Metabolic remodeling during Bacillus subtilis biofilm development
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA529199 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8787220.fastq.gz | Fastqsanger.gz | |||
| SRR8787230.fastq.gz | Fastqsanger.gz | |||
| SRR8787240.fastq.gz | Fastqsanger.gz | |||
| SRR8787221.fastq.gz | Fastqsanger.gz | |||
| SRR8787231.fastq.gz | Fastqsanger.gz |
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Project description:Biofilms are structured communities of tightly associated cells that constitute the predominant state of bacterial growth in natural and human-made environments. Although the core genetic circuitry that controls biofilm formation in model bacteria such as Bacillus subtilis has been well characterized, little is known about the role that metabolism plays in this complex developmental process. Here, we performed a time-resolved analysis of the metabolic changes associated with pellicle biofilm formation and development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. We report a surprisingly widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. Most of these metabolic alterations were hitherto unrecognized as biofilm-associated. For example, we observed increased activity of the tricarboxylic acid (TCA) cycle during early biofilm growth, a shift from fatty acid biosynthesis to fatty acid degradation, reorganization of iron metabolism and transport, and a switch from acetate to acetoin fermentation. Close agreement between metabolomic, transcriptomic, and proteomic measurements indicated that remodeling of metabolism during biofilm development was largely controlled at the transcriptional level. Our results also provide insights into the transcription factors and regulatory networks involved in this complex metabolic remodeling. Following these results, we demonstrate that acetoin production via acetolactate synthase is essential for robust biofilm growth and has the dual role of conserving redox balance and maintaining extracellular pH. This study represents a comprehensive systems-level investigation of the metabolic remodeling occurring during B. subtilis biofilm development that will serve as a useful roadmap for future studies on biofilm physiology.
2019-03-27 | GSE128875 | GEO
Project description:Biofilms are structured communities of tightly associated cells that constitute thepredominant state of bacterial growth in naturaland human-madeenvironments. Although the core genetic circuitry that controls biofilm formation in model bacteria such as Bacillus subtilishas been well characterized, little is known about the role that metabolism plays in this complex developmental process. Here, weperformed a time-resolved analysisof the metabolic changes associated with pellicle biofilm formation and development inB. subtilisby combining metabolomic, transcriptomic, and proteomic analyses. We report a surprisingly widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. Most of these metabolic alterations were hithertounrecognized as biofilm-associated.For example, we observed increased activity of the tricarboxylic acid (TCA) cycle during early biofilm growth, a shift from fatty acid biosynthesis to fatty acid degradation, reorganization of iron metabolism and transport, and a switch from acetate to acetoin fermentation. Close agreement between metabolomic, transcriptomic, and proteomic measurements indicated that remodeling of metabolism during biofilm development was generally controlled at the transcriptional level. Our resultsalsoprovide insights into the transcription factors and regulatory networks involved in thiscomplexmetabolic remodeling. Following upon these results, we demonstrate that acetoin production via acetolactate synthase is essential for robust biofilm growthand has the dual role of conservingredox balance and maintaining extracellularpH.This study represents a comprehensive systems-level investigation of the metabolic remodeling occurring during B. subtilisbiofilm development that will serve as a useful roadmap for future studies on biofilm physiology.
2019-04-30 | PXD013307 | Pride
Project description:Investigation of the kinetics of whole genome gene expression level changes in Bacillus subtilis NDmed strain during formation of submerged biofilm and pellicle. The Bacillus subtilis NDmed strain analyzed in this study is able to form thick and highly structured submerged biofilms as described in Bridier et al., (2011) The Spatial Architecture of Bacillus subtilis Biofilms Deciphered Using a Surface-Associated Model and In Situ Imaging. PLoS ONE 6(1):e16177.
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Project description:Transcriptome comparison of Bacillus subtilis 168 grown on solid agar (sample 1-3) or aerated liquid (sample 4-7) 2xSG medium with and without of 0.1 mM manganese.
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Project description:The objective of the study was to uncover the developmental dynamics in Bacillus subtilis biofilms on a transcriptome level. The experiment covered a developmental timeline over two months of biofilm growth.
2020-10-05 | GSE141305 | GEO
Project description:Biofilms are structured communities of tightly associated cells that constitute the predominant state of bacterial growth in natural and human-made environments. Although the core genetic circuitry that controls biofilm formation in model bacteria such as Bacillus subtilis has been well characterized, little is known about the role that metabolism plays in this complex developmental process. Here, we performed a time-resolved analysis of the metabolic changes associated with pellicle biofilm formation and development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. We report surprisingly widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. Most of these metabolic alterations were hitherto unrecognized as biofilm associated. For example, we observed increased activity of the tricarboxylic acid (TCA) cycle during early biofilm growth, a shift from fatty acid biosynthesis to fatty acid degradation, reorganization of iron metabolism and transport, and a switch from acetate to acetoin fermentation. Close agreement between metabolomic, transcriptomic, and proteomic measurements indicated that remodeling of metabolism during biofilm development was largely controlled at the transcriptional level. Our results also provide insights into the transcription factors and regulatory networks involved in this complex metabolic remodeling. Following upon these results, we demonstrated that acetoin production via acetolactate synthase is essential for robust biofilm growth and has the dual role of conserving redox balance and maintaining extracellular pH. This report represents a comprehensive systems-level investigation of the metabolic remodeling occurring during B. subtilis biofilm development that will serve as a useful road map for future studies on biofilm physiology.IMPORTANCE Bacterial biofilms are ubiquitous in natural environments and play an important role in many clinical, industrial, and ecological settings. Although much is known about the transcriptional regulatory networks that control biofilm formation in model bacteria such as Bacillus subtilis, very little is known about the role of metabolism in this complex developmental process. To address this important knowledge gap, we performed a time-resolved analysis of the metabolic changes associated with bacterial biofilm development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. Here, we report a widespread and dynamic remodeling of metabolism affecting central carbon metabolism, primary biosynthetic pathways, fermentation pathways, and secondary metabolism. This report serves as a unique hypothesis-generating resource for future studies on bacterial biofilm physiology. Outside the biofilm research area, this work should also prove relevant to any investigators interested in microbial physiology and metabolism.
| S-EPMC6529636 | biostudies-literature
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:Biofilm hydrophobicity in environmental isolates of Bacillus subtilis
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Project description:The natural biotope of Bacillus subtilis is the upper layer of soil where it grows as a biofilm. To mimic this physiological development and study the impact of nanoparticles during the formation of a biofilm in a contaminated soil, we have studied the proteomic response of the ancestral strain Bacillus subtilis 3610, which is able to form biofilm contrary to the 168 laboratory strain. The bacteria were grown on soft agar plates containing n-ZnO, n-TiO2 or ZnSO4 metal ion.
2018-10-24 | PXD006444 | Pride
Project description:Soybeans fermented by Bacillus subtilis BJ3-2 exhibits strong ammonia taste in medium temperature below 37℃ and prominent soy sauce-like aroma moderate temperatures above 45℃. The transcriptome sequencing of Bacillus subtilis BJ3-2 (incubating at 37°C and 45°C) has been completed, screening of differentially expressed genes (DEGs) through data analysis, and analyzing their metabolic pathways, laying a foundation for exploring the regulatory mechanism of soy sauce-like aroma formation.
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