scholarly journals PaReBrick: PArallel REarrangements and BReaks identification toolkit

2021 ◽  
Author(s):  
Alexey Zabelkin ◽  
Yulia Yakovleva ◽  
Olga Bochkareva ◽  
Nikita Alexeev
Keyword(s):  
Antigenic Variation ◽  
Phenotypic Diversity ◽  
Genome Rearrangements ◽  
Supplementary Information ◽  
High Plasticity ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Phyletic Pattern ◽  
Bacterial Populations ◽  
Different Strains

Abstract Motivation High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions, and duplications may independently occur in different strains, providing parallel adaptation or phenotypic diversity. Specifically, such rearrangements might be responsible for virulence, antibiotic resistance, and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. Results Here we define the term “parallel rearrangements” as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial populations as a tool PaReBrick. The tool takes a collection of strains represented as a sequence of oriented synteny blocks and a phylogenetic tree as input data. It identifies rearrangements, tests them for consistency with a tree, and sorts the events by their parallelism score. The tool provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved.We demonstrated PaReBrick’s efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. Availability PaReBrick is written in Python and is available on GitHub https://github.com/ctlab/parallelrearrangements Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals PaReBrick: PArallel REarrangements and BReakpoints identification toolkit

2021 ◽  
Author(s):  
Alexey Zabelkin ◽  
Yulia Yakovleva ◽  
Olga Bochkareva ◽  
Nikita Alexeev
Keyword(s):  
Antigenic Variation ◽  
Genome Rearrangements ◽  
High Plasticity ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Phyletic Pattern ◽  
Consistency Results ◽  
Algorithmic Solution ◽  
Synteny Blocks ◽  
Different Strains

Motivation: High plasticity of bacterial genomes is provided by numerous mechanisms including horizontal gene transfer and recombination via numerous flanking repeats. Genome rearrangements such as inversions, deletions, insertions, and duplications may independently occur in different strains, providing parallel adaptation. Specifically, such rearrangements might be responsible for multi-virulence, antibiotic resistance, and antigenic variation. However, identification of such events requires laborious manual inspection and verification of phyletic pattern consistency. Results: Here we define the term "parallel rearrangements" as events that occur independently in phylogenetically distant bacterial strains and present a formalization of the problem of parallel rearrangements calling. We implement an algorithmic solution for the identification of parallel rearrangements in bacterial population, as a tool PaReBrick. The tool takes synteny blocks and a phylogenetic tree as input and outputs rearrangement events. The tool tests each rearrangement for consistency with a tree, and sorts the events by their parallelism score and provides diagrams of the neighbors for each block of interest, allowing the detection of horizontally transferred blocks or their extra copies and the inversions in which copied blocks are involved. We proved PaReBrick's efficiency and accuracy and showed its potential to detect genome rearrangements responsible for pathogenicity and adaptation in bacterial genomes. Availability: PaReBrick is written in Python and is available on GitHub: https://github.com/ctlab/parallel-rearrangements .

scholarly journals Genotypic and Phenotypic Diversity among Induced, stx2-Carrying Bacteriophages from Environmental Escherichia coli Strains

2008 ◽  
Vol 75 (2) ◽  
pp. 329-336 ◽  
Author(s):  
Cristina García-Aljaro ◽  
Maite Muniesa ◽  
Juan Jofre ◽  
Anicet R. Blanch
Keyword(s):  
Escherichia Coli ◽  
Shiga Toxin ◽  
Phenotypic Diversity ◽  
Morphological Diversity ◽  
Lytic Cycle ◽  
Animal Origin ◽  
Bacterial Populations ◽  
Shiga Toxin 2 ◽  
Different Strains ◽  
High Level

