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opencc-by-4.0Sep 2022View details →

Shared biophysical mechanisms determine early biofilm architecture development across different bacterial species

These data are the numerical values that underlie the Figures 1 - 4, and the Supplementary Figures 1 - 10 for the article "Shared biophysical mechanisms determine early biofilm architecture development across different bacterial species" by the same authors. The content of the data files is organized according to the figures and figure panels of this article.

opencc-by-4.0Mar 2023View details →

SI Figure 4: SEM images of either unwashed (left) or washed (right) E. antarcticus nematodes. A. Unwashed head region with arrows pointing to attached material and possible fungal hyphae. B. Washed head region with arrows pointing to the remaining attached material. C. Unwashed annules with arrows pointing to commonly attached foreign material. D. Washed annules with arrows pointing to remaining attached material. E. Unwashed somatic pore with arrows pointing to the common organic material. F. Washed vulva with an arrow pointing to remaining attached organic material. G. Unwashed cuticle with arrows showing a possible biofilm. H. Washed cuticle showing single attached cells indicated with arrows. I. Unwashed cuticle showing an off-axis line of attached material. J. Washed cuticle showing a similar off-axis line of material (as indicated with arrow) but reduced in quantity compared to the unwashed. in External and internal microbiomes of Antarctic nematodes are distinct, but more similar to each other than the surrounding environment

SI Figure 4: SEM images of either unwashed (left) or washed (right) E. antarcticus nematodes. A. Unwashed head region with arrows pointing to attached material and possible fungal hyphae. B. Washed head region with arrows pointing to the remaining attached material. C. Unwashed annules with arrows pointing to commonly attached foreign material. D. Washed annules with arrows pointing to remaining attached material. E. Unwashed somatic pore with arrows pointing to the common organic material. F. Washed vulva with an arrow pointing to remaining attached organic material. G. Unwashed cuticle with arrows showing a possible biofilm. H. Washed cuticle showing single attached cells indicated with arrows. I. Unwashed cuticle showing an off-axis line of attached material. J. Washed cuticle showing a similar off-axis line of material (as indicated with arrow) but reduced in quantity compared to the unwashed.

opencc-by-4.0Dec 2022View details →

Figure 1 in Effect of Mauritia flexuosa L. leaf extract on Staphylococcus aureus and Staphylococcus haemolyticus biofilms adhered to stainless steel surface

Figure 1. Gas chromatographic profile of extracts from Mauritia flexuosa L. leaves. (A) Ethanolic extract and (B) Aqueous extract. The peaks numbers correspond to the phenolic compounds and carbohydrates listed in Table 1.

opencc-by-4.0Mar 2018View details →

Quantifying biostabilisation effects of biofilm-secreted and extracted extracellular polymeric substances (EPS) on sandy substrate

This dataset provides the data underlying the manuscript Quantifying biostabilisation effects of biofilm-secreted and extracted extracellular polymeric substances (EPS) on sandy substrate published in Earth Surface Dynamics - an interactive open-access journal of the European Geosciences Union. The work was conducted in the Total Environment Simulator at the University of Hull as part of Task 9.3 of the Hydralab+ inititiative.  Microbial assemblages ('biofilms') preferentially develop at water-sediment interfaces and are known to have a considerable influence on sediment stability and erodibility. There is potential for significant impacts on sediment transport and morphodynamics and, hence, on the longer-term evolution of coastal and fluvial environments. However, the biostabilisation effects remain poorly understood and quantified due to the inherent complexity of biofilms and the large spatial and temporal (i.e. seasonality) variations involved. Here, we use controlled laboratory tests to systematically quantify the effects of natural biofilm colonisation as well as extracted extracellular polymeric substances (EPS) on sediment stability. Extracted EPS may be useful to simulate biofilm-mediated biostabilisation, and potentially provides a method of speeding up time scales of physical modelling experiments investigating biostabilisation effects. We find a mean biostabilisation effect due to natural biofilm colonisation and development of almost four times that of the uncolonised sand. The presented cumulative probability distribution of measured critical threshold for erosion of colonised sand reflects the large spatial and temporal variations generally seen in natural biostabilised environments. For identical sand, engineered sediment stability from the addition of extracted EPS compares well across the measured range of the critical threshold for erosion and behaves in a linear and predictable fashion. Yet, the effectiveness of extracted EPS to stabilise sediment is sensitive to the preparation procedure, time after application and environmental conditions such as salinity, pH and temperature. These findings are expected to improve bio-physical experimental models in fluvial and coastal environments and provide much-needed quantification of biostabilisation to improve predictions of sediment dynamics in aquatic ecosystems.

