>-regulated virulence factors. However, this has not been studied. We show that periodically disturbing biofilms composed of <em>S. aureus</em> using a physical force affects the expression of <em>agr</em>-regulated virulence factors. In nutrient-poor environments, disturbance increased the expression of <em>coa</em>, <em>fnbpA</em>, <em>lukS</em>, and <em>splA</em>. Disturbance into a nutrient-rich environment at low or high disturbance amplitudes moderately reduced expression of <em>coa</em> and <em>fnbpA</em> but increased expression of <em>lukS</em> and <em>splA</em>. Interestingly, at an intermediate amplitude, the overall expression of <em>agr-</em>regulated virulence factors was the lowest; expression of <em>lukS</em> and <em>splA</em> remained unchanged relative to an undisturbed biofilm while expression of <em>coa</em> and <em>fnbpA</em> significantly decreased. We hypothesize that these changes are a result of disturbance-driven changes in access to AIP and nutrients. Our results may allow the identification of environments where virulence is enhanced, or reduced, owing to disturbance.</p>
Dataset of paper "Growth and prevalence of antibiotic-resistant bacteria in microplastic biofilm from wastewater treatment plant effluents"
<p>Dataset of paper "Growth and prevalence of antibiotic-resistant bacteria in microplastic biofilm from wastewater treatment plant effluents":</p> <ul> <li>Raw 16srRNA forward and reverse sequence data</li> <li>16srRNA partial sequence data for submission to public database</li> <li>Nucleotide BLAST result from National Centre of Biotechnology Information (NCBI) database</li> <li>Summary of sample metadata and bacterial colony forming units (CFUs)</li> <li>Summary of sample metadata and quantified genes</li> </ul>
Spatial Mapping and Host Linking of Mobile Genetic Elements in Complex Microbiomes - Mapping MGEs in oral plaque biofilms at high specificity
<p>We stained for the GFP gene in samples that contained mixtures of plaque and GFP-transformed E. coli. We mapped mefE, an AMR gene located on a plasmid and encoding an antibiotic efflux pump, in the plaque metagenomic data of volunteer A but not volunteer B. To test the efficacy of gel embedding and clearing, we used orthogonal FISH probes, designed to not target any sequence in the plaque. We identified a T7-like prophage via metagenomic analysis and developed probes targeting its capsB gene, which encodes the minor capsid protein. We identified a highly prevalent prophage of the class Caudoviricetes with a large terminase gene, termL, and were able to design a large set of FISH probes to stain in three different colors simultaneously. We identified three non-plasmid AMR genes within metagenome assembled genomes: patA, patB, and adeF.</p>
Data for: Extensive cellular multi-tasking within Bacillus subtilis biofilms
<p><em>Bacillus subtilis</em> is a soil-dwelling bacterium that can form biofilms, or communities of cells surrounded by a self-produced extracellular matrix. In biofilms, genetically identical cells often exhibit heterogeneous transcriptional phenotypes, so that subpopulations of cells carry out essential yet costly cellular processes that allow the entire population to thrive. Surprisingly, the extent of phenotypic heterogeneity and the relationships between subpopulations of cells within biofilms of even in well-studied bacterial systems like <em>B. subtilis</em> remains largely unknown. To determine relationships between these subpopulations of cells, we created 182 strains containing pairwise combinations of fluorescent transcriptional reporters for the expression state of 14 different genes associated with potential cellular subpopulations. We determined the spatial organization of the expression of these genes within biofilms using confocal microscopy, which revealed that many reporters localized to distinct areas of the biofilm, some of which were co-localized. We used flow cytometry to quantify reporter coexpression, which revealed that many cells "multi-task," simultaneously expressing two reporters. These data indicate that prior models describing <em>B. subtilis</em> cells as differentiating into specific cell types, each with a specific task or function, were oversimplified. Only a few subpopulations of cells, including surfactin and plipastatin producers, as well as sporulating and competent cells, appear to have distinct roles based on the set of genes examined here. These data will provide us with a framework with which to further study and make predictions about the roles of diverse cell phenotypes in <em>B. subtilis </em>biofilms.</p>
