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 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.

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 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.

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 bcgTree: automatized phylogenetic tree building from bacterial core genomes

Genome ◽  
2016 ◽  
Vol 59 (10) ◽  
pp. 783-791 ◽  
Author(s):  
Markus J. Ankenbrand ◽  
Alexander Keller
Keyword(s):  
Markov Models ◽  
Bacterial Species ◽  
Single Copy ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Sequencing Technologies ◽  
Genus Lactobacillus ◽  
Standard Task ◽  
Tree Building ◽  
High Level

The need for multi-gene analyses in scientific fields such as phylogenetics and DNA barcoding has increased in recent years. In particular, these approaches are increasingly important for differentiating bacterial species, where reliance on the standard 16S rDNA marker can result in poor resolution. Additionally, the assembly of bacterial genomes has become a standard task due to advances in next-generation sequencing technologies. We created a bioinformatic pipeline, bcgTree, which uses assembled bacterial genomes either from databases or own sequencing results from the user to reconstruct their phylogenetic history. The pipeline automatically extracts 107 essential single-copy core genes, found in a majority of bacteria, using hidden Markov models and performs a partitioned maximum-likelihood analysis. Here, we describe the workflow of bcgTree and, as a proof-of-concept, its usefulness in resolving the phylogeny of 293 publically available bacterial strains of the genus Lactobacillus. We also evaluate its performance in both low- and high-level taxonomy test sets. The tool is freely available at github ( https://github.com/iimog/bcgTree ) and our institutional homepage ( http://www.dna-analytics.biozentrum.uni-wuerzburg.de ).

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

2021 ◽  
Author(s):  
Ezequiel G Mogro ◽  
Nicolás M Ambrosis ◽  
Mauricio J Lozano
Keyword(s):  
Insertion Sequence ◽  
Bacterial Genome ◽  
Draft Genome ◽  
Genome Plasticity ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
A Genome ◽  
Phenotypic Variations ◽  
Genome Assemblies ◽  
Straightforward Approach

Abstract Bacterial genomes are composed of core and accessory genomes. The first is composed of housekeeping and essential genes, while the second is highly enriched in 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 (DLISs) on assembled genomes. Here, we introduce ISCompare, a new program 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 analyze multiple ISs at the same time and outputs a list of candidate DLISs. ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes.

scholarly journals Pathogenic Escherichia coli – virulence mechanisms

2016 ◽  
Vol 72 (6) ◽  
pp. 352-357
Author(s):  
Katarzyna Półtorak ◽  
Kinga Wieczorek ◽  
Jacek Osek
Keyword(s):  
Bloodstream Infections ◽  
Epidemiological Data ◽  
Intestinal Epithelial ◽  
Bacterial Strains ◽  
Internal Organs ◽  
E Coli ◽  
Cellular Processes ◽  
Pathogenic Escherichia Coli ◽  
Different Strains

E. coli are the predominant microorganisms in the human gastrointestinal tract. In most cases, they exist as harmless comensals, and some of them are beneficial to their host in balancing gut flora and absorption of nutrients. However, there are pathogenic strains that cause a broad range of diseases in humans and animals, from diarrhea to bloodstream infections. Among bacterial strains causing these symptoms, seven pathotypes are now recognized: enteropathogenic E. coli (EPEC), shiga toxin-producing E. coli (STEC), enterotoxigenic E. coli (ETEC), enteroinvasive E. coli (EIEC), enteroaggregative E. coli (EAEC), diffusely adherent E. coli (DAEC), and adherent-invasive E. coli (AIEC). Several different strains cause diverse diseases by means of virulence factors that facilitate their interactions with the host, including colonization of the intestinal epithelial surfaces, crossing of the mucosal barriers, invasion of the bloodstream and internal organs or producing toxins that affect various cellular processes. Pathogenic E. coli are commonly studied in humans, animals, food and the environment, in developed and developing countries. The presented paper reviews recent information concerning the pathogenic mechanisms of E. coli, the role of animals and food in the transmission chain and a short overview of epidemiological data.

scholarly journals MCF-7 Human Breast Adenocarcinoma Anticancer and Antimicrobial, in silico Docking and ADME Prediction Studies of Furan Moiety Containing Substituted 2-Aminopyrimidine Derivatives