opencc-by-4.0Dec 2018View details →

Erosion threshold and mode of failure of biofilm surrogates

This dataset provides the raw data from laboratory experiments investigating the failure mechanisms and erosion thresholds of surrogate biofilms. The experiments were conducted as part of HYDRALAB+ JRA 1 RECIPE. More than 60 erosion experiments were carried out at the FZK (Forschungszentrum Küste) using different mixtures of Xanthan Gum and sand fractions.

Figure 10. A in Epilithic biofilms of the Eastern Caspian (Aktau region, Kazakhstan) under conditions of falling sea level

Figure 10. A thin biofilm that has practically grown into the surface of crumbling sandstone in the abrasive section of an open pseudolittoral (a). Fragment of colonial settlment by Halamphora borealis (b). Scale bars: a — 5 cm, b — 10 µm. Photos by Philipp Sapozhnikov, Olga Kalinina.

Figure 9 in Epilithic biofilms of the Eastern Caspian (Aktau region, Kazakhstan) under conditions of falling sea level

Figure 9. Fragment of cheesy ("moss") biofilm (a) on flat blocks of sandstone, in the middle pseudolittoral zone. Mixed colonial settlements of Halamphora coffeaeformis and H. hybrida (b, c) growing in the form of "clouds" (flakes) on Enteromorpha filaments. Designations: h — cells of various species of Halamphora, ep — cell of Entomoneis paludosa. Puddles of the upper pseudolittoral, April 2023. Scale bar: a – 5 cm, b – 100 µm, c – 25 µm. Photos by Philipp Sapozhnikov.

Figure 3 in Epilithic biofilms of the Eastern Caspian (Aktau region, Kazakhstan) under conditions of falling sea level

Figure 3. Map of microepiliton sampling points in various coastal locations in the city of Aktau: a - map of the Caspian Sea with a highlighted area of the coast of the Mangystau region, b - section of the coast of the Mangystau region with a highlighted area of the city of Aktau, c - coast in the area of the city of Aktau and its immediate suburbs, d - locations of sampling in October 2022, e - locations of sampling in April 2023.

Figure 1. A in Epilithic biofilms of the Eastern Caspian (Aktau region, Kazakhstan) under conditions of falling sea level

Figure 1. A view of the impact of the wind waves on the newly dry bottom at the shoreline in the center of Aktau on 20 October 2022. Photo by Andrey Kostianoy.

opencc-by-4.0Jun 2024View details →

Curation of Vibrio biofilm matrix cluster and associated proteins

The supplementary data and other supporting materials for the paper titled "Comprehensive Genomic and Evolutionary Analysis of Biofilm Matrix Clusters and Proteins in the Vibrio Genus".

