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646 results for “Pseudomonas aeruginosa”
Data from: Spatial structure maintains diversity of pyocin inhibition in household Pseudomonas aeruginosa
<p><span><span><span><span><span><span><span><span><span><span><span>Nearly all bacteria produce narrow-spectrum antibiotics called bacteriocins. Studies have shown that bacteriocins can mediate microbial interactions, but the mechanisms underlying patterns of inhibition are less well understood. We assembled a spatially structured collection of isolates of <i>Pseudomonas aeruginosa</i> from bathroom and kitchen sink drains in nine households. Growth inhibition of these <i>P. aeruginosa </i>by bacteriocins, known as pyocins in this species, was measured using pairwise inhibition assays. Carbon source usage of these isolates was measured and genetic distance was estimated using multilocus sequencing. We found that as the distance between sites of isolation increased, there was a significantly higher probability of inhibition, and that pyocin inhibition and susceptibility vary greatly among isolates collected from different houses. We also detected support for other mechanisms influencing diversity: inhibition outcomes were influenced by the type of drain from which isolates were collected, and while we found no indication that carbon source utilization influences inhibition, inhibition was favored at an intermediate genetic distance. Overall, these results suggest that the combined effects of dispersal limitation among sites and competitive exclusion within them maintain diversity in pyocin inhibition and susceptibility phenotypes, and that additional processes such as local adaptation and effects of phylogenetic distance could further contribute to spatial variability.</span></span></span></span></span></span></span></span></span></span></span></p>
Spatial structure affects phage efficacy in infecting dual-strain biofilms of Pseudomonas aeruginosa
Bacterial viruses, or phage, are key members of natural microbial communities. Yet much research on bacterial-phage interactions has been conducted in liquid cultures involving single bacterial strains. Here we explored how bacterial diversity affects the success of lytic phage in structured communities. We infected a susceptible Pseudomonas aeruginosa strain PAO1 with a lytic phage Pseudomonas 352 in the presence versus absence of an insensitive P. aeruginosa strain PA14, in liquid culture versus colonies on agar. We found that both in liquid and in colonies, inter-strain competition reduced resistance evolution in the susceptible strain and decreased phage population size. However, while all sensitive bacteria died in liquid, bacteria in colonies could remain sensitive yet escape phage infection, due mainly to reduced growth in colony centers. In sum, spatial structure can protect bacteria against phage infection, while the presence of competing strains reduces the evolution of resistance to phage.
Data from: Mridha S and Kümmerli R (2022) Enforced specialization fosters mutual cheating and not division of labour in the bacterium Pseudomonas aeruginosa
<p><span>A common way for bacteria to cooperate is via the secretion of beneficial public goods (proteases, siderophores, biosurfactants) that can be shared among individuals in a group. Bacteria often simultaneously deploy multiple public goods with complementary functions. This raises the question whether natural selection could favour division of labour where subpopulations or species specialise in the production of a single public good, whilst sharing the complementary goods at the group level. Here we use an experimental system, where we mix engineered specialists of the bacterium <em>Pseudomonas aeruginosa</em> that can each only produce one of the two siderophores, pyochelin or pyoverdine, and explore the conditions under which specialization can lead to division of labour. When growing pyochelin and pyoverdine specialists at different mixing ratios under different levels of iron limitation, we found that specialists could only successfully complement each other in environments with moderate iron limitation and grow as good as the generalist wildtype but not better. Under more stringent iron limitation, the dynamics in specialist communities was characterized by mutual cheating and with higher proportions of pyochelin producers greatly compromising group productivity. Nonetheless, specialist communities remained stable through negative frequency-dependent selection. Our work shows that specialization in a bacterial community can be spurred by cheating and does not necessarily result in beneficial division of labour. We propose that natural selection might favour fine-tuned regulatory mechanisms in generalists over division of labour because the former enables generalists to remain flexible and adequately adjust public good investments in fluctuating environments. </span></p>