ABSTRACT Shiga toxin 2 (stx 2) gene-carrying bacteriophages have been shown to convert Escherichia coli strains to Shiga toxin-producing Escherichia coli (STEC). In this study, 79 E. coli strains belonging to 35 serotypes isolated from wastewaters of both human and animal origin were examined for the presence of stx2 -carrying bacteriophages in their genomes. The lytic cycle of the bacteriophages was induced by mitomycin, and the bacteriophage fraction was isolated and used for morphological and genetic characterization. The induced bacteriophages showed morphological diversity, as well as restriction fragment length polymorphism variation, in the different strains belonging to different serotypes. The ability to infect new hosts was highly variable, although most of the induced phages infected Shigella sonnei host strain 866. In summary, in spite of carrying either the same or different stx 2 variants and in spite of the fact that they were isolated from strains belonging to the same or different serotypes, the induced bacteriophages were highly variable. The high level of diversity and the great infectious capacity of these phages could enhance the spread of the stx 2 gene and variants of this gene among different bacterial populations in environments to which humans may be exposed.

scholarly journals Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare

2020 ◽  
Author(s):  
E.G. Mogro ◽  
N. Ambrosis ◽  
M.J. Lozano
Keyword(s):  
Bacterial Genome ◽  
Draft Genome ◽  
Supplementary Information ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Link Type ◽  
A Genome ◽  
Phenotypic Variations ◽  
Genome Assemblies ◽  
Straightforward Approach

AbstractMotivationBacterial genomes are composed by a core and an accessory genome. The first composed of housekeeping and essential genes, while the second is composed, in its majority, of mobile genetic elements, including transposable elements (TEs). Insertion sequences (ISs), the smallest TEs, have an important role in genome evolution, and contribute to bacterial genome plasticity and adaptability. ISs can spread in a genome, presenting different locations in nearly related strains, and producing phenotypic variations. Few tools are available which can identify differentially located ISs (DLIS) on assembled genomes.ResultsWe developed ISCompare to profile IS mobilization events in related bacterial strains using complete or draft genome assemblies. ISCompare was validated using artificial genomes with simulated random IS insertions and real sequences, achieving the same or better results than other available tools, with the advantage that ISCompare can analyse multiple ISs at the same time and outputs a list of candidate DLIS. We think that ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes.Availability and implementationISCompare was implemented in python3 and its source code is freely available for download at https://github.com/maurijlozano/ISCompare.Supplementary informationSupplementary data are available at https://github.com/maurijlozano/ISCompare.

Antioxidant and Antibacterial Activities of Artemisia herba-alba Asso Essential Oil from Middle Atlas, Morocco

2018 ◽  
Vol 16 (S1) ◽  
pp. S48-S54
Author(s):  
Y. Ez zoubi ◽  
S. Lairini ◽  
A. Farah ◽  
K. Taghzouti ◽  
A. El Ouali Lalami
Keyword(s):  
Antibacterial Activity ◽  
Essential Oil ◽  
Foodborne Pathogens ◽  
Food Systems ◽  
Antibacterial Activities ◽  
Culture Collection ◽  
Bornyl Acetate ◽  
Bacterial Strains ◽  
Disk Diffusion Assay ◽  
Different Strains

The purpose of this study was to determine the chemical composition and to evaluate the antioxidant and antibacterial effects of the Moroccan Artemisia herba-alba Asso essential oil against foodborne pathogens. The essential oil of Artemisia herba-alba was analyzed by gas chromatography coupled with mass spectroscopy. The antibacterial activity was assessed against three bacterial strains isolated from foodstuff and three bacterial strains referenced by the ATCC (American Type Culture Collection) using the disk diffusion assay and the macrodilution method. The antioxidant activity was evaluated using the DPPH (2, 2-diphenyl-1- picrylhydrazyl) method. The fourteen compounds of the Artemisia herba-alba essential oil were identified; the main components were identified as β-thujone, chrysanthenone, α-terpineol, α-thujone, α-pinene, and bornyl acetate. The results of the antibacterial activity obtained showed a sensitivity of the different strains to Artemisia herba-alba essential oil with an inhibition diameter of 8.50 to 17.00 mm. Concerning the MICs (minimum inhibitory concentrations), the essential oil exhibited much higher antibacterial activity with MIC values of 2.5 μl/ml against Bacillus subtilis ATCC and Lactobacillus sp. The essential oil was found to be active by inhibiting free radicals with an IC50 (concentration of an inhibitor where the response is reduced by half) value of 2.9 μg/ml. These results indicate the possible use of the essential oil on food systems as an effective inhibitor of foodborne pathogens, as a natural antioxidant, and for potential pharmaceutical applications. However, further research is needed in order to determine the toxicity, antibacterial, and antioxidant effects in edible products.

