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prophage induction

Aleksandra Dydecka, Bożena Nejman-Faleńczyk, Sylwia Bloch, Gracja Topka, Agnieszka Necel, Logan W Donaldson, Grzegorz Węgrzyn, Alicja Węgrzyn
The exo-xis region of lambdoid bacteriophage genomes contains several established and potential genes that are evolutionarily conserved, but not essential for phage propagation under laboratory conditions. Nevertheless, deletion or overexpression of either the whole exo-xis region and important regulatory elements can significantly influence the regulation of phage development. This report defines specific roles for orf60a and orf61 in bacteriophage λ and Φ24B , a specific Shiga toxin-converting phage with clinical relevance...
October 11, 2018: Viruses
Raphael Freiherr von Boeselager, Eugen Pfeifer, Julia Frunzke
Phenotypic diversification is key to microbial adaptation. Currently, advanced technological approaches offer insights into cell-to-cell variation of bacterial populations at a spatiotemporal resolution. However, the underlying molecular causes or consequences often remain obscure. In this study, we developed a workflow combining fluorescence-activated cell sorting and RNA-sequencing, thereby allowing transcriptomic analysis of 106 bacterial cells. As a proof of concept, the workflow was applied to study prophage induction in a subpopulation of Corynebacterium glutamicum...
October 5, 2018: Scientific Reports
Svetlana Alexeeva, Jesús Adrián Guerra Martínez, Maciej Spus, Eddy J Smid
BACKGROUND: In complex microbial ecosystems such as the marine environment, the gastrointestinal tract, but also in mixed culture fermentations, bacteriophages are frequently found to be a part of the microbial community. Moreover, prophages or prophage-like elements are frequently identified in sequenced bacterial genomes. The mixed undefined starter cultures represent an ecosystem which is shaped by long term evolution under relatively defined environmental conditions and provides an interesting model to study co-evolution of phages and their hosts as well as the impact of diversity on microbial community stability...
September 24, 2018: BMC Microbiology
Travis N Mavrich, Eoghan Casey, Joana Oliveira, Francesca Bottacini, Kieran James, Charles M A P Franz, Gabriele Andrea Lugli, Horst Neve, Marco Ventura, Graham F Hatfull, Jennifer Mahony, Douwe van Sinderen
In the current report, we describe the identification of three genetically distinct groups of prophages integrated into three different chromosomal sites of human gut-associated Bifidobacterium breve and Bifidobacterium longum strains. These bifidobacterial prophages are distantly related to temperate actinobacteriophages of several hosts. Some prophages, integrated within the dnaJ2 gene, are competent for induction, excision, replication, assembly and lysis, suggesting that they are fully functional and can generate infectious particles, even though permissive hosts have not yet been identified...
August 24, 2018: Scientific Reports
Mengyu Shen, Yuhui Yang, Wei Shen, Lujia Cen, Jeffrey S McLean, Wenyuan Shi, Shuai Le, Xuesong He
The human oral cavity is home to a large number of bacteria and bacteriophages (phages). However, the biology of oral phages as members of the human microbiome is not well understood. Recently, we isolated Actinomyces odontolyticus subsp. actinosynbacter strain XH001 from the human oral cavity, and genomic analysis revealed the presence of an intact prophage named xhp1. Here, we demonstrated that xhp1 is a linear plasmid-like prophage, which is a newly identified phage of A. odontolyticus The prophage xhp1 genome is a 35-kb linear double-stranded DNA with 10-bp single-stranded, 3' cohesive ends...
September 1, 2018: Applied and Environmental Microbiology
Alfred Fillol-Salom, Roser Martínez-Rubio, Rezheen F Abdulrahman, John Chen, Robert Davies, José R Penadés
Phage-inducible chromosomal islands (PICIs) are a recently discovered family of pathogenicity islands that contribute substantively to horizontal gene transfer, host adaptation and virulence in Gram-positive cocci. Here we report that similar elements also occur widely in Gram-negative bacteria. As with the PICIs from Gram-positive cocci, their uniqueness is defined by a constellation of features: unique and specific attachment sites, exclusive PICI genes, a phage-dependent mechanism of induction, conserved replication origin organization, convergent mechanisms of phage interference, and specific packaging of PICI DNA into phage-like infectious particles, resulting in very high transfer frequencies...
September 2018: ISME Journal
Shaohua Hu, Lin Cao, Yiyin Wu, Yajun Zhou, Tao Jiang, Liqiang Wang, Qiujing Wang, Desong Ming, Shicheng Chen, Mingxi Wang
Myroides odoratimimus is an important nosocomial pathogen. Management of M. odoratimimus infection is difficult owing to the multidrug resistance and the unknown pathogenesis mechanisms. Based on our previous genomic sequencing data of M. odoratimimus PR63039 (isolated from a patient with the urinary tract infection), in this study, we further performed comparative genomic analysis for 10 selected Myroides strains. Our results showed that these Myroides genome contexts were very similar and phylogenetically related...