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Radial topographies of biofilm colonies

During the biofilm life cycle, bacteria attach to a surface and then reproduce, forming crowded, growing communities. Difficulties in accurately measuring biofilm height across relevant time and length scales have prevented testing diverse biophysical models empirically. Using white light interferometry, we measure the heights of microbial colonies with nanometer precision from inoculation to their final equilibrium height, producing a novel and detailed empirical characterization of vertical growth dynamics. This dataset corresponds to the profiles of developing biofilms, measured through white-light interferometry. This dataset represents novel high-resolution characterizations of developing biofilms in the vertical direction, empirical measurements that can be utilized to test models for biofilm development, ranging from bulk-dynamics to surface fluctuations.

opencc-zeroFeb 2023View details →

opencc-by-4.0Aug 2022View details →

Single cell annotations in 3D bacterial biofilms of Vibrio cholerae

This repository contains the data to reproduce the study `Single-cell segmentation in bacterial biofilms with optimized convolutional neural networks enables tracking of cell lineages and measurements of growth rates` by Jelli, Ohmura, Netter, et al. It contains the following four subfolders:   - `training-data-from-experimentally-acquired-images`: the dataset that was created to train segmentation models - `trained-models`: contains five models trained on the trainind dataset to be used for predictions - `segmentation-predictions-for-different-species`: segmentations based on a trained model on biofilms of different species - `training-data-synthetic`: Synthetic microscope images and their corresponding label images together with scripts to create the data

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Supporting isotopic data for: Differential utilization of submerged leaf litter by microbial biofilms and macroinvertebrates in a large dryland river

Open the record for dataset details and reuse information.

publicOct 2025View details →

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Radial topographies of biofilm colonies

Open the record for dataset details and reuse information.

publicFeb 2023View details →

opencc-by-4.0Dec 2019View details →

Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms

Data extracted from confocal microscopy associated with the paper "Stochastic pulsing of gene expression enables the generation of spatial patterns in Bacillus subtilis biofilms" Stochastic pulsing of gene expression can generate phenotypic diversity in a genetically identical population of cells, but it is unclear whether it has a role in the development of multicellular systems. Here, we show how stochastic pulsing of gene expression enables spatial patterns to form in a model multicellular system, Bacillus subtilis bacterial biofilms. We use quantitative microscopy and time-lapse imaging to observe pulses in the activity of the general stress response sigma factor σB in individual cells during biofilm development. Both σB and sporulation activity increase in a gradient, peaking at the top of the biofilm, even though σB represses sporulation. As predicted by a simple mathematical model, increasing σB expression shifts the peak of sporulation to the middle of the biofilm. Our results demonstrate how stochastic pulsing of gene expression can play a key role in pattern formation during biofilm development.

opencc-by-4.0May 2020View details →

Phenotypic modulation of biofilm formation in a Staphylococcus epidermidis orthopedic clinical isolate grown under different mechanical stimuli: contribution from a combined proteomic study

One of the major causes of prosthetic joint failure is infection. Recently, coagulase negative Staphylococcus epidermidis has been identified as an emergent, nosocomial pathogen involved in subclinical prosthetic join infections (PJIs). The diagnosis of PJIs mediated by S. epidermidis is usually complex and difficulties due to the absence of acute clinical signs derived from the host immune system response. Therefore, analysis of protein patterns in biofilm-producing S. epidermidis allows for the examination of the molecular basis of biofilm formation. Thus, in the present study, the proteome of a clinical isolate S. epidermidis was analyzed when cultured in its planktonic or sessile form to examine protein expression changes depending on culture conditions. After 24 hours of culture, sessile bacteria exhibited increased gene expression for ribosomal activity and for expression of proteins related to the initial attachment phase, involved in the capsular polysaccharide/adhesin, surface associated proteins and peptidoglycan biosynthesis. Likewise, planktonic S. epidermidis was able to aggregate after 24 hours, synthesizing the accumulation associate protein and cell-wall molecules through the activation of the YycFG and ArlRS, two component regulatory pathways. Prolonged culture under vigorous agitation generated a stressful growing environment triggering aggregation in a biofilm-like matrix as a mechanism to survive harsh conditions. Further studies will be essential to support these findings in order to further delineate the complex mechanisms of biofilm formation of S. epidermidis and they could provide the groundwork for the development of new drugs against biofilm-related infections, as well as the identification of novel biomarkers of subclinical or chronic infections mediated by these emerging, low virulence pathogens.

