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283 results for “Bacillus Subtilis”
Code and data for 'Bacillus subtilis histidine kinase KinC activates biofilm formation by controlling heterogeneity of single-cell responses'
<p>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</p>
The role of cell-envelope synthesis for envelope growth and cytoplasmic density in Bacillus subtilis
<p>All cells must increase their volumes in response to biomass growth to maintain intracellular mass density within physiologically permissive bounds. Here, we investigate the regulation of volume growth in the Gram-positive bacterium <em>Bacillus subtilis</em>. To increase volume, bacteria enzymatically expand their cell envelopes and insert new envelope material. First, we demonstrate that cell-volume growth is determined indirectly, by expanding their envelopes in proportion to mass growth, similarly to the Gram-negative <em>Escherichia coli</em>, despite their fundamentally different envelope structures. Next, we studied, which pathways might be responsible for robust surface-to-mass coupling: We found that both peptidoglycan synthesis and membrane synthesis are required for proper surface-to-mass coupling. However, surprisingly, neither pathway is solely rate-limiting, contrary to wide-spread belief, since envelope growth continues at a reduced rate upon complete inhibition of either process. To arrest cell-envelope growth completely, the simultaneous inhibition of both envelope-synthesis processes is required. Thus, we suggest that multiple envelope-synthesis pathways collectively confer an important aspect of volume regulation, the coordination between surface growth and biomass growth.</p>
Lactic Acid Bacteria and Bacillus subtilis as Potential Protective Cultures for Biopreservation in the Food Industry
<div> <p>This dataset contains the raw data corresponding to the figures and tables of the publication with DOI <a href="https://doi.org/10.3390/app14104016">10.3390/app14104016</a>, as well as the accession numbers assigned to the related sequencing data.</p> </div>
Probiotic Bacillus subtilis Protects against a-Synuclein Aggregation in C. elegans (fluorescence microscopy data)
<p>This project has been submitted by the Maria Doitsidou Lab.<br> <br> Project contents:<br> This project contains datasets of z-stack images of <em>C. elegans</em> strains used to study how the gut microbiome affects Parkinson’s disease. Each strain contains a chromosomal insertion containing YFP fused to α-synuclein (pkIs2386[Punc-54::α-synuclein::YFP + unc-119(+)]). The following<em> C. elegans</em> strains were used and/or created for this project:<br> NL5901 pkIs2386[Punc-54::α-synuclein::YFP + unc-119(+)]<br> MDH586 daf-2(e1370) III; pkIs2386<br> MDH585 daf-16(mu86) I; pkIs2386<br> MDH587 hsf-1(sy441) I; pkIs2386<br> MDH657 daf-2(e1370) III; daf-16(mu86) I; pkIs2386<br> MDH614 daf-2(gk390525) III; pkIs2386<br> MDH611 eat-2(ad465) II; pkIs2386<br> MDH711 lagr-1(gk331) I, pkIs2386<br> MDH725 sptl-3(ok1927) II; pkIs2386<br> MDH724 asm-3(ok1744) IV; pkIs2386.<br> <br> High magnification (40x objective) z stack images of the head region were obtained by using a Zeiss Axio imager 2 microscope.<br> <br> <br> Aim:<br> Study how a probiotic<em> B. subtilis</em> strain affects alpha-synuclein protein aggregation.<br> <br> Main results:<br> The authors showed that the probiotic<em> B. subtilis</em> strain PXN21 inhibits and clears a-synuclein aggregation in a <em>C. elegans </em>model. The bacterium acts via metabolites and biofilm formation to activate protective pathways in the host, including DAF-16/FOXO and sphingolipid metabolism.<br> <br> Contributors:<br> Maria Eugenia Goya, Feng Xue, Cristina Sampedro-Torres-Quevedo, Sofia Arnaouteli, Lourdes Riquelme-Dominguez, Andres Romanowski, Jack Brydon, Kathryn L. Ball, Nicola R. Stanley-Wall and Maria Doitsidou<br> <br> These datasets were used in the following publication:<br> <br> Probiotic Bacillus subtilis Protects against a-Synuclein Aggregation in <em>C. elegans</em><br> <br> Maria Eugenia Goya, Feng Xue, Cristina Sampedro-Torres-Quevedo, Sofia Arnaouteli, Lourdes Riquelme-Dominguez, Andres Romanowski, Jack Brydon, Kathryn L. Ball, Nicola R. Stanley-Wall and Maria Doitsidou<br> <br> Cell Reports January 14, 2020 30 367-380; first published January 14, 2020 <a href="https://doi.org/10.1016/j.celrep.2019.12.078">https://doi.org/10.1016/j.celrep.2019.12.078</a></p>
Data for: Sigma-B responses of Bacillus subtilis exposed to different environmental stressors and containing different single RsbR proteins or hybrid fusions of RsbRs