Structural insights into the inhibition site in the phosphorylcholine phosphatase enzyme of Pseudomonas aeruginosa
<p>Inputs for the simulations (MDs and FEP), plus scripts used to obtain results of the manuscript entitled "Structural insights into the inhibition site in the phosphorylcholine phosphatase enzyme of Pseudomonas aeruginosa"</p>
The effects of antibiotic combination treatments on Pseudomonas aeruginosa tolerance evolution and coexistence with Stenotrophomonas maltophilia
<p><em>Pseudomonas aeruginosa</em> bacterium is a common pathogen of Cystic Fibrosis (CF) patients due to its ability to evolve resistance to antibiotics during treatments. While <em>P. aeruginosa</em> resistance evolution is well characterised in monocultures, it is less well understood in polymicrobial CF infections. Here, we investigated how exposure to ciprofloxacin, colistin, or tobramycin antibiotics, administered at sub-MIC doses alone and in combination, shaped the tolerance evolution of <em>P. aeruginosa</em> (PAO1 lab and clinical CF LESB58 strains) in the absence and presence of a commonly co-occurring species, <em>Stenotrophomonas maltophilia</em>. Increases in antibiotic tolerances were primarily driven by the presence of that antibiotic in the treatment. We observed a reciprocal cross-tolerance between ciprofloxacin and tobramycin, and when combined these antibiotics selected increased MICs for all antibiotics. Though the presence of <em>S. maltophilia</em> did not affect the tolerance or the MIC evolution, it drove <em>P. aeruginosa</em> into extinction more frequently in the presence of tobramycin due to its relatively greater innate tobramycin tolerance. In contrast, <em>P. aeruginosa</em> dominated and drove <em>S. maltophilia</em> extinct in most other treatments. Together, our findings suggest that besides driving high-level antibiotic tolerance evolution, sub-MIC antibiotic exposure can alter competitive bacterial interactions, leading to target pathogen extinctions in multi-species communities.</p>
Arms-race and fluctuating-selection dynamics in Pseudomonas aeruginosa bacteria coevolving with phage OMKO1
<p class="MsoNormal">Experimental evolution studies have examined coevolutionary dynamics between bacteria and lytic phages, where two models for antagonistic coevolution dominate: arms-race dynamics (ARD) and fluctuating-selection dynamics (FSD). Here, we tested the ability for <em>Pseudomonas aeruginosa </em>to coevolve with phage OMKO1 during 10 passages in the laboratory; whether ARD versus FSD coevolution occurred; and how coevolution affected a predicted phenotypic trade-off between phage resistance and antibiotic sensitivity. We used a unique "deep" sampling design, where 96 bacterial clones per passage were obtained from the three replicate coevolving communities. Next, we examined phenotypic changes in growth ability, susceptibility to phage attack, and resistance against antibiotics. Results confirmed that the bacteria and phages coexisted throughout the study with one community undergoing ARD while the other two showed evidence for FSD. Surprisingly, only the ARD bacteria demonstrated the anticipated trade-off. Whole genome sequencing revealed that treatment populations of bacteria accrued more <em>de novo</em> mutations, relative to a control bacterial population. Additionally, coevolved bacteria presented mutations in genes for biosynthesis of flagella, type-IV pilus and lipopolysaccharide, with three mutations fixing contemporaneously with the occurrence of the phenotypic trade-off in the ARD-coevolved bacteria. Our study demonstrates that both ARD and FSD coevolution outcomes are possible in a single interacting bacteria-phage system, and that occurrence of predicted phage-driven evolutionary trade-offs may depend on the genetics underlying evolution of phage-resistance in bacteria. These results are relevant for the ongoing development of lytic phages, such as OMKO1, in personalized treatment of human patients, as an alternative to antibiotics. </p>
