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It has become widely accepted that bacteriophages are extremely abundant and are enormously influential on the biosphere. Bacteriophages kill between 4-50% of the entire bacteria population daily (Suttle, 2005). The aim of this study was to screen soil samples for Pseudomonas aeruginosa lytic phages, select and characterize an isolate morphologically for genome analysis using next generation lllumina sequencing. The lytic isolate was detected using the spot method on lawns of P. aeruginosa. Using the described procedure (Jordan, et al. 2010), LY218 was successfully isolated from soil samples. Transmission electron microscopy (TEM) performed by the University of Alabama at Birmingham (UAB), High Resolution Imaging Facility (HRIF) and lllumina Next Generation Sequencing (NGS) also at UAB, were performed to determine the morphology of the phage. The TEM images reveal that this isolate has a short tail when compared to other Myoviridae phages. Upon performing the Blast NCBI sequence comparison analysis, it was determined that this isolate is 73083 bp and it is 97% identical to the Pseudomonas phage Phi 176, a phage isolated and sequenced in Bath, England. Phi 176, was submitted to the GenBank database with accession number K.M411960. A total of 88 presumptive genes have been identified. Presumptive function of 86 proteins were called based on homology determined by Predict Protein. The 3% difference between these two phage sequences is centered on two proteins of indeterminant function. Sequencing of the LY218 genome revealed a dsDNA with 54.9% G+C content and 356 open reading frames (ORFs) were predicted to be coding sequences. The full nucleotide sequence of the genome of LY218 has been determined, and this has been deposited (the NCBI accession number in MN906996)., INTRODUCTION After returning to France in 1915, the Franco-Canadian microbiologist Felix d'Herelle noticed some mysterious clear spots within his cultures of coccobacilli which he concluded were zones of dead bacteria [...]

Over the past decade, the development of next-generation sequencing for human microbiota has led to remarkable discoveries. The characterization of gastric microbiota has enabled the examination of genera associated with several diseases, including gastritis, precancerous lesions, and gastric cancer. Helicobacter pylori (H. pylori) is well known to cause gastric dysbiosis by reducing diversity, because this bacterium is the predominant bacterium. However, as the diseases developed into more severe stages, such as atrophic gastritis, premalignant lesion, and gastric adenocarcinoma, the dominance of H. pylori began to be displaced by other bacteria, including Streptococcus, Prevotella, Achromobacter, Citrobacter, Clostridium, Rhodococcus, Lactobacillus, and Phyllobacterium. Moreover, a massive reduction in H. pylori in cancer sites was observed as compared with noncancer tissue in the same individual. In addition, several cases of H. pylori-negative gastritis were found. Among these individuals, there was an enrichment of Paludibacter, Dialister, Streptococcus, Haemophilus parainfluenzae, and Treponema. These remarkable findings suggest the major role of gastric microbiota in the development of gastroduodenal diseases and led us to the hypothesis that H. pylori might not be the only gastric pathogen. The gastric microbiota point of view of disease development should lead to a more comprehensive consideration of this relationship. Keywords: Gastric microbiota, Helicobacter pylori, Cancer, Gastric cancer, Gastritis, Precancerous lesion, Author(s): Langgeng Agung Waskito[sup.1,2], Yudith Annisa Ayu Rezkitha[sup.2,3], Ratha-korn Vilaichone[sup.4,5,6,7], Titong Sugihartono[sup.7], Syifa Mustika[sup.8], I Dewa Nyoman Wibawa[sup.9], Yoshio Yamaoka[sup.7,10,11] and Muhammad Miftahussurur[sup.2,7] Background Gastrointestinal (GI) diseases have caused an [...]

The cyclic GMP-AMP synthase (cGAS)-STING pathway is a central component of the cell-autonomous innate immune system in animals.sup.1,2. The cGAS protein is a sensor of cytosolic viral DNA and, upon sensing DNA, it produces a cyclic GMP-AMP (cGAMP) signalling molecule that binds to the STING protein and activates the immune response.sup.3-5. The production of cGAMP has also been detected in bacteria.sup.6, and has been shown, in Vibrio cholerae, to activate a phospholipase that degrades the inner bacterial membrane.sup.7. However, the biological role of cGAMP signalling in bacteria remains unknown. Here we show that cGAMP signalling is part of an antiphage defence system that is common in bacteria. This system is composed of a four-gene operon that encodes the bacterial cGAS and the associated phospholipase, as well as two enzymes with the eukaryotic-like domains E1, E2 and JAB. We show that this operon confers resistance against a wide variety of phages. Phage infection triggers the production of cGAMP, which--in turn--activates the phospholipase, leading to a loss of membrane integrity and to cell death before completion of phage reproduction. Diverged versions of this system appear in more than 10% of prokaryotic genomes, and we show that variants with effectors other than phospholipase also protect against phage infection. Our results suggest that the eukaryotic cGAS-STING antiviral pathway has ancient evolutionary roots that stem from microbial defences against phages. cGAMP signalling in bacteria mediates anti-phage defence, as part of a genetic system suggested to be the ancient ancestor of the animal cGAS-STING innate immune pathway., Author(s): Daniel Cohen [sup.1] , Sarah Melamed [sup.1] , Adi Millman [sup.1] , Gabriela Shulman [sup.1] , Yaara Oppenheimer-Shaanan [sup.1] , Assaf Kacen [sup.2] , Shany Doron [sup.1] , Gil [...]

Cytosolic inflammasome complexes mediated by a pattern recognition receptor (PRR) defend against pathogen infection by activating caspase 1. Pyrin, a candidate PRR, can bind to the inflammasome adaptor ASC to form a caspase 1-activating complex (1,2). Mutations in the Pyrin-encoding gene, MEFV, cause a human autoinflammatory disease known as familial Mediterranean fever (3-5). Despite important roles in immunity and disease, the physiological function of Pyrin remains unknown. Here we show that Pyrin mediates caspase 1 inflammasome activation in response to Rho-glucosylation activity of cytotoxin TcdB (6-8), a major virulence factor of Clostridium difficile, which causes most cases of nosocomial diarrhoea. The glucosyltransferase-inactive TcdB mutant loses the inflammasome-stimulating activity. Other Rho-inactivating toxins, including FIC-domain adenylyltransferases (Vibrio parahaemolyticus VopS and Histophilus somni IbpA) and Clostridium botulinum ADP-ribosylating C3 toxin, can also biochemically activate the Pyrin inflammasome in their enzymatic activitydependent manner. These toxins all target the Rho subfamily and modify a switch-I residue. We further demonstrate that Burkholderia cenocepacia inactivates RHOA by deamidating Asn41, also in the switch-I region, and thereby triggers Pyrin inflammasome activation, both of which require the bacterial type VI secretion system (T6SS). Loss of the Pyrin inflammasome causes elevated intra-macrophage growth of B. cenocepacia and diminished lung inflammation in mice. Thus, Pyrin functions to sense pathogen modification and inactivation of Rho GTPases, representing a new paradigm in mammalian innate immunity., C. difficile is the major cause of hospital-acquired infectious diarrhoea and antibiotic-associated pseudomembranous colitis. The major virulence factors of C. difficile are two secreted protein toxins (TcdA and TcdB) (7,8). [...]

TTC ATT AAT ACG ACT CAC TTC, Organisms are defined by the information encoded in their genomes, and since the origin of life this information has been encoded using a two-base-pair genetic alphabet (A-T and G-C). In [...]