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22 results for “bacteriocins”
Deep Learning Neural Network Development for the Classification of Bacteriocin Sequences Produced by Lactic Acid Bacteria
<p>This project contains the following underlying data:</p> <h3> Software-Related Files</h3> <p><strong> · </strong><strong>BacLABNet_script.ipynb</strong> (Deep Learning Neural Network for classification of Bacteriocin Sequences) </p> <p><strong> · </strong><strong>embed_proteins.py </strong>(Recurrent Neural Network to obtained the embedding vectors)</p> <p> · <strong> </strong><strong>model_I22.h5</strong> (This file contains the trained weights of the trained model)</p> <p> · <strong>model_I22.json</strong> (This file contains the structure of the trained model)</p> <p><strong> · </strong><strong>rnn_gru.pt</strong> (Initial weights of the Recurrent Neural Network to obtain embedding vectors)</p> <p><strong> · </strong><strong>List_kmers.csv</strong> (List of 5-mers and 7-mers obtained from dataset after it filtered sequences shorter than 50 aa and longer than 2000 aa)</p> <p><strong> </strong></p> <p> <strong>Files Used for Training, Testing, and Validation of the Neural Network</strong></p> <p> <strong>· </strong> <strong>data_nonBacLAB.csv</strong> (25000 nonBacLAB amino acid sequences retrieved from Uniprot)</p> <p> <strong>· data_BacLAB.csv</strong> (24964 BacLAB amino acid sequences retrieved from Uniprot)</p> <p> <strong> </strong></p> <p><strong> Additional Files</strong></p> <p><strong> · data_BacLAB_and_nonBacLAB.csv </strong>(Combination of sequences from data_BacLAB.csv and data_nonBacLAB.csv)</p> <p> <strong> · </strong><strong>all k.mers list.xlsx </strong>(Table of all k-mers obtained for k=3,5,7,15,20)</p> <p> </p> <p><strong>Note:</strong> Codes are additionally available on GitHub. </p> <p><span>Data are available under the terms of the Creative Commons Zero "No rights reserved" data waiver (CC0 1.0 Public domain dedication)(http://creativecommons.org/publicdomain/zero/1.0/)</span></p>
The cost and benefit of quorum sensing controlled bacteriocin production in Lactobacillus plantarum
Bacteria eliminate competitors via 'chemical warfare' with bacteriocins. Some species appear to adjust bacteriocin production conditionally in response to the social environment. We tested whether variation in the cost and benefit of producing bacteriocins could explain such conditional behaviour, in the bacteria Lactobacillus plantarum. We found that: (1) bacterial bacteriocin production could be upregulated by either the addition of a synthetic autoinducer peptide (PLNC8IF; signalling molecule), or by a plasmid which constitutively encodes for the production of this peptide; (2) bacteriocin production is costly, leading to reduced growth when grown in poor and, to a lesser extent, in rich media; (3) bacteriocin production provides a fitness advantage, when grown in competition with sensitive strains; (4) the fitness benefits provided by bacteriocin production is greater at higher cell densities. These results show how the costs and benefits of upregulating bacteriocin production can depend upon abiotic and biotic conditions.
Draft Genome Sequences of Two Bacteriocin-Producing Enterococcus faecium Strains Isolated from Nonfermented Animal Foods in Spain
<p>Raw sequences of two bacteriocin-producing Enterococcus faecium.</p> <p> </p>
Data from: Plastic responses to competition: does bacteriocin production increase in the presence of nonself competitors?