Complete dataset for the publication "Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication"
<p>This dataset enlists all individual datapoints shown in the publication "Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication" (https://doi.org/10.1038/s41467-023-44157-3). For detailed information regarding the individual contributions please check the "Author information" section in the publication. </p>
Movies of Pseudomonas aeruginosa twitching
<p><strong><span>Movie S1. </span></strong><span>Bacteria twitching in the confined condition. It can be clearly seen that some of the bacteria exhibit obvious twitching movements while others are stationary. The playback speed of the video is 10 times the actual speed.</span></p> <p><strong><span>Movie S2. </span></strong><span>Bacteria twitching in the free condition. The playback speed of the video is 10 times the actual speed.</span></p>
MD simulation data for Pseudomonas aeruginosa TonB-CTD, Amber ff99SB-ILDN, tip4p, 298K, Gromacs
<p>MD simulation data for Pseudomonas aeruginosa TonB-CTD. Simulated with Amber ff99SB-ILDN force field, tip4p water model at 298K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Pseudomonas aeruginosa TonB-CTD, Amber ff99SB-ILDN, OPC4, 310K, Gromacs
<p>MD simulation data for Pseudomonas aeruginosa TonB-CTD. Simulated with Amber ff99SB-ILDN force field, OPC4 water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Pseudomonas aeruginosa TonB-CTD, Amber ff99SB-ILDN, tip4p, 310K, Gromacs
<p>MD simulation data for Pseudomonas aeruginosa TonB-CTD. Simulated with Amber ff99SB-ILDN force field, tip4p water model at 310K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
MD simulation data for Pseudomonas aeruginosa TonB-CTD, Amber ff99SB-ILDN, tip3p, 298K, Gromacs
<p>MD simulation data for Pseudomonas aeruginosa TonB-CTD. Simulated with Amber ff99SB-ILDN force field, tip3p water model at 298K, Gromacs software package.</p> <p>Simulation reported in "Rotational dynamics of proteins from spin relaxation times and molecular dynamics simulations", Ollila et al. Submitted (2017).</p>
[PART 3] A twist of fate: the helix-turn-helix motif in Pseudomonas aeruginosa ExsA can allosterically stabilize the ligand-binding domain
<p>1273- ExsA - Dimer1 without DNA - alphaFold compact - 230ns/day 10x500ns<br>*1274- ExsA - Dimer2 without DNA - xtal extended (like 1026) - 10x1µs (not everything is 1 µs)<br>1275- ExsA - Dimer3 without DNA - made by hand / 150ns/day (reps 1-5 broken, reps 6-10 correct)<br>*1276- ExsA- monomer - Site1-PexoT - 240 ns/day - 10x1µs (some replicas have pieces missing)<br>*1277- ExsA- monomer - Site2-PexoT - 10x1µs<br>*1278- ExsA - Dimer2 with broken DNA - xtal extended (like 1026) - 5x200ns?</p>
[PART 2] A twist of fate: the helix-turn-helix motif in Pseudomonas aeruginosa ExsA can allosterically stabilize the ligand-binding domain
<p>1273- ExsA - Dimer1 without DNA - alphaFold compact <br>1274- ExsA - Dimer2 without DNA - xtal extended <br>1275- ExsA - Dimer3 without DNA - made by hand (reps 1-5 broken, reps 6-10 correct)<br>1276- ExsA- monomer - Site1-PexoT <br>1277- ExsA- monomer - Site2-PexoT<br>1278- ExsA - Dimer2 with broken DNA</p>
A novel mechanism that maintains outer membrane lipid asymmetry in Pseudomonas aeruginosa
<p>Newick file the PA2800 phylogenetic tree in "A novel mechanism that maintains outer membrane lipid asymmetry in Pseudomonas aeruginosa"</p>
Interactions between metabolism and growth can determine the co-existence of Staphylococcus aureus and Pseudomonas aeruginosa
<p>Most bacteria exist and interact within polymicrobial communities. These interactions produce unique compounds, increase virulence and augment antibiotic resistance. One community associated with negative healthcare outcomes consists of <em>Pseudomonas aeruginosa</em> and <em>Staphylococcus aureus</em>. When co-cultured, virulence factors secreted by <em>P. aeruginosa</em> reduce metabolism and growth in <em>S. aureus</em>. When grown in vitro, this allows <em>P. aeruginosa</em> to drive <em>S. aureus</em> toward extinction. However, when found <em>in vivo</em>, both species can co-exist. Previous work has noted that this may be due to altered gene expression or mutations. However, little is known about how the growth environment could influence the co-existence of both species. Using a combination of mathematical modeling and experimentation, we show that changes to bacterial growth and metabolism caused by differences in the growth environment can determine