Data from: Biofilms as self-shaping growing nematics
<p>Active nematics are the nonequilibrium analog of passive liquid crystals in which anisotropic units consume free energy to drive emergent behavior. Similar to liquid crystal (LC) molecules in displays, ordering and dynamics in active nematics are sensitive to boundary conditions; however, unlike passive liquid crystals, active nematics, such as those composed of living matter, have the potential to regulate their boundaries through self-generated stresses. Here, using bacterial biofilms confined by a hydrogel as a model system, we show how a three-dimensional, living nematic can actively shape itself and its boundary in order to regulate its internal architecture through growth-induced stresses. We show that biofilms exhibit a sharp transition in shape from <em>domes</em> to <em>lenses</em> upon changing environmental stiffness or cell-substrate friction, which is explained by a theoretical model considering the competition between confinement and interfacial forces. The growth mode defines the progression of the boundary, which in turn determines the trajectories and spatial distribution of cell lineages. We further demonstrate that the evolving boundary defines the orientational ordering of cells and the emergence of topological defects in the interior of the biofilm. Our findings reveal novel self-organization phenomena in confined active matter and provide strategies for guiding the development of programmed microbial consortia with emergent material properties.</p>
Biofilm formation and plasmid-mediated quinolone resistance genes at varying quinolone inhibitory concentrations in quinolone-resistant bacteria superinfecting COVID-19 inpatients
<p>The likelihood of treatment failure in COVID-19 patients with bacterial superinfection stems from phenotypic, viz., biofilms, and genotypic mechanisms. This cross-sectional study aimed to determine the inhibitory concentrations of quinolones—nalidixic acid, norfloxacin, ciprofloxacin, ofloxacin, and levofloxacin—in biofilm formers [minimum biofilm inhibitory concentration (MBIC)] and non-formers [minimum inhibitory concentration (MIC)] as well as correlate the quinolones' folds with the presence of plasmid-mediated quinolone-resistance (PMQR) genes in quinolone-resistant bacteria isolated from COVID-19 inpatients. Quinolone-resistant isolates (n=193), verified through disc diffusion, were tested for quinolone inhibitory concentrations and biofilm formation with broth microdilution and microtiter plate methods, respectively. Polymerase chain reaction was used to detect PMQR genes. MIC to MBIC median increase in folds for ciprofloxacin, ofloxacin, and levofloxacin was 128 (2-8,192), 64 (4-1,024), and 32 (4-512) in gram-positive cocci (GPC), respectively, while it was 32 (4-8,192), 32 (4-2,048), and 16 (2-1,024) in fermentative-gram-negative bacilli (F-GNB), and 16 (4-4,096), 64 (2-64), and 16 (8-512) in non-fermentative-gram-negative bacilli (NF-GNB). Biofilm-forming F-GNB (32/126) and NF-GNB (10/24) harbored <em>qnrB</em> [11/32 versus (vs.) 3/10], <em>aac(6')-Ib-cr </em>(10/32 vs. 4/10), and <em>qnrS</em> (9/32 vs. 0/10) genes, respectively. A 32-fold median increase in ciprofloxacin was significantly associated with <em>qnrA</em> and <em>qnrS</em> in F-GNB and NF-GNB, respectively. F-GNB and NF-GNB biofilms were significantly associated with <em>aac(6')-Ib-cr</em> and <em>qnrS</em> genes, respectively. Nearly one-third of the superinfecting bacteria in COVID-19 patients formed biofilms, and had at least one PMQR gene, increasing the need for quinolone inhibitory concentrations.</p>
Lateral interactions govern self-assembly of the bacterial biofilm matrix protein BslA (experimental and simulation data)
<p>The soil bacterium Bacillus subtilis is a model organism to investigate the formation of biofilms, the predominant form of microbial life. The secreted protein BslA self-assembles at the surface of the biofilm to give the B. subtilis biofilm its characteristic hydrophobicity. To understand the mechanism of BslA self-assembly at interfaces, here we built a molecular model based on the previous BslA crystal structure and the newly determined crystal structure of the BslA paralogue YweA. Our analysis revealed two conserved protein-protein interaction interfaces supporting BslA self-assembly into an infinite 2d lattice that fits previously determined transmission microscopy images. Molecular dynamics simulations and in vitro protein assays further support our model of BslA elastic film formation, while mutagenesis experiments highlight the importance of the identified interactions for biofilm structure. Based on this knowledge, YweA was engineered to form more stable elastic films and rescue biofilm structure in bslA deficient strains. These findings shed new light on protein film assembly and will inform the development of BslA technologies which range from surface coatings to emulsions in fast-moving consumer goods.</p>