May 23, 2018: MicrobiologyOpen
Joanna Mokracka, Sylwia Krzymińska, Danił Ałtunin, Dariusz Wasyl, Ryszard Koczura, Krzysztof Dudek, Monika Dudek, Zofia Anna Chyleńska, Anna Ekner-Grzyb
The aim of this study was to estimate virulence potential of Salmonella enterica strains colonizing the gut of free-living sand lizards (Lacerta agilis L.). The strains belonged to three Salmonella serovars: Abony, Schleissheim, and Telhashomer. Adhesion and invasion abilities of the strains were determined in quantitative assays using the gentamicin protection method. Induction of apoptosis was assessed using HeLa cell monolayers. PCR assays were used for detection of 26 virulence genes localised within mobile elements: pathogenicity islands, virulence plasmids, and prophage sequences...
October 2018: Antonie Van Leeuwenhoek
Gaylen A Uhlich, Elisa Andreozzi, Bryan J Cottrell, Erin R Reichenberger, Xinmin Zhang, George C Paoli
The high frequency of prophage insertions in the mlrA gene of clinical serotype O157:H7 isolates renders such strains deficient in csgD-dependent biofilm formation but prophage induction may restore certain mlrA properties. In this study we used transcriptomics to study the effect of high and low sulfamethoxazole-trimethoprim (SMX-TM) concentrations on prophage induction, biofilm regulation, and virulence gene expression in strain PA20 under environmental conditions following 5-hour and 12-hour exposures in broth or on agar...
2018: PloS One
Dolonchapa Chakraborty, Eric Clark, Steven A Mauro, Gerald B Koudelka
Shiga toxin (Stx)-encoding E. coli (STEC) strains are responsible for sporadic outbreaks of food poisoning dating to 1982, when the first STEC strain, E. coli O157:H7, was isolated. Regardless of STEC serotype, the primary symptoms of STEC infections are caused by Stx that is synthesized from genes resident on lambdoid prophage present in STEC. Despite similar etiology, the severity of STEC-mediated disease varies by outbreak. However, it is unclear what modulates the severity of STEC-mediated disease. Stx production and release is controlled by lytic growth of the Stx-encoding bacteriophage, which in turn, is controlled by the phage repressor...
April 29, 2018: Viruses
J Dylan Shropshire, Jungmin On, Emily M Layton, Helen Zhou, Seth R Bordenstein
Wolbachia are maternally inherited, intracellular bacteria at the forefront of vector control efforts to curb arbovirus transmission. In international field trials, the cytoplasmic incompatibility (CI) drive system of w Mel Wolbachia is deployed to replace target vector populations, whereby a Wolbachia -induced modification of the sperm genome kills embryos. However, Wolbachia in the embryo rescue the sperm genome impairment, and therefore CI results in a strong fitness advantage for infected females that transmit the bacteria to offspring...
May 8, 2018: Proceedings of the National Academy of Sciences of the United States of America
Margarita Andreevskaya, Elina Jääskeläinen, Per Johansson, Anne Ylinen, Lars Paulin, Johanna Björkroth, Petri Auvinen
Psychrotrophic lactic acid bacteria (LAB) are the prevailing spoilage organisms in packaged cold-stored meat products. Species composition and metabolic activities of such LAB spoilage communities are determined by the nature of the meat product, storage conditions, and interspecies interactions. Our knowledge of system level responses of LAB during such interactions is very limited. To expand it, we studied interactions between three common psychrotrophic spoilage LAB ( Leuconostoc gelidum , Lactococcus piscium , and Lactobacillus oligofermentans ) by comparing their time course transcriptome profiles obtained during their growth in individual, pairwise, and triple cultures...
July 1, 2018: Applied and Environmental Microbiology
Jeffrey K Cornuault, Marie-Agnès Petit, Mahendra Mariadassou, Leandro Benevides, Elisabeth Moncaut, Philippe Langella, Harry Sokol, Marianne De Paepe
BACKGROUND: Viral metagenomic studies have suggested a role for bacteriophages in intestinal dysbiosis associated with several human diseases. However, interpretation of viral metagenomic studies is limited by the lack of knowledge of phages infecting major human gut commensal bacteria, such as Faecalibacterium prausnitzii, a bacterial symbiont repeatedly found depleted in inflammatory bowel disease (IBD) patients. In particular, no complete genomes of phages infecting F. prausnitzii are present in viral databases...
