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https://www.readbyqxmd.com/read/28811754/comparative-genome-analysis-of-rathayibacter-tritici-ncppb-1953-with-rathayibacter-toxicus-strains-can-facilitate-studies-on-mechanisms-of-nematode-association-and-host-infection
#1
Jungwook Park, Pyeong An Lee, Hyun-Hee Lee, Kihyuck Choi, Seon-Woo Lee, Young-Su Seo
Rathayibacter tritici, which is a Gram positive, plant pathogenic, non-motile, and rod-shaped bacterium, causes spike blight in wheat and barley. For successful pathogenesis, R. tritici is associated with Anguina tritici, a nematode, which produces seed galls (ear cockles) in certain plant varieties and facilitates spread of infection. Despite significant efforts, little research is available on the mechanism of disease or bacteria-nematode association of this bacterium due to lack of genomic information. Here, we report the first complete genome sequence of R...
August 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/28811656/phageterm-a-tool-for-fast-and-accurate-determination-of-phage-termini-and-packaging-mechanism-using-next-generation-sequencing-data
#2
Julian R Garneau, Florence Depardieu, Louis-Charles Fortier, David Bikard, Marc Monot
The worrying rise of antibiotic resistance in pathogenic bacteria is leading to a renewed interest in bacteriophages as a treatment option. Novel sequencing technologies enable description of an increasing number of phage genomes, a critical piece of information to understand their life cycle, phage-host interactions, and evolution. In this work, we demonstrate how it is possible to recover more information from sequencing data than just the phage genome. We developed a theoretical and statistical framework to determine DNA termini and phage packaging mechanisms using NGS data...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28811613/transcriptomic-analysis-of-nickel-exposure-in-sphingobium-sp-ba1-cells-using-rna-seq
#3
M Volpicella, C Leoni, C Manzari, M Chiara, E Picardi, E Piancone, F Italiano, A D'Erchia, M Trotta, D S Horner, G Pesole, L R Ceci
Nickel acts as cofactor for a number of enzymes of many bacteria species. Its homeostasis is ensured by proteins working as ion efflux or accumulation systems. These mechanisms are also generally adopted to counteract life-threatening high extra-cellular Ni(2+) concentrations. Little is known regarding nickel tolerance in the genus Sphingobium. We studied the response of the novel Sphingobium sp. ba1 strain, able to adapt to high Ni(2+) concentrations. Differential gene expression in cells cultured in 10 mM Ni(2+), investigated by RNA-seq analysis, identified 118 differentially expressed genes...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28809851/grape-pomace-compost-harbors-organohalide-respiring-dehalogenimonas-species-with-novel-reductive-dehalogenase-genes
#4
Yi Yang, Steven A Higgins, Jun Yan, Burcu Şimşir, Karuna Chourey, Ramsunder Iyer, Robert L Hettich, Brett Baldwin, Dora M Ogles, Frank E Löffler
Organohalide-respiring bacteria have key roles in the natural chlorine cycle; however, most of the current knowledge is based on cultures from contaminated environments. We demonstrate that grape pomace compost without prior exposure to chlorinated solvents harbors a Dehalogenimonas (Dhgm) species capable of using chlorinated ethenes, including the human carcinogen and common groundwater pollutant vinyl chloride (VC) as electron acceptors. Grape pomace microcosms and derived solid-free enrichment cultures were able to dechlorinate trichloroethene (TCE) to less chlorinated daughter products including ethene...
August 15, 2017: ISME Journal
https://www.readbyqxmd.com/read/28809850/function-related-replacement-of-bacterial-siderophore-pathways
#5
Hilke Bruns, Max Crüsemann, Anne-Catrin Letzel, Mohammad Alanjary, James O McInerney, Paul R Jensen, Stefan Schulz, Bradley S Moore, Nadine Ziemert
Bacterial genomes are rife with orphan biosynthetic gene clusters (BGCs) associated with secondary metabolism of unrealized natural product molecules. Often up to a tenth of the genome is predicted to code for the biosynthesis of diverse metabolites with mostly unknown structures and functions. This phenomenal diversity of BGCs coupled with their high rates of horizontal transfer raise questions about whether they are really active and beneficial, whether they are neutral and confer no advantage, or whether they are carried in genomes because they are parasitic or addictive...