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The cost and benefit of quorum sensing controlled bacteriocin production in Lactobacillus plantarum
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Data from: Suppression of bacteriocin resistance using live, heterospecific competitors
Rapidly spreading antibiotic resistance has led to the need for novel alternatives and sustainable strategies for antimicrobial use. Bacteriocins are a class of proteinaceous anticompetitor toxins under consideration as novel therapeutic agents. However, bacteriocins, like other antimicrobial agents, are susceptible to resistance evolution, and will require the development of sustainable strategies to prevent or decelerate the evolution of resistance. Here we conduct proof-of-concept experiments to test whether introducing a live, heterospecific competitor along with a bacteriocin dose can effectively suppress the emergence of bacteriocin resistance in vitro. Previous work with conventional chemotherapeutic agents suggests that competition between conspecific sensitive and resistant pathogenic cells can effectively suppress the emergence of resistance in pathogenic populations. However, the threshold of sensitive cells required for such competitive suppression of resistance may often be too high to maintain host health. Therefore, here we aim to ask whether the principle of competitive suppression can be effective if a heterospecific competitor is used. Our results show that a live competitor introduced in conjunction with low bacteriocin dose can effectively control resistance and suppress sensitive cells. Further, this efficacy can be matched by using a bacteriocin-producing competitor without any additional bacteriocin. These results provide strong proof-of-concept for the effectiveness of competitive suppression using live, heterospecific competitors. Currently in-use probiotic strains or commensals may provide promising candidates for the therapeutic use of bacteriocin-mediated competitive suppression.
Data from: The role of bacteriocins as selfish genetic elements
Bacteria produce a wide arsenal of toxic compounds in order to kill competing species. Bacteriocins, protein-based toxins produced by nearly all bacteria, have generally been considered a ubiquitous anti-competitor strategy, used to kill competing bacterial strains. Some of these bacteriocins are encoded on plasmids, which also code for closely linked immunity compounds (thereby rendering toxin producing cells immune to their own toxin). However, the production of bacteriocins can also be interpreted as a means to promote plasmid stability by preferentially selecting for cells carrying the plasmid. If, for example, a cell were to lose the plasmid, it would no longer produce the immunity compound and would be killed by its bacteriocin-producing clone mates. In this respect, bacteriocins can be regarded as similar to previously described toxin–antitoxin systems that are able promote the stable transmission of plasmids to daughter cells. In order to test this prediction, we carried out an experimental evolution study using the bacterium Escherichia coli, finding that bacteriocins can indeed select for the stable maintenance of plasmids. This suggests that bacteriocins can act primarily as selfish genetic elements promoting their own transmission in the population, which may help explain their unique ecology and evolution.
Data from: Suppression of bacteriocin resistance using live, heterospecific competitors
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Data from: Bacteriocins and the assembly of natural Pseudomonas fluorescens populations
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Data from: The role of bacteriocins as selfish genetic elements
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Horizontal transfer of bacteriocin biosynthesis genes requires metabolic adaptation to improve compound production and cellular fitness
GEO Series GSE208001. Staphylococcus aureus subsp. aureus RN4220. 9 samples. Type: Expression profiling by high throughput sequencing.
Insensitivity of the studied APEC strains to antibiotics and bacteriocins
<p>An .xls file with all the data for the submitted manuscript.</p>
Transcriptional changes associated to resistance to the cell wall active bacteriocin Lcn972
GEO Series GSE38349. Lactococcus lactis subsp. lactis; Lactococcus cremoris subsp. cremoris MG1363. 4 samples. Type: Expression profiling by array.
Effect of bacteriocin NC8 on human intestinal flora
GEO Series GSE199735. Homo sapiens. 30 samples. Type: Expression profiling by high throughput sequencing.
Characterization of a potential ABC-type bacteriocin exporter protein from Treponema denticola
GEO Series GSE83445. Treponema denticola. 2 samples. Type: Expression profiling by array.
Identification of a Novel Bacteriocin Regulatory System in Streptococcus mutans
GEO Series GSE22902. Streptococcus mutans. 2 samples. Type: Expression profiling by array.
Peptide alarmone signalling triggers an auto-active bacteriocin necessary for genetic competence
GEO Series GSE22019. Streptococcus mutans; Streptococcus mutans UA159. 6 samples. Type: Expression profiling by array.
Data for "Uncovering natural sources of LAB bacteriocins through the use of metagenomics"
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Transcriptional response of Enterococcus faecali to the glycosylated bacteriocin glycocin F
GEO Series GSE138552. Enterococcus faecalis. 39 samples. Type: Expression profiling by high throughput sequencing.
Lactic acid bacteria derived bacteriocin targets purine and histidine metabolisms of gut microbiota to alleviate colitis
GEO Series GSE274981. Mus musculus. 18 samples. Type: Expression profiling by high throughput sequencing.
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