<p>Bacteria use a variety of systems to sense stress and mount an appropriate response to assure fitness and survival. <em>Bacillus subtilis</em> uses stressosomes—cytoplasmic multiprotein complexes—to sense environmental stressors and enact the general stress response by activating the alternative sigma factor σ<sup>B</sup>. Each stressosome includes 40 RsbR proteins, representing four paralogous (RsbRA, RsbRB, RsbRC, and RsbRD) putative stress sensors. Population-level analyses suggested that the RsbR paralogs are largely redundant, while our prior work using microfluidics-coupled fluorescence microscopy uncovered differences among the RsbR paralogs' σ<sup>B</sup> response profiles with respect to timing and intensity when facing an identical stressor.</p> <p>We used microfluidics and fluorescence microscopy to address the question of whether the σ<sup>B</sup> responses mediated by each paralog differ in the presence of different environmental stressors: can they distinguish among stressors? Wild-type cells (with all four paralogs) and RsbRA-only cells activate σ<sup>B</sup> with characteristic transient response timing irrespective of stressor but show varying response magnitude. However, cells with other individual RsbR paralogs show distinct timing and magnitude in their responses to ethanol, salt, oxidative and acid stress, implying that RsbR proteins can distinguish among stressors. To show this distinct timing, we quantified time-lapse image series of cells with a fluorescent σ<sup>B</sup> transcriptional reporter. Representative videos of time-lapse image series and the results of our quantitation for each RsbR paralog in each stress condition are included in this dataset.</p> <p>We also probed the relative importance of each half of each RsbR paralog. Experiments with hybrid fusion proteins comprising the N-terminal half of one paralog and the C-terminal half of another argued that the N-terminal identity influences response magnitude and that determinants in both halves of RsbRA are important for its stereotypical transient σ<sup>B</sup> response timing. Time-lapse videos for each hybrid fusion protein and the corresponding quantification of these data are also included in the dataset.</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>
Evaluation of Bacillus Subtilis R0179 in Healthy Young Adults
ClinicalTrials.gov study NCT01802151. IPD Sharing: Not stated. Countries: 1. Publications: 6.
In vitro assessment of Bacillus subtilis DSM29784 secreted metabolites on gut chicken microbiota
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Data for: Sigma-B responses of Bacillus subtilis exposed to different environmental stressors and containing different single RsbR proteins or hybrid fusions of RsbRs
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The role of cell-envelope synthesis for envelope growth and cytoplasmic density in Bacillus subtilis
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Data for: Extensive cellular multi-tasking within Bacillus subtilis biofilms
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Data from: Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas
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Supplementary dataset for cell-free supernatant proteome analysis from Bacillus subtilis and Lactobacillus helveticus in response to pH changes
<p>Data obtained through Scaffold 5 was used for quantification of the proteins based on spectra count values. These spectral count values were normalized, and analysis of variance (ANOVA) performed to detect differential abundance among the treatments at the 95 % confidence level (p < 0.05).<br> </p>
Bacillus subtilis prophages_clustered to vOTUs
<p><span>This dataset comprises </span><span>genomic sequences of predicted </span><span>prophage elements from <em>Bacillus subtilis</em> genomes, organized into separate FASTA files based on clustering results. A total of 64 FASTA files are provided. Within each file, individual prophage sequences are listed, each preceded by a header in the following format: </span><span>>AP011541.2_Phage_7_Pos_3240205-3266407</span><span>. This format denotes the host genome ID, phage identifier, and the prophage coordinates within the host genome. Each FASTA file is uniquely numbered to correspond with a viral Operational Taxonomic Unit (vOTU), representing the prophage group to which the sequences belong.</span></p> <p><span>The prophage elements were sourced from both complete <em>B. subtilis</em> genome sequences available in NCBI's database (191 genomes; last accessed March 2023) and from 40 local soil microscale isolates (PS strains; PRJNA437002). Prophage coordinates within the bacterial genomes were identified using the PHASTER web tool. Functional categories assigned by PHASTER (complete, questionable, incomplete) were disregarded, and all predicted prophage elements were included.</span></p> <p><span>These prophage elements were then clustered using the vContact2 tool. Briefly, prophage genes were predicted using Prodigal, translated into proteins, and subjected to reference-free phylogenetic clustering via vContact2. This tool constructs a network based on the number of shared proteins between phages. The ClusterOne algorithm was then applied to this network to infer groups of related phages, which were used to define vOTUs for further analysis.</span></p> <p><span>In addition to the vOTU-based clusters, two artificial clusters were created: Outliers and Singletons. Outliers share some proteins with different vOTUs but fall below the 20% similarity threshold, while Singletons represent prophage elements with no similarity to other clusters.</span></p> <p><span>Dataset is described in publication: </span><span><strong><span>doi:</span></strong></span><span><span> https://doi.org/10.1101/2024.07.03.601884</span></span></p>