August 15, 2017: ISME Journal
https://www.readbyqxmd.com/read/28809146/mycobacterium-talmoniae-sp-nov-a-slowly-growing-mycobacterium-isolated-from-human-respiratory-samples
#6
Rebecca M Davidson, Mary Ann DeGroote, Jamie L Marola, Sarah Buss, Victoria Jones, Michael R McNeil, Alison G Freifeld, L Elaine Epperson, Nabeeh A Hasan, Mary Jackson, Peter C Iwen, Max Salfinger, Michael Strong
A novel slowly growing, non-chromogenic species of the class Actinobacteria was isolated from a human respiratory sample in Nebraska, USA, in 2012. Analysis of the internal transcribed spacer sequence supported placement into the genus Mycobacterium with high sequence similarity to a previously undescribed strain isolated from a patient respiratory sample from Oregon, USA, held in a collection in Colorado, USA, in 2000. The two isolates were subjected to phenotypic testing and whole genome sequencing and found to be indistinguishable...
August 15, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28809143/bacillus-swezeyi-sp-nov-and-bacillus-haynesii-sp-nov-isolated-from-desert-soil
#7
Christopher A Dunlap, David A Schisler, Elizabeth B Perry, Nora Connor, Frederick M Cohan, Alejandro P Rooney
Two isolates of Gram-reaction-positive, facultatively anaerobic, motile, rod-shaped, endospore-forming bacteria were identified during a survey of the diversity of strains belonging to the genus Bacillus deposited in the Agriculture Research Service Culture Collection. These strains were originally isolated from soil in Evolution Canyon III (Israel) in a survey of ecological diversification. Phylogenetic analysis of the 16S rRNA gene of strains NRRL B-41294T and NRRL B-41327T determined they were closely related to members of the Bacillus licheniformis clade...
August 15, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28808742/a-more-comprehensive-community-of%C3%A2-ammonia-oxidizing-archaea-aoa-revealed-by-genomic-dna-and-rna-analyses-of-amoa-gene-in-subtropical-acidic-forest-soils
#8
Ruo-Nan Wu, Han Meng, Yong-Feng Wang, Wensheng Lan, Ji-Dong Gu
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4...
August 14, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28808230/environmental-drivers-of-a-microbial-genomic-transition-zone-in-the-ocean-s-interior
#9
Daniel R Mende, Jessica A Bryant, Frank O Aylward, John M Eppley, Torben Nielsen, David M Karl, Edward F DeLong
The core properties of microbial genomes, including GC content and genome size, are known to vary widely among different bacteria and archaea (1,2) . Several hypotheses have been proposed to explain this genomic variability, but the fundamental drivers that shape bacterial and archaeal genomic properties remain uncertain (3-7) . Here, we report the existence of a sharp genomic transition zone below the photic zone, where bacterial and archaeal genomes and proteomes undergo a community-wide punctuated shift...
August 14, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28808132/defining-electron-bifurcation-in-the-electron-transferring-flavoprotein-family
#10
Amaya M Garcia Costas, Saroj Poudel, Anne-Frances Miller, Gerrit J Schut, Rhesa N Ledbetter, Kathryn R Fixen, Lance C Seefeldt, Michael W W Adams, Caroline S Harwood, Eric S Boyd, John W Peters
Electron bifurcation is the coupling of exergonic and endergonic redox reactions to simultaneously generate (or utilize) low and high potential electrons. It is the third recognized form of energy conservation in biology and has recently been described in select electron transferring flavoproteins (Etfs). Etfs are flavin-containing heterodimers best known for donating electrons derived from fatty acid and amino acid oxidation to an electron transfer respiratory chain via ETF quinone oxidoreductase. Canonical examples contain a flavin adenine dinucleotide (FAD) that is involved in electron transfer as well as a non-redox active adenosine monophosphate (AMP)...