April 3, 2018: Microbiome
Sylwia Bloch, Bożena Nejman-Faleńczyk, Karolina Pierzynowska, Ewa Piotrowska, Alicja Węgrzyn, Christelle Marminon, Zouhair Bouaziz, Pascal Nebois, Joachim Jose, Marc Le Borgne, Luciano Saso, Grzegorz Węgrzyn
Oxidative stress may be the major cause of induction of Shiga toxin-converting (Stx) prophages from chromosomes of Shiga toxin-producing Escherichia coli (STEC) in human intestine. Thus, we aimed to test a series of novel antioxidant compounds for their activities against prophage induction, thus, preventing pathogenicity of STEC. Forty-six compounds (derivatives of carbazole, indazole, triazole, quinolone, ninhydrine, and indenoindole) were tested. Fifteen of them gave promising results and were further characterized...
December 2018: Journal of Enzyme Inhibition and Medicinal Chemistry
Philip Kelleher, Jennifer Mahony, Katharina Schweinlin, Horst Neve, Charles M Franz, Douwe van Sinderen
Lactococcus lactis is a lactic acid bacterium that is intensively and globally exploited in commercial dairy food fermentations. Though the presence of prophages in lactococcal genomes is widely reported, only limited studies pertaining to the stability of prophages in lactococcal genomes have been performed. The current study reports on the complete genome exploration of thirty lactococcal strains for the presence of potentially intact prophages, so as to assess their genomic diversity and the associated risk or benefit of harbouring such prophages...
May 2, 2018: International Journal of Food Microbiology
Núria Daranas, Anna Bonaterra, Jesús Francés, Jordi Cabrefiga, Emilio Montesinos, Esther Badosa
A viability quantitative PCR (v-qPCR) assay was developed for the unambiguous detection and quantification of Lactobacillus plantarum PM411 viable cells in aerial plant surfaces. A 972-bp region of a PM411 predicted prophage with mosaic architecture enabled the identification of a PM411 strain-specific molecular marker. Three primer sets with different amplicon lengths (92, 188, and 317 bp) and one TaqMan probe were designed. All the qPCR assays showed good linearity over a 4-log range and good efficiencies but differed in sensitivity...
May 15, 2018: Applied and Environmental Microbiology
A Krüger, J Burgán, A W Friedrich, J W A Rossen, P M A Lucchesi
Shiga toxins (Stx) are the main virulence factor of a pathogroup of Escherichia coli strains that cause severe human diseases. These toxins are encoded in prophages (Stx prophages), and generally their expression depends on prophage induction. Several studies have reported high diversity among both Stx prophages and Stx. In particular, the toxin subtype Stx2a is associated with high virulence and HUS. Here, we report the genome of ArgO145, an inducible Stx2a prophage identified in a bovine O145:H- strain which produced high levels of Shiga toxin and Stx phage particles...
June 2018: Infection, Genetics and Evolution
María Soledad Vela Gurovic, Fátima R Viceconte, Marcelo T Pereyra, Maximiliano A Bidegain, María Amelia Cubitto
ETHNOPHARMACOLOGICAL RELEVANCE: Ganoderma lucidum (Lingzhi or Reishi) is a medicinal mushroom historically used in Asian countries to treat a wide variety of diseases and prolong life. In the last years, G. lucidum has been internationally recognized as an effective adjuvant in cancer treatment. Among active components, the most recent research indicates that polysaccharides modulate the immune response favoring the recovery from toxicity of chemo and radiotherapy while triterpenes are cytotoxic to tumoral cells mainly by altering gene expression...
May 10, 2018: Journal of Ethnopharmacology
Amelia R I Lindsey, Danny W Rice, Sarah R Bordenstein, Andrew W Brooks, Seth R Bordenstein, Irene L G Newton
The bacterial endosymbiont Wolbachia manipulates arthropod reproduction to facilitate its maternal spread through host populations. The most common manipulation is cytoplasmic incompatibility (CI): Wolbachia-infected males produce modified sperm that cause embryonic mortality, unless rescued by embryos harboring the same Wolbachia. The genes underlying CI, cifA and cifB, were recently identified in the eukaryotic association module of Wolbachia's prophage WO. Here, we use transcriptomic and genomic approaches to address three important evolutionary facets of the cif genes...
February 1, 2018: Genome Biology and Evolution
Alexander Harms, Cinzia Fino, Michael A Sørensen, Szabolcs Semsey, Kenn Gerdes
Bacterial persisters are phenotypic variants that survive antibiotic treatment in a dormant state and can be formed by multiple pathways. We recently proposed that the second messenger (p)ppGpp drives Escherichia coli persister formation through protease Lon and activation of toxin-antitoxin (TA) modules. This model found considerable support among researchers studying persisters but also generated controversy as part of recent debates in the field. In this study, we therefore used our previous work as a model to critically examine common experimental procedures to understand and overcome the inconsistencies often observed between results of different laboratories...
December 12, 2017: MBio
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