scholarly journals A mechanism for migrating bacterial populations to non-genetically adapt to new environments

2021 ◽  
Author(s):  
Henry H Mattingly ◽  
Thierry Emonet
Keyword(s):  
Collective Behavior ◽  
Group Composition ◽  
Phenotypic Diversity ◽  
Population Expansion ◽  
Migration Speed ◽  
Diverse Population ◽  
Genetic Inheritance ◽  
Bacterial Populations ◽  
Physical Environments ◽  
Varying Environments

Populations of chemotactic bacteria can rapidly expand into new territory by consuming and chasing an attractant cue in the environment, increasing the population's overall growth in nutrient-rich environments. Although the migrating fronts driving this expansion contain cells of multiple swimming phenotypes, the consequences of non-genetic diversity for population expansion are unknown. Here, through theory and simulations, we predict that expanding populations non-genetically adapt their phenotype composition to migrate effectively through multiple physical environments. Swimming phenotypes in the migrating front are spatially sorted by chemotactic performance, but the mapping from phenotype to performance depends on the environment. Therefore, phenotypes that perform poorly localize to the back of the group, causing them to selectively fall behind. Over cell divisions, the group composition dynamically enriches for high-performers, enhancing migration speed and overall growth. Furthermore, non-genetic inheritance controls a trade-off between large composition shifts and slow responsiveness to new environments, enabling a diverse population to out-perform a non-diverse one in varying environments. These results demonstrate that phenotypic diversity and collective behavior can synergize to produce emergent functionalities. Non-genetic inheritance may generically enable bacterial populations to transiently adapt to new situations without mutations, emphasizing that genotype-to-phenotype mappings are dynamic and context-dependent.

scholarly journals Recognition of conserved antigens by Th17 cells provides broad protection against pulmonaryHaemophilus influenzaeinfection

2018 ◽  
Vol 115 (30) ◽  
pp. E7149-E7157 ◽  
Author(s):  
Wenchao Li ◽  
Xinyun Zhang ◽  
Ying Yang ◽  
Qingqin Yin ◽  
Yan Wang ◽  
...  
Keyword(s):  
Th17 Cells ◽  
Antigenic Variation ◽  
Vaccine Development ◽  
Community Acquired Pneumonia ◽  
Chronic Obstructive ◽  
Current Effort ◽  
Obstructive Pulmonary Disease ◽  
Th17 Response ◽  
Homologous Strain ◽  
Different Strains

NontypeableHaemophilus influenzae(NTHi) is a major cause of community acquired pneumonia and exacerbation of chronic obstructive pulmonary disease. A current effort in NTHi vaccine development has focused on generating humoral responses and has been greatly impeded by antigenic variation among the numerous circulating NTHi strains. In this study, we showed that pulmonary immunization of mice with killed NTHi generated broad protection against lung infection by different strains. While passive transfer of immune antibodies protected only against the homologous strain, transfer of immune T cells conferred protection against both homologous and heterologous strains. Further characterization revealed a strong Th17 response that was cross-reactive with different NTHi strains. Responding Th17 cells recognized both cytosolic and membrane-associated antigens, while immune antibodies preferentially responded to surface antigens and were highly strain specific. We further identified several conserved proteins recognized by lung Th17 cells during NTHi infection. Two proteins yielding the strongest responses were tested as vaccine candidates by immunization of mice with purified proteins plus an adjuvant. Immunization induced antigen-specific Th17 cells that recognized different strains and, upon adoptive transfer, conferred protection. Furthermore, immunized mice were protected against challenge with not only NTHi strains but also a fully virulent, encapsulated strain. Together, these results show that the immune mechanism of cross-protection against pneumonia involves Th17 cells, which respond to a broad spectrum of antigens, including those that are highly conserved among NTHi strains. These mechanistic insights suggest that inclusion of Th17 antigens in subunit vaccines offers the advantage of inducing broad protection and complements the current antibody-based approaches.