August 14, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28806924/essential-genome-of-campylobacter-jejuni
#11
Rabindra K Mandal, Tieshan Jiang, Young Min Kwon
BACKGROUND: Campylobacter species are a leading cause of bacterial foodborne illness worldwide. Despite the global efforts to curb them, Campylobacter infections have increased continuously in both developed and developing countries. The development of effective strategies to control the infection by this pathogen is warranted. The essential genes of bacteria are the most prominent targets for this purpose. In this study, we used transposon sequencing (Tn-seq) of a genome-saturating library of Tn5 insertion mutants to define the essential genome of C...
August 14, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28806750/characterization-of-novel-bangle-lectin-from-photorhabdus-asymbiotica-with-dual-sugar-binding-specificity-and-its-effect-on-host-immunity
#12
Gita Jančaříková, Josef Houser, Pavel Dobeš, Gabriel Demo, Pavel Hyršl, Michaela Wimmerová
Photorhabdus asymbiotica is one of the three recognized species of the Photorhabdus genus, which consists of gram-negative bioluminescent bacteria belonging to the family Morganellaceae. These bacteria live in a symbiotic relationship with nematodes from the genus Heterorhabditis, together forming a complex that is highly pathogenic for insects. Unlike other Photorhabdus species, which are strictly entomopathogenic, P. asymbiotica is unique in its ability to act as an emerging human pathogen. Analysis of the P...
August 14, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28805302/torix-group-rickettsia-are-widespread-in-culicoides-biting-midges-diptera-ceratopogonidae-reach-high-frequency-and-carry-unique-genomic-features
#13
Jack Pilgrim, Mats Ander, Claire Garros, Matthew Baylis, Gregory D D Hurst, Stefanos Siozios
There is increasing interest in the heritable bacteria of invertebrate vectors of disease as they present novel targets for control initiatives. Previous studies on biting midges (Culicoides spp.), known to transmit several RNA viruses of veterinary importance, have revealed infections with the endosymbiotic bacteria, Wolbachia and Cardinium. However, rickettsial symbionts in these vectors are underexplored. Here, we present the genome of a previously uncharacterized Rickettsia endosymbiont from Culicoides newsteadi (RiCNE)...
August 14, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28803698/genomics-and-ecology-of-novel-n2o-reducing-microorganisms
#14
REVIEW
Sara Hallin, Laurent Philippot, Frank E Löffler, Robert A Sanford, Christopher M Jones
Microorganisms with the capacity to reduce the greenhouse gas nitrous oxide (N2O) to harmless dinitrogen gas are receiving increased attention due to increasing N2O emissions (and our need to mitigate climate change) and to recent discoveries of novel N2O-reducing bacteria and archaea. The diversity of denitrifying and nondenitrifying microorganisms with capacity for N2O reduction was recently shown to be greater than previously expected. A formerly overlooked group (clade II) in the environment include a large fraction of nondenitrifying N2O reducers, which could be N2O sinks without major contribution to N2O formation...
August 10, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28802691/the-genome-analysis-of-oleiphilus-messinensis-me102-dsm-13489-t-reveals-backgrounds-of-its-obligate-alkane-devouring-marine-lifestyle
#15
Stepan V Toshchakov, Alexei A Korzhenkov, Tatyana N Chernikova, Manuel Ferrer, Olga V Golyshina, Michail M Yakimov, Peter N Golyshin
Marine bacterium Oleiphilus messinensis ME102 (DSM 13489(T)) isolated from the sediments of the harbor of Messina (Italy) is a member of the order Oceanospirillales, class Gammaproteobacteria, representing the physiological group of marine obligate hydrocarbonoclastic bacteria (OHCB) alongside the members of the genera Alcanivorax, Oleispira, Thalassolituus, Cycloclasticus and Neptunomonas. These organisms play a crucial role in the natural environmental cleanup in marine systems. Despite having the largest genome (6...