Data from: Clinical antibiotic-resistance plasmids have small effects on biofilm formation and population growth in Escherichia coli in vitro
<div> <div> <div> <p>Antimicrobial resistance (AR) mechanisms encoded on plasmids can affect other phenotypic traits in bacteria, including biofilm formation. These effects may be important contributors to the spread of AR and the evolutionary success of plasmids, but it is not yet clear how common such effects are for clinical plasmids/bacteria, and how they vary among different plasmids and host strains. Here, we used a combinatorial approach to test the effects of clinical AR plasmids on biofilm formation and population growth in clinical and laboratory Escherichia coli strains. In most of the 25 plasmid-bacterium combinations tested, we observed no significant change in biofilm formation upon plasmid introduction, contrary to the notion that plasmids frequently alter biofilm formation. In a few cases we detected altered biofilm formation, and these effects were specific to particular plasmid-bacterium combinations. By contrast, we found a relatively strong effect of a chromosomal streptomycin-resistance mutation (in rpsL) on biofilm formation. Further supporting weak and host-strain- dependent effects of clinical plasmids on bacterial phenotypes in the combinations we tested, we found growth costs associated with plasmid carriage (measured in the absence of antibiotics) were moderate and varied among bacterial strains. These findings suggest some key clinical resistance plasmids cause only mild phenotypic disruption to their host bacteria, which may contribute to the persistence of plasmids in the absence of antibiotics.</p> </div> </div> </div>
Dynamic social interactions and keystone species shape the diversity and stability of mixed-species biofilms – an example from dairy isolates - Dataset
<p>We previously reported a bacterial four-species biofilm model comprising <i>Stenotrophomonas rhizophila </i>(SR), <i>Bacillus licheniformis </i>(BL), <i>Microbacterium lacticum </i>(ML), and <i>Calidifontibacter indicus</i> (CI) that were isolated from the surface of a dairy pasteuriser after cleaning and disinfection. These bacteria produced 3.13-fold more biofilm mass compared to the sum of biofilm masses in monoculture (<a href="https://doi.org/10.3389/fmicb.2023.1159434">https://doi.org/10.3389/fmicb.2023.1159434</a>). In a subsequent experiment we confirmed that the observed community synergy resulted from dynamic social interactions among various species pairs, encompassing commensalism, exploitation, and amensalism. <i>M. lacticum</i> appeared to be the keystone species as it increased the growth of all other species that led to the synergy in biofilm mass. Interactions among the other three species (in the absence of <i>M. lacticum</i>) also contributed towards the synergy in biofilm mass. Bacterial cell-free-supernatants were also investigated to assess the nature of the observed synergy. The first four sheets of the Excel file contain raw cell count data for the four species (SR, BL, ML, and CI), recorded every 4 h over a 24 h period on the surface of stainless steel (SS) in the presence of brain-heart-infusion (BHI) medium and skim-milk (SM). Data related to individual bacterial cell counts in various mixed-species biofilms are also presented. These biofilms were developed on SS in BHI for h. Data related to bacterial biofilm masses in different mixed-species biofilm combinations are also presented, showcasing the effect of replacing one strain with its CFS. Species written in red indicate that their CFS was used, not their viable form. </p>
Larval Debridement Therapy Versus Sharp Debridement to Remove Biofilm
ClinicalTrials.gov study NCT02294175. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Confocal images for Mycobacteria biofilm from: Lipoarabinomannan regulates septation in Mycobacterium smegmatis
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A temporary cholesterol-rich diet and bacterial extracellular matrix factors favor Salmonella spp. biofilm formation in the cecum
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OpenNeuro
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