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https://www.readbyqxmd.com/read/29331569/salinivibrio-kushneri-sp-nov-a-moderately-halophilic-bacterium-isolated-from-salterns
#1
Clara López-Hermoso, Rafael R de la Haba, Cristina Sánchez-Porro, Antonio Ventosa
Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184T, IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37°C, at pH 7.2-7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAGT (99...
December 21, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29325559/pangenome-analyses-of-the-wheat-pathogen-zymoseptoria-tritici-reveal-the-structural-basis-of-a-highly-plastic-eukaryotic-genome
#2
Clémence Plissonneau, Fanny E Hartmann, Daniel Croll
BACKGROUND: Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence...
January 11, 2018: BMC Biology
https://www.readbyqxmd.com/read/29324905/strains-of-bacterial-species-induce-a-greatly-varied-acute-adaptive-immune-response-the-contribution-of-the-accessory-genome
#3
Uri Sela, Chad W Euler, Joel Correa da Rosa, Vincent A Fischetti
A fundamental question in human susceptibility to bacterial infections is to what extent variability is a function of differences in the pathogen species or in individual humans. To focus on the pathogen species, we compared in the same individual the human adaptive T and B cell immune response to multiple strains of two major human pathogens, Staphylococcus aureus and Streptococcus pyogenes. We found wide variability in the acute adaptive immune response induced by various strains of a species, with a unique combination of activation within the two arms of the adaptive response...
January 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29247056/genome-sequencing-links-persistent-outbreak-of-legionellosis-in-sydney-to-an-emerging-clone-of-legionella-pneumophila-st211
#4
Verlaine J Timms, Rebecca Rockett, Nathan L Bachmann, Elena Martinez, Qinning Wang, Sharon C-A Chen, Neisha Jeoffreys, Peter J Howard, Anna Smith, Sheena Adamson, Robin Gilmour, Vicky Sheppeard, Vitali Sintchenko
The city of Sydney, Australia, experienced a persistent outbreak of Legionella pneumophila serogroup 1 (Lp1) pneumonia in 2016. To elucidate the source and guide public health actions the genomes of clinical and environmental Lp1 isolates recovered over 7 weeks were examined. A total of 48 isolates from human cases and cooling towers were sequenced and compared using SNP-based, core-genome MLST and pangenome approaches. All three methods confirmed phylogenetic relatedness between isolates associated with outbreaks in the Central Business District (CBD) in March and May and Suburb 1...
December 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29247013/whole-genome-sequencing-reveals-transmission-of-gonococcal-antibiotic-resistance-among-men-who-have-sex-with-men-an-observational-study
#5
Jason C Kwong, Eric P F Chow, Kerrie Stevens, Timothy P Stinear, Torsten Seemann, Christopher K Fairley, Marcus Y Chen, Benjamin P Howden
OBJECTIVES: Drug-resistant Neisseria gonorrhoeae are now a global public health threat. Direct transmission of antibiotic-resistant gonococci between individuals has been proposed as a driver for the increased transmission of resistance, but direct evidence of such transmission is limited. Whole-genome sequencing (WGS) has superior resolution to investigate outbreaks and disease transmission compared with traditional molecular typing methods such as multilocus sequence typing (MLST) and N...
December 15, 2017: Sexually Transmitted Infections
https://www.readbyqxmd.com/read/29237792/zoonotic-transfer-of-clostridium-difficile-harboring-antimicrobial-resistance-between-farm-animals-and-humans
#6
C W Knetsch, N Kumar, S C Forster, T R Connor, H P Browne, C Harmanus, I M Sanders, S R Harris, L Turner, T Morris, M Perry, F Miyajima, P Roberts, M Pirmohamed, J G Songer, J S Weese, A Indra, J Corver, M Rupnik, B W Wren, T V Riley, E J Kuijper, T D Lawley
The emergence of Clostridium difficile as a significant human diarrheal pathogen is associated with the production of highly transmissible spores and the acquisition of antimicrobial resistance genes (ARGs) and virulence factors. Unlike the hospital associated C. difficile RT027 lineage, the community associated C. difficile RT078 lineage is isolated from both humans and farm animals; however, the geographical population structure and transmission networks remain unknown. Here we applied whole genome phylogenetic analysis of 248 C...
December 13, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29212929/nucleic-acid-polymers-are-active-against-hepatitis-delta-virus-infection-in-vitro
#7
Frauke Beilstein, Matthieu Blanchet, Andrew Vaillant, Camille Sureau
In this study, an in vitro infection model for the hepatitis delta virus (HDV) was used to evaluate the antiviral effects of phosphorothioate nucleic acid polymers (NAPs) and investigate their mechanism of action. The results show that NAPs inhibit HDV infection at less than 4 micromolar concentrations in cultures of differentiated human hepatoma cells. NAPs were shown to be active at viral entry, but inactive post entry on HDV RNA replication. Inhibition was independent of the NAPs nucleotide sequence, but dependent on both size and amphipathicity of the polymer...