2021 ◽  
Vol 33 (7) ◽  
pp. 1504-1512
Author(s):  
Manju Mathew ◽  
Muthuvel Ramanathan Ezhilarasi
Keyword(s):  
In Silico ◽  
Antimicrobial Activities ◽  
Docking Studies ◽  
Breast Adenocarcinoma ◽  
Bacterial Strains ◽  
In Silico Docking ◽  
In Silico Studies ◽  
Furan Moiety ◽  
Different Strains

A series of 4(5-(4-chlorophenyl)furan-2-yl)-6-phenylpyrimidin-2-amine derivatives (5a-h) were synthesized from 2-(4-chlorophenyl)-5-styrylfuran (3a-h) with guanidine nitrate in absolute ethanol under conventional method and evaluated for their in vitro anticancer, antimicrobial activities and in silico studies. The chemical structure of the furan moiety containing substituted amino pyrimidine derivatives (5a-h) were elucidated from spectroscopic analysis like infrared, 1H & 13C NMR spectral data and CHN analysis. in silico docking studies were predicted for the synthesized compounds (5a-h) using bacterial protein 1UAG and in silico ADME predictions were also carried for the synthesized compounds (5a-h). The in vitro anticancer study was carried the compound 5b by MMT assay. Compound 5b shows the LC50 value of 120.15 ± 0.003 μg/mL. in vitro Antimicrobial activities were screened for the compounds (5a-h) using different strains. Compound 5h has electron withdrawing group in benzene ring substituted in the para position showed good antimicrobial activity against all the bacterial strains and fungal strains. in silico studies, compound 5h shows excellent docking score (-9.7 kcal/mol) compared with ciprofloxacin (-7.8 kcal/mol).

scholarly journals PLaBAse: A comprehensive web resource for analyzing the plant growth-promoting potential of plant-associated bacteria

2021 ◽  
Author(s):  
Sascha Patz ◽  
Anupam Gautam ◽  
Becker Matthias ◽  
Silke Ruppel ◽  
Pablo Rodriguez Palenzuela ◽  
...  
Keyword(s):  
Plant Growth ◽  
Marker Gene ◽  
Plant Production ◽  
Symbiotic Bacteria ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
Associated Bacteria ◽  
Web Resource ◽  
Plant Growth Promoting ◽  
Growth Promoting

Plant-beneficial microorganisms are gaining importance for sustainable plant production and phytosanitary practices. Yet there is a lack of computational approaches targeting bacterial traits associated with plant growth-promotion (PGP), which hinders the in-silico identification, comparison, and selection of phytostimulatory bacterial strains. To address this problem, we have developed the new web resource PLaBAse (v1.01, http://plabase.informatik.uni-tuebingen.de/pb/plabase.php), which provides a number of services, including (i) a database for screening 5,565 plant-associated bacteria (PLaBA-db), (ii) a tool for predicting plant growth-promoting traits (PGPTs) of single bacterial genomes (PGPT-Pred), and (iii) a tool for the prediction of bacterial plant-association by marker gene identification (PIFAR-Pred). The latter was developed by Martĺnez-Garcĺa et al. and is now hosted at University of Tuebingen. The PGPT-Pred tool is based on our new PGPT ontology, a literature- and OMICs-curated, comprehensive, and hierarchical collection of ~6,900 PGPTs that are associated with 6,965,955 protein sequences. To study the distribution of the PGPTs across different environments, we applied it to 70,540 bacterial strains associated with (i) seven different environments (including plants), (iii) five different plant spheres (organs), and (iii) two bacteria-induced plant phenotypes. This analysis revealed that plant-symbiotic bacteria generally have a larger genome size and a higher count of PGPT-annotated protein encoding genes. Obviously, not all reported PGPTs are restricted to -or only enriched in- plant-associated and plant symbiotic bacteria. Some also occur in human- and animal-associated bacteria, perhaps due to the transmission of PGP bacteria (PGPBs) between environments, or because some functions are involved in adaption processes to various environments. Here we provide an easy-to-use approach for screening of PGPTs in bacterial genomes across various phyla and isolation sites, using PLaBA-db, and for standardized annotation, using PGPT-Pred. We believe that this resource will improve our understanding about the entire PGP processes and facilitate the prediction of PGPB as bio-inoculants and for biosafety strategies, so as to help to establish sustainable and targeted bacteria-incorporated plant production systems in the future.

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