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Disinfectant efficacy on mixed biofilms comprising Escherichia coli and spoilage microorganisms

This study aimed to investigate the impact of temperature and the presence of other microorganisms on the susceptibility of STEC to biocides. Mature biofilms were formed at both 10°C and 25°C. An inoculum of planktonic bacteria comprising 106 CFU/ml of spoilage bacteria and 103 CFU/ml of a single E. coli strain (O157, O111, O103, and O12) was used to form mixed biofilms. The following bacterial combinations were tested: T1: Carnobacterium piscicola + Lactobacillus bulgaricus +STEC, T2: Comamonas koreensis + Raoultella terrigena + STEC, and T3: Pseudomonas aeruginosa + C. koreensis + STEC. Tested biocides included quaternary ammonium compounds (Quats), sodium hypochlorite (Shypo), sodium hydroxide (SHyd), hydrogen peroxide (HyP), and BioDestroy®-organic peroxyacetic acid (PAA). Biocides were applied to 6-day-old biofilms. Minimum Bactericidal Concentrations (MBC) and Biofilm Eradication Concentrations (BEC) were determined. Planktonic cells and single-species biofilms exhibited greater susceptibility to sanitizers (P < 0.0001). Lactobacillus and Carnobacterium were more susceptible than the rest of the tested bacteria (P < 0.0001). Single species biofilms formed by E. coli O111, O121, O157, and O45 showed resistance (100%) to Shypo sanitizer (200 ppm) at 25°C. From the most effective to the least effective, sanitizer performance on single-species biofilms was PAA > Quats > HyP > SHyd > Shypo. In multi-species biofilms, spoilage bacteria within T1, T2, and T3 biofilms showed elevated resistance to SHyd (30%), followed by quats (23.25%), HyP (15.41%), SHypo (9.70%), and BioDestroy® (3.42%) (P < 0.0001). Within T1, T2, and T3, the combined STEC strains exhibited superior survival to Quats (23.91%), followed by HyP (19.57%), SHypo (18.12%), SHyd (16.67%), and BioDestroy® (4.35%) (P < 0.0001). O157:H7-R508 strains were less tolerant to Quats and Shypo when combined with T2 and T3 (P < 0.0001). O157:H7 and O103:H2 strains in mixed biofilms T1, T2, and T3 exhibited higher biocide resistance than the weak biofilm former, O145:H2 (P < 0.0001). The study shows that STEC within multi-species biofilms' are more tolerant to disinfectants.

opencc-zeroMar 2024View details →

opencc-by-4.0Nov 2021View details →

Code and data for 'Bacillus subtilis histidine kinase KinC activates biofilm formation by controlling heterogeneity of single-cell responses'

Code and data used in the paper 'Bacillus subtilis histidine  kinase KinC activates biofilm formation by controlling heterogeneity of single-cell responses'  https://doi.org/10.1128/mBio.01694-21

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The role of surface adhesion on the macroscopic wrinkling of biofilms

Biofilms, bacterial communities of cells encased by a self-produced matrix, exhibit a variety of three-dimensional structures. Specifically, channel networks formed within the bulk of the biofilm have been identified to play an important role in the colonies viability by promoting the transport of nutrients and chemicals. Here, we study channel formation and focus on the role of the adhesion of the biofilm matrix to the substrate in Pseudomonas aeruginosa biofilms grown under constant flow in microfluidic channels. We perform phase contrast and confocal laser scanning microscopy to examine the development of the biofilm structure as a function of the substrates surface energy. The formation of the wrinkles and folds is triggered by a mechanical buckling instability, controlled by biofilm growth rate and the film's adhesion to the substrate. The three-dimensional folding gives rise to hollow channels that rapidly increase the overall volume occupied by the biofilm and facilitate bacterial movement inside them. The experiments and analysis on mechanical instabilities for the relevant case of a bacterial biofilm grown during flow enable us to predict and control the biofilm morphology.

opencc-zeroDec 2021View details →