Connecting Microbial Population Genetics with Microbial Pathogenesis Engineering Microfluidic Cell Arrays for High-throughput Interrogation of Host-Pathogen Interaction

2011 ◽  
pp. 533-548
Author(s):  
Palaniappan Sethu ◽  
Kalyani Putty ◽  
Yongsheng Lian ◽  
Awdhesh Kalia
Keyword(s):  
High Throughput ◽  
Bacterial Species ◽  
Human Cells ◽  
Bacterial Strains ◽  
Cell Array ◽  
Bacterial Populations ◽  
Host Pathogen Interaction ◽  
Gradient Generator ◽  
Molecular Events ◽  
Host Pathogen

A bacterial species typically includes heterogeneous collections of genetically diverse isolates. How genetic diversity within bacterial populations influences the clinical outcome of infection remains mostly indeterminate. In part, this is due to a lack of technologies that can enable contemporaneous systems-level interrogation of host-pathogen interaction using multiple, genetically diverse bacterial strains. This chapter presents a prototype microfluidic cell array (MCA) that allows simultaneous elucidation of molecular events during infection of human cells in a semi-automated fashion. It shows that infection of human cells with up to sixteen genetically diverse bacterial isolates can be studied simultaneously. The versatility of MCAs is enhanced by incorporation of a gradient generator that allows interrogation of host-pathogen interaction under four different concentrations of any given environmental variable at the same time. Availability of high throughput MCAs should foster studies that can determine how differences in bacterial gene pools and concentration-dependent environmental variables affect the outcome of host-pathogen interaction.

scholarly journals T4SP Database 2.0: An Improved Database for Type IV Secretion Systems in Bacterial Genomes with New Online Analysis Tools

2016 ◽  
Vol 2016 ◽  
pp. 1-4 ◽  
Author(s):  
Na Han ◽  
Weiwen Yu ◽  
Yujun Qiang ◽  
Wen Zhang
Keyword(s):  
Recipient Cell ◽  
Bacterial Species ◽  
Genetic Material ◽  
Type Iv Secretion ◽  
Bacterial Strains ◽  
Secretion Systems ◽  
Bacterial Genomes ◽  
Type Iv ◽  
Type Iv Secretion Systems ◽  
User Friendly

Type IV secretion system (T4SS) can mediate the passage of macromolecules across cellular membranes and is essential for virulent and genetic material exchange among bacterial species. The Type IV Secretion Project 2.0 (T4SP 2.0) database is an improved and extended version of the platform released in 2013 aimed at assisting with the detection of Type IV secretion systems (T4SS) in bacterial genomes. This advanced version provides users with web server tools for detecting the existence and variations of T4SS genes online. The new interface for the genome browser provides a user-friendly access to the most complete and accurate resource of T4SS gene information (e.g., gene number, name, type, position, sequence, related articles, and quick links to other webs). Currently, this online database includes T4SS information of 5239 bacterial strains.Conclusions. T4SS is one of the most versatile secretion systems necessary for the virulence and survival of bacteria and the secretion of protein and/or DNA substrates from a donor to a recipient cell. This database on virB/D genes of the T4SS system will help scientists worldwide to improve their knowledge on secretion systems and also identify potential pathogenic mechanisms of various microbial species.

scholarly journals Prophages and Past Prophage-Host Interactions Revealed by CRISPR Spacer Content in a Fish Pathogen