December 6, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29205771/homoeologous-exchange-is-a-major-cause-of-gene-presence-absence-variation-in-the-amphidiploid-brassica-napus
#8
Bhavna Hurgobin, Agnieszka A Golicz, Philipp E Bayer, Chon-Kit Kenneth Chan, Soodeh Tirnaz, Aria Dolatabadian, Sarah V Schiessl, Birgit Samans, Juan D Montenegro, Isobel A P Parkin, J Chris Pires, Boulos Chalhoub, Graham J King, Rod Snowdon, Jacqueline Batley, David Edwards
Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In the present study we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B...
December 4, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29183332/a-novel-ruminococcus-gnavus-clade-enriched-in-inflammatory-bowel-disease-patients
#9
Andrew Brantley Hall, Moran Yassour, Jenny Sauk, Ashley Garner, Xiaofang Jiang, Timothy Arthur, Georgia K Lagoudas, Tommi Vatanen, Nadine Fornelos, Robin Wilson, Madeline Bertha, Melissa Cohen, John Garber, Hamed Khalili, Dirk Gevers, Ashwin N Ananthakrishnan, Subra Kugathasan, Eric S Lander, Paul Blainey, Hera Vlamakis, Ramnik J Xavier, Curtis Huttenhower
BACKGROUND: Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes. METHODS: We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2...
November 28, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29079617/staphylococcus-edaphicus-sp-nov-isolated-in-antarctica-harbours-mecc-gene-and-genomic-islands-with-suspected-role-in-adaptation-to-extreme-environment
#10
Roman Pantůček, Ivo Sedláček, Adéla Indráková, Veronika Vrbovská, Ivana Mašlaňová, Vojtěch Kovařovic, Pavel Švec, Stanislava Králová, Lucie Krištofová, Jana Kekláková, Petr Petráš, Jiří Doškař
Two Gram-stain-positive, coagulase-negative staphylococcal strains were isolated from abiotic sources, stone fragments and sandy soil in James Ross Island, Antarctica. Here we describe properties of novel species of the genus Staphylococcus that has near identical 16S rRNA gene sequence to Staphylococcus saprophyticus However, compared to S. saprophyticus and the next closest relatives, the new species demonstrates considerable phylogenetic distance at whole genome level, average nucleotide identity <85 %, and inferred DNA-DNA hybridization <30%...
October 27, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29077859/panx-pan-genome-analysis-and-exploration
#11
Wei Ding, Franz Baumdicker, Richard A Neher
Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates-the pan-genome-is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization for interactive exploration of the pan-genome...
October 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29068466/too-much-eukaryote-lgt
#12
REVIEW
William F Martin
The realization that prokaryotes naturally and frequently disperse genes across steep taxonomic boundaries via lateral gene transfer (LGT) gave wings to the idea that eukaryotes might do the same. Eukaryotes do acquire genes from mitochondria and plastids and they do transfer genes during the process of secondary endosymbiosis, the spread of plastids via eukaryotic algal endosymbionts. From those observations it, however, does not follow that eukaryotes transfer genes either in the same ways as prokaryotes do, or to a quantitatively similar degree...
October 25, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29067021/comparative-genomics-of-facultative-bacterial-symbionts-isolated-from-european-orius-species-reveals-an-ancestral-symbiotic-association
#13
Xiaorui Chen, Matthew D Hitchings, José E Mendoza, Virginia Balanza, Paul D Facey, Paul J Dyson, Pablo Bielza, Ricardo Del Sol
Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29049350/an-integrative-in-silico-approach-for-therapeutic-target-identification-in-the-human-pathogen-corynebacterium-diphtheriae
#14
Syed Babar Jamal, Syed Shah Hassan, Sandeep Tiwari, Marcus V Viana, Leandro de Jesus Benevides, Asad Ullah, Adrián G Turjanski, Debmalya Barh, Preetam Ghosh, Daniela Arruda Costa, Artur Silva, Richard Röttger, Jan Baumbach, Vasco A C Azevedo
Corynebacterium diphtheriae (Cd) is a Gram-positive human pathogen responsible for diphtheria infection and once regarded for high mortalities worldwide. The fatality gradually decreased with improved living standards and further alleviated when many immunization programs were introduced. However, numerous drug-resistant strains emerged recently that consequently decreased the efficacy of current therapeutics and vaccines, thereby obliging the scientific community to start investigating new therapeutic targets in pathogenic microorganisms...