the final population composition. We found that changing the carbon source in growth media affects the ratio of ATP to growth rate for both species, a metric we call absolute growth. We found that as a growth environment increases the absolute growth for one species, that species will increasingly dominate the co-culture. This is due to interactions between growth, metabolism, and metabolism-altering virulence factors produced by <em>P. aeruginosa</em>. Finally, we show that the relationship between absolute growth and the final population composition can be perturbed by altering the spatial structure in the community. Our results demonstrate that differences in growth environment can account for conflicting observations regarding the co-existence of these bacterial species in the literature, provides support for the intermediate disturbance hypothesis, and may offer a novel mechanism to manipulate polymicrobial populations.</p>
Periodically disturbing biofilms reduces expression of quorum sensing regulated virulence factors in Pseudomonas aeruginosa
<p>The opportunistic pathogen <em>Pseudomonas aeruginosa</em> uses quorum sensing to control the expression of multiple virulence factors. In this dataset, we provide raw data demonstrating that periodically disturbing biofilms composed of <em>P. aeruginosa</em> using a physical force reduces the expression of multiple quorum sensing regulated virulence factors from the three major regulons. This dataset also contains cell density measurements of bacteria both the in biofilm and planktonic state under a variety of conditions that use physical force to manipulate the spatial positioning of bacteria. Finally, the data set contains raw outputs from a network logic model that described the core quorum sensing network. This data is affiliated with the manuscript entitled "Periodically disturbing biofilms reduces expression of quorum sensing regulated virulence factors in <em>Pseudomonas aeruginosa</em>."</p>
Datasets for phylogeny-guided analysis of pseudogenes in Pseudomonas aeruginosa
<p>In the study entitled "A large-scale phylogeny-guided analysis of pseudogenes in <em>Pseudomonas aeruginosa</em> bacterium" we analyzed the genomic data of 4699 strains of the bacterium <em>Pseudomonas aeruginosa P. aeruginosa)</em> as they exhibit high variability in the number of annotated pseudogenes. In particular, we looked for correlations between the number of pseudogenes and other genomic- and meta- features of the strains. We identified orthologous genes and pseudogenes and compared cluster size distributions and length homogeneity within clusters. We mapped and examined orthology relationships between genes and pseudogenes. We generated a phylogenetic tree of the strains and found that phylogenetically related strains are more homogeneous in the number of pseudogenes and share a significant amount of pseudogenes. Finally, we dived into clusters of orthologues genes and pseudogenes and quantified their phylogenetic neighborhood, classifying pseudogenes into evolutionary preserved pseudogenes, misannotated pseudogenes, or pseudogenes formed by failed horizontal transfer events. This in-depth study provides important insights that can be incorporated into pseudogene annotation pipelines in the future.<br> <br> We provide the following files:</p> <p>protein_seq.zip: A fasta file containing 28,948,105 protein sequences of coding genes across all strains.</p> <p>pseudo_seq.zip: A fasta file containing 86,273 DNA sequences of pseudogenes across all strains. </p> <p>protein_clustering_output.zip: Clustering of protein sequences with CD-HIT clustering algorithm and the following parameters: similarity threshold of 70%, word size of 5, and the slow mode version.</p> <p>pseudo_clustering_output.zip: Clustering of pseudogene sequences with CD-HIT-EST clustering algorithm and the following parameters: similarity threshold of 80\%, word size of 5, and the slow mode version.</p> <p> </p>
Figure 16: Antibiotic sensitivity and resistance pattern of Pseudomonas aeruginosa
<p><strong>Figure 16: Antibiotic sensitivity and resistance pattern of Pseudomonas aeruginosa </strong></p>
Figure 17: Theoretical Prediction of Imipenem Resistance in Pseudomonas aeruginosa (2020-2030)
<p><strong>Figure 17: Theoretical Prediction of Imipenem Resistance in Pseudomonas aeruginosa (2020-2030)</strong></p>
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Allen Brain Atlas
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.