August 9, 2017: Marine Genomics
https://www.readbyqxmd.com/read/28802266/functional-analysis-of-genes-encoded-by-the-locus-of-heat-resistance-lhr-in-escherichia-coli
#16
Ryan Mercer, Oanh Nguyen, Qixing Ou, Lynn McMullen, Michael G Gänzle
The locus of heat resistance (LHR) is a 15 - 19 kb genomic island conferring exceptional heat resistance to organisms in the family Enterobacteriaceae including pathogenic strains of Salmonella enterica and Escherichia coli The complement of LHR-encoded genes that is necessary for heat resistance and the stress- or growth-phase induced expression of LHR-encoded genes are unknown. This study determined the contribution of the 7 LHR-encoded genes yfdX1GI, yfdX2, hdeDGI, orf11, trxGI, kefB, and psiEGI by comparison of the heat resistance of E...
August 11, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28802036/transcription-replication-conflicts-orientation-matters
#17
Yea-Lih Lin, Philippe Pasero
Interference between DNA replication and transcription represents a major source of genomic instability. In this issue of Cell, Lang et al. and Hamperl et al. show that head-on collisions, but not codirectional collisions, impede fork progression in bacteria and in human cells by promoting the formation of RNA-DNA hybrids known as R-loops.
August 10, 2017: Cell
https://www.readbyqxmd.com/read/28801673/photosensitizer-in-lipid-nanoparticle-a-nano-scaled-approach-to-antibacterial-function
#18
Bishakh Rout, Chi-Hsien Liu, Wei-Chi Wu
Photosensitization-based antimicrobial therapy (PAT) is an alternative therapy aimed at achieving bacterial inactivation. Researchers use various photosensitizers to achieve bacterial inactivation. However, the most widely used approach involves the use of photosensitizers dispersed in aqueous solution, which could limit the effectiveness of photodynamic inactivation. Therefore, the approaches to encapsulate the photosensitizer in appropriate vehicles can enhance the delivery of the photosensitizer. Herein, Toluidine Blue O (TBO) was the photosensitizer, and lipid nanoparticles were used for its encapsulation...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28800585/comparative-pathogenomics-of-clostridium-tetani
#19
Jonathan E Cohen, Rong Wang, Rong-Fong Shen, Wells W Wu, James E Keller
Clostridium tetani and Clostridium botulinum produce two of the most potent neurotoxins known, tetanus neurotoxin and botulinum neurotoxin, respectively. Extensive biochemical and genetic investigation has been devoted to identifying and characterizing various C. botulinum strains. Less effort has been focused on studying C. tetani likely because recently sequenced strains of C. tetani show much less genetic diversity than C. botulinum strains and because widespread vaccination efforts have reduced the public health threat from tetanus...
2017: PloS One
https://www.readbyqxmd.com/read/28800137/chemical-dispersants-enhance-the-activity-of-oil-and-gas-condensate-degrading-marine-bacteria
#20
Julien Tremblay, Etienne Yergeau, Nathalie Fortin, Susan Cobanli, Miria Elias, Thomas L King, Kenneth Lee, Charles W Greer
Application of chemical dispersants to oil spills in the marine environment is a common practice to disperse oil into the water column and stimulate oil biodegradation by increasing its bioavailability to indigenous bacteria capable of naturally metabolizing hydrocarbons. In the context of a spill event, the biodegradation of crude oil and gas condensate off eastern Canada is an essential component of a response strategy. In laboratory experiments, we simulated conditions similar to an oil spill with and without the addition of chemical dispersant under both winter and summer conditions and evaluated the natural attenuation potential for hydrocarbons in near-surface sea water from the vicinity of crude oil and natural gas production facilities off eastern Canada...
August 11, 2017: ISME Journal
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