2017: PloS One
https://www.readbyqxmd.com/read/29048510/donor-derived-mycoplasma-hominis-and-an-apparent-cluster-of-m-hominis-cases-in-solid-organ-transplant-recipients
#15
Olivia C Smibert, Heather L Wilson, Asma Sohail, Shanti Narayanasamy, Mark B Schultz, Susan A Ballard, Jason C Kwong, Jim de Boer, C Orla Morrissey, Anton Y Peleg, Greg I Snell, Miranda A Paraskeva, Adam W J Jenney
Background: Invasive and disseminated Mycoplasma hominis infections are well recognized but uncommon complications in solid organ transplant recipients. In a single center, a cluster of M. hominis infections were identified in lung transplant recipients from the same thoracic intensive care unit (ICU). We sought to determine the source(s) of these infections. Methods: Medical records of the donor and infected transplant recipients were reviewed for clinical characteristics...
October 16, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29047329/genome-sequencing-of-39-akkermansia-muciniphila-isolates-reveals-its-population-structure-genomic-and-functional-diverisity-and-global-distribution-in-mammalian-gut-microbiotas
#16
Xianfeng Guo, Shenghui Li, Jiachun Zhang, Feifan Wu, Xiangchun Li, Dan Wu, Min Zhang, Zihao Ou, Zhuye Jie, Qiulong Yan, Peng Li, Jiangfeng Yi, Yongzheng Peng
BACKGROUND: Akkermansia muciniphila is one of the most dominant bacteria that resides on the mucus layer of intestinal tract and plays key role in human health, however, little is known about its genomic content. RESULTS: Herein, we for the first time characterized the genomic architecture of A. muciniphila based on whole-genome sequencing, assembling, and annotating of 39 isolates derived from human and mouse feces. We revealed a flexible open pangenome of A. muciniphila currently consisting of 5644 unique proteins...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29020009/genome-sequences-of-lower-great-lakes-microcystis-sp-reveal-strain-specific-genes-that-are-present-and-expressed-in-western-lake-erie-blooms
#17
Kevin Anthony Meyer, Timothy W Davis, Susan B Watson, Vincent J Denef, Michelle A Berry, Gregory J Dick
Blooms of the potentially toxic cyanobacterium Microcystis are increasing worldwide. In the Laurentian Great Lakes they pose major socioeconomic, ecological, and human health threats, particularly in western Lake Erie. However, the interpretation of "omics" data is constrained by the highly variable genome of Microcystis and the small number of reference genome sequences from strains isolated from the Great Lakes. To address this, we sequenced two Microcystis isolates from Lake Erie (Microcystis aeruginosa LE3 and M...
2017: PloS One
https://www.readbyqxmd.com/read/28977764/comparative-genomic-and-plasmid-analysis-of-beer-spoiling-and-non-beer-spoiling-lactobacillus-brevis-isolates
#18
Jordyn Bergsveinson, Barry Ziola
Beer-spoilage-related lactic acid bacteria (BSR LAB) belong to multiple genera and species; however, beer-spoilage capacity is isolate-specific and partially acquired via horizontal gene transfer within the brewing environment. Thus, the extent to which genus-, species-, or environment- (i.e., brewery-) level genetic variability influences beer-spoilage phenotype is unknown. Publicly available Lactobacillus brevis genomes were analyzed via BlAst Diagnostic Gene findEr (BADGE) for BSR genes and assessed for pangenomic relationships...
October 4, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28970823/new-insights-into-the-diversity-of-the-genus-faecalibacterium
#19
Leandro Benevides, Sriti Burman, Rebeca Martin, Véronique Robert, Muriel Thomas, Sylvie Miquel, Florian Chain, Harry Sokol, Luis G Bermudez-Humaran, Mark Morrison, Philippe Langella, Vasco A Azevedo, Jean-Marc Chatel, Siomar Soares
Faecalibacterium prausnitzii is a commensal bacterium, ubiquitous in the gastrointestinal tracts of animals and humans. This species is a functionally important member of the microbiota and studies suggest it has an impact on the physiology and health of the host. F. prausnitzii is the only identified species in the genus Faecalibacterium, but a recent study clustered strains of this species in two different phylogroups. Here, we propose the existence of distinct species in this genus through the use of comparative genomics...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28957508/phenetic-comparison-of-prokaryotic-genomes-using-k-mers
#20
Maxime Déraspe, Frédéric Raymond, Sébastien Boisvert, Alexander Culley, Paul H Roy, François Laviolette, Jacques Corbeil
Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated the methodology using simulated genomes and previously published phylogenomic studies of Streptococcus pneumoniae and Pseudomonas aeruginosa. We also investigated the relationship of specific genetic determinants with bacterial population structures...
October 1, 2017: Molecular Biology and Evolution
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