Annotation files of Bacillus subtilis ICS
<p>This serves as an accompanying dataset to MRA00736-24 "Draft Genome of <em>Bacillus subtilis</em> ICS Isolated from Okra (A<em>belmoschus esculentus</em>) Exhibited Genes Related to Plant Growth Promoting Potential".</p>
Expression of degQ gene and its effect on lipopeptide production as well as formation of secretory proteases in Bacillus subtilis strains
<p><em>Bacillus subtilis</em> is described as a promising production strain for lipopeptides. In case of <em>B. subtilis</em> strains JABs24 and DSM10<sup>T</sup>, surfactin and plipastatin are produced. Lipopeptide formation is controlled, among others, by the DegU response regulator. The activating phospho-transfer by the DegS sensor kinase is stimulated by the pleiotropic regulator DegQ, resulting in enhanced DegU activation. In <em>B. subtilis</em> 168, a point mutation in the <em>degQ</em> promoter region leads to a reduction in gene expression. Corresponding reporter strains showed a 14-fold reduced expression. This effect on <em>degQ</em> expression and the associated impact on lipopeptide formation was examined for <em>B. subtilis</em> JABs24, a lipopeptide-producing derivative of strain 168, and <em>B. subtilis</em> wild-type strain DSM10<sup>T</sup>, which has a native <em>degQ</em> expression. Based on stimulatory effects of the DegU regulator on secretory protease formation, the impact of <em>degQ</em> expression on extracellular protease activity was additionally investigated. To follow the impact of <em>degQ</em>, a deletion mutant was constructed for DSM10<sup>T</sup>, while a natively expressed <em>degQ</em> version was integrated into strain JABs24. This allowed strain-specific quantification of the stimulatory effect of <em>degQ</em> expression on plipastatin and the negative effect on surfactin production in strains JABs24 and DSM10<sup>T</sup>. While an unaffected <em>degQ</em> expression reduced surfactin production in JABs24 about 25%, a 6-fold increase in plipastatin was observed. In contrast, <em>degQ</em> deletion in DSM10<sup>T</sup> increased surfactin titer by 3-fold but decreased plipastatin production by 5-fold. In addition, although significant differences in extracellular protease activity were detected, no decrease in plipastatin and surfactin produced during cultivation was observed.</p>
Bacillus subtilis metabolomics
<p>Bacillus subtilis metabolomics:</p> <p>Analyses were performed using an UHPLC (1290 Infinity LC, Agilent Technologies) coupled to a QTRAP MS (AB 6500+, ABSciex) in Shanghai Applied Protein Technology Co., Ltd. The analytes were separated on HILIC (Waters UPLC BEH Amidecolumn, 2.1 mm × 100 mm, 1.7μm) and C18 columns (Waters UPLC BEH C18-2.1x100 mm, 1.7 μm).</p> <p>For HILIC separation, the column temperature was set at 35 ℃; and the injection volume was 2 μL. Mobile phase A: 90%H2O + 2 mM ammonium formate + 10% acetonitrile , mobile phase B: 0.4% formic acid in acetonitrile. A gradient (85% B at 0-1 min, 80% B at 3-4 min, 70% B at 6 min, 50% B at 10-15.5 min, 85% B at 15.6 -23 min ) was then initiated at a flow rate of 300μL/min.</p> <p>For RPLC separation, the column temperature was set at 40℃, and the injection volume was 2 μL. Mobile phase A: 5 mMammonium acetate in water, mobile phase B: 99.5% acetonitrile.A gradient (5% B at 0 min, 60% B at 5 min, 100% B at 11-13min, 5% B at 13.1-16 min ) was then initiated at a flow rate of 400 μL/min. The sample was placed at 4 ℃ during the wholeanalysis process.</p> <p>6500+ QTRAP (AB SCIEX) was performed in positive and negative switch mode. The ESI positive source conditions were asfollows: Source temperature: 580℃; Ion Source Gas1 (GS1): 45; Ion Source Gas2 (GS2): 60; Curtain Gas (CUR): 35; IonSprayVoltage(IS): +4500 V; The ESI negative source conditions were as follows: Source temperature: 580℃; Ion Source Gas1(GS1): 45; Ion Source Gas2 (GS2): 60; Curtain gas (CUR): 35; IonSpray Voltage(IS): -4500 V. MRM method was used for massspectrometry quantitative data acquisition. The MRM ion pairs are showed in the attached file. A polled quality control (QC)samples were set in the sample queue to evaluate the stability and repeatability of the system.</p>
Effect of Bacillus Subtilis BS50 Supplementation on Gastrointestinal Symptoms in Healthy Adults
ClinicalTrials.gov study NCT05004454. IPD Sharing: NO. Countries: 1. Publications: 1.
Effect of Bacillus Subtilis ATCC 122264 Supplementation on Gas Symptoms and Quality of Life in Participants With Functional Bloating
ClinicalTrials.gov study NCT06308146. IPD Sharing: NO. Countries: 1. Publications: 1.
A Study to Evaluate OPTI-BIOME™ Bacillus Subtilis MB40 on Abdominal Discomfort, Gas and Bloating in a Healthy Population
ClinicalTrials.gov study NCT02950012. IPD Sharing: NO. Countries: 2. Publications: 1.
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