2020 ◽  
Vol 8 (12) ◽  
pp. 1919
Author(s):  
Elina Laanto ◽  
Janne J. Ravantti ◽  
Lotta-Riina Sundberg
Keyword(s):  
Flavobacterium Columnare ◽  
Strain Atcc ◽  
Human Pathogens ◽  
Fish Pathogen ◽  
Bacterial Strains ◽  
Host Interactions ◽  
Different Strains ◽  
Gene Orthologs ◽  
Similar Genome Organization

The role of prophages in the evolution, diversification, or virulence of the fish pathogen Flavobacterium columnare has not been studied thus far. Here, we describe a functional spontaneously inducing prophage fF4 from the F. columnare type strain ATCC 23463, which is not detectable with commonly used prophage search methods. We show that this prophage type has a global distribution and is present in strains isolated from Finland, Thailand, Japan, and North America. The virions of fF4 are myoviruses with contractile tails and infect only bacterial strains originating from Northern Finland. The fF4 resembles transposable phages by similar genome organization and several gene orthologs. Additional bioinformatic analyses reveal several species in the phylum Bacteroidetes that host a similar type of putative prophage, including bacteria that are important animal and human pathogens. Furthermore, a survey of F. columnare Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) spacers indicate a shared evolutionary history between F. columnare strains and the fF4 phage, and another putative prophage in the F. columnare strain ATCC 49512, named p49512. First, CRISPR spacer content from the two CRISPR loci (types II-C and VI-B) of the fF4 lysogen F. columnare ATCC 23463 revealed a phage terminase protein-matching spacer in the VI-B locus. This spacer is also present in two Chinese F. columnare strains. Second, CRISPR analysis revealed four F. columnare strains that contain unique spacers targeting different regions of the putative prophage p49512 in the F. columnare strain ATCC 49512, despite the geographical distance or genomovar of the different strains. This suggests a common ancestry for the F. columnare prophages and different host strains.

scholarly journals Crab Apple Blossoms as a Model for Research on Biological Control of Fire Blight

1997 ◽  
Vol 87 (11) ◽  
pp. 1096-1102 ◽  
Author(s):  
P. L. Pusey
Keyword(s):  
Fire Blight ◽  
Biocontrol Agents ◽  
Suitable Model ◽  
Bacterial Strains ◽  
Bacterial Populations ◽  
Cold Room ◽  
Series Of Experiments ◽  
Population Interactions ◽  
Intact Crab ◽  
Crab Apple

Nonseasonal availability of pomaceous flowers could improve laboratory detection and prefield testing of biocontrol agents for fire blight of pear and apple. Crab apple was selected as a model because of its high flower productivity on 1-year-old wood, high susceptibility to fire blight, and availability from nurseries. Cultivars Manchurian and Snowdrift were manipulated to bloom once by transferring dormant nursery trees from a cold room to a greenhouse and a second time by defoliating trees and applying 1% cytokinin and 0.1% gibberellins to the buds with a brush. Different sets of trees were induced at different times to bloom, so that flowers were produced 12 months in the year. When known bacterial antagonists (Erwinia herbicola strain C9-1 and Pseudomonas fluorescens strain A506) were applied alone or in combination to the stigmas of detached crab apple blossoms prior to inoculation with the pathogen (E. amylovora strain Ea153), population interactions over time were comparable to those reported in previous studies involving pear or apple. In a subsequent series of experiments, the relative effects of 12 bacterial strains on stigmatic populations of strain Ea153 were similar for detached blossoms of crab apple in the laboratory, blossoms of intact crab apple trees in the greenhouse, and blossoms of pear and apple in the field. Additionally, when stigmas of detached crab apple blossoms were inoculated with antagonists (strains C9-1 and A506) and the pathogen, and later subjected to a 24-h wetting period, bacterial populations in the flower hypanthium increased and disease was suppressed. These studies indicate that crab apple blossoms can serve as a suitable model for year-round evaluation and study of biocontrol agents for fire blight.

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