Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7230050.fastq.gz | Fastqsanger.gz | |||
| SRR7230060.fastq.gz | Fastqsanger.gz | |||
| SRR7230051.fastq.gz | Fastqsanger.gz | |||
| SRR7230061.fastq.gz | Fastqsanger.gz | |||
| SRR7230052.fastq.gz | Fastqsanger.gz |
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Project description:Multispecies biofilms consist of complex communities where extracellular polymeric substances (EPS) are vital in their structure, adaptability, and function. However, characterizing the components of EPS, particularly glycans and proteins, remains a challenge due to the diverse species and their interactions within the matrix. This study examined how interactions between different species affect EPS components' production and spatial organization. We utilized a consortium of four bacterial soil isolates that have previously demonstrated various intrinsic properties in biofilm communities: Microbacterium oxydans, Paenibacillus amylolyticus, Stenotrophomonas rhizophila, and Xanthomonas retroflexus. We used fluorescence lectin-binding analysis (FLBA) to identify specific glycan components and meta-proteomics to characterize matrix proteins in mono- and multispecies biofilms. Our results revealed diverse glycan structures and compositions, including fucose and different amino sugar-containing polymers, with substantial differences between monospecies and multispecies biofilms. In isolation, M. oxydans produced galactose/N-Acetylgalactosamine network-like structures and influenced the matrix composition in multispecies biofilms. Proteomic analysis revealed flagellin proteins in Xanthomonas and Paenibacillus, particularly in multispecies biofilms. Additionally, surface-layer proteins and a unique peroxidase were found in P. amylolyticus multispecies biofilms, indicating enhanced oxidative stress resistance and structural stability under these conditions. This study highlights the crucial role of interspecies interactions in shaping biofilm matrices and the production of glycans and proteins. These findings deepen our understanding of biofilm complexity and may lead to new approaches for controlling biofilms in various environments.
2025-03-31 | PXD057669 | Pride
Project description:The human protozoan parasiteEntamoeba histolyticais responsible for amebiasis, a disease endemic to developing countries.E. histolyticatrophozoites colonize the large intestine, primarily feeding on bacteria. However, in the GI, as well as in aquatic and soil microenvironments, bacterial cells form aggregates or structured communities, called biofilm, too large for phagocytosis. However, trophozoites are still able to invade and degrade bacteria under biofilm form by a mechanism mimicking digestive exophagy. E.histolytica cysteine proteinase degrade TasA, one of the main component of the biofilm matrix. Biofilm also play an important role protecting trophozoites against oxidative stress. The specific mechanism suggests that amoeba is adapted to biofilm predation and may serve as a new unexplored reservoir of novel therapeutic approaches to treat biofilms. Consistently, amoeba’s products restored antibiotic sensitivity to biofilm cells. Furthermore, our findings here show that probiotic biofilms may serve as a protective shield for mammalian cells, hindering the progression of the parasite towards them.
2023-10-25 | GSE233645 | GEO
Project description:Ravindra Garde, Bashar Ibrahim & Stefan Schuster. Extending the minimal model of metabolic oscillations in Bacillus subtilis biofilms. Scientific Reports 10, 1 (2020).
Biofilms are composed of microorganisms attached to a solid surface or floating on top of a liquid surface. They pose challenges in the field of medicine but can also have useful applications in industry. Regulation of biofilm growth is complex and still largely elusive. Oscillations are thought to be advantageous for biofilms to cope with nutrient starvation and chemical attacks. Recently, a minimal mathematical model has been employed to describe the oscillations in Bacillus subtilis biofilms. In this paper, we investigate four different modifications to that minimal model in order to better understand the oscillations in biofilms. Our first modification is towards making a gradient of metabolites from the center of the biofilm to the periphery. We find that it does not improve the model and is therefore, unnecessary. We then use realistic Michaelis-Menten kinetics to replace the highly simple mass-action kinetics for one of the reactions. Further, we use reversible reactions to mimic the diffusion in biofilms. As the final modification, we check the combined effect of using Michaelis-Menten kinetics and reversible reactions on the model behavior. We find that these two modifications alone or in combination improve the description of the biological scenario.
2024-09-02 | BIOMD0000001053 | BioModels
Project description:Biofilms offer an excellent example of ecological interaction among bacteria. Temporal and spatial oscillations in biofilms are an emerging topic. In this paper, we describe the metabolic oscillations in Bacillus subtilis biofilms by applying the smallest theoretical chemical reaction system showing Hopf bifurcation proposed by Wilhelm and Heinrich in 1995. The system involves three differential equations and a single bilinear term. We specifically select parameters that are suitable for the biological scenario of biofilm oscillations. We perform computer simulations and a detailed analysis of the system including bifurcation analysis and quasi-steady-state approximation. We also discuss the feedback structure of the system and the correspondence of the simulations to biological observations. Our theoretical work suggests potential scenarios about the oscillatory behaviour of biofilms and also serves as an application of a previously described chemical oscillator to a biological system.
2024-09-02 | BIOMD0000000932 | BioModels
Project description:We examined the differential gene expression of Staphylococcus epidermidis and Staphylococcus epidermidis in dual species biofilms. Therefore, we performed RNA-Seq on single and dual species biofilms and we compared the gene expression levels in dual species biofilms to those in single species biofilms.
2016-05-27 | GSE79575 | GEO
Project description:The physiological and transcriptional response of Nitrosomonas europaea biofilms to phenol and toluene was examined and compared to suspended cells. Biofilms were grown in Drip Flow Biofilm Reactors under continuous flow conditions of growth medium containing ammonia as growth substrate. The responses of N. europaea biofilms to the aromatic hydrocarbons phenol and toluene were determined during short-term (3 h) additions of each compound to the biofilms. Ammonia oxidation in the biofilms was inhibited 50% by 60 uM phenol and 100 uM toluene. These concentrations were chosen for microarray analysis of phenol- and toluene-exposed N. europaea biofilms. Liquid batch cultures of exponentially growing N. europaea cells were harvested alongside the biofilms to determine differential gene expression between attached and suspended growth of N. europaea.
2010-07-20 | GSE22646 | GEO
Project description:We performed comparative analysis of transcriptomes of S. mutans in single biofilms and in mixed-biofilms with A. actinomycetemcomitans. We also compared the transcriptomic profiles of A. actinomycetemcomitans in single biofilms and A. actinomycetemcomitans in mixed biofilms with S. mutans. Finally we looked at the changes in gene expression in both organisms in time.
2017-03-31 | GSE75019 | GEO