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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
https://www.readbyqxmd.com/read/28945251/graphtyper-enables-population-scale-genotyping-using-pangenome-graphs
#12
Hannes P Eggertsson, Hakon Jonsson, Snaedis Kristmundsdottir, Eirikur Hjartarson, Birte Kehr, Gisli Masson, Florian Zink, Kristjan E Hjorleifsson, Aslaug Jonasdottir, Adalbjorg Jonasdottir, Ingileif Jonsdottir, Daniel F Gudbjartsson, Pall Melsted, Kari Stefansson, Bjarni V Halldorsson
A fundamental requirement for genetic studies is an accurate determination of sequence variation. While human genome sequence diversity is increasingly well characterized, there is a need for efficient ways to use this knowledge in sequence analysis. Here we present Graphtyper, a publicly available novel algorithm and software for discovering and genotyping sequence variants. Graphtyper realigns short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths...
November 2017: Nature Genetics
https://www.readbyqxmd.com/read/28894437/evolution-of-stenotrophomonas-maltophilia-in-cystic-fibrosis-lung-over-chronic-infection-a-genomic-and-phenotypic-population-study
#13
Alfonso Esposito, Arianna Pompilio, Clotilde Bettua, Valentina Crocetta, Elisabetta Giacobazzi, Ersilia Fiscarelli, Olivier Jousson, Giovanni Di Bonaventura
Stenotrophomonas maltophilia has been recognized as an emerging multi-drug resistant opportunistic pathogen in cystic fibrosis (CF) patients. We report a comparative genomic and phenotypic analysis of 91 S. maltophilia strains from 10 CF patients over a 12-year period. Draft genome analyses included in silico Multi-Locus Sequence Typing (MLST), Single-Nucleotide Polymorphisms (SNPs), and pangenome characterization. Growth rate, biofilm formation, motility, mutation frequency, in vivo virulence, and in vitro antibiotic susceptibility were determined and compared with population structure over time...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28890711/horizontally-acquired-genes-are-often-shared-between-closely-related-bacterial-species
#14
Evgeni Bolotin, Ruth Hershberg
Horizontal gene transfer (HGT) serves as an important source of innovation for bacterial species. We used a pangenome-based approach to identify genes that were horizontally acquired by four closely related bacterial species, belonging to the Enterobacteriaceae family. This enabled us to examine the extent to which such closely related species tend to share horizontally acquired genes. We find that a high percent of horizontally acquired genes are shared among these closely related species. Furthermore, we demonstrate that the extent of sharing of horizontally acquired genes among these four closely related species is predictive of the extent to which these genes will be found in additional bacterial species...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28887423/forensic-human-identification-using-skin-microbiomes
#15
Sarah E Schmedes, August E Woerner, Bruce Budowle
The human microbiome contributes significantly to the genetic content of the human body. Genetic and environmental factors help shape the microbiome, and as such, the microbiome can be unique to an individual. Previous studies have demonstrated the potential to use microbiome profiling for forensic applications, however a method has yet to identify stable features of skin microbiomes that produce high classification accuracies for samples collected over reasonably long time intervals. A novel approach is described to classify skin microbiomes to their donors by comparing two features types, Propionibacterium acnes pangenome presence/absence features and nucleotide diversities of stable clade-specific markers...
September 8, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28878862/permanent-draft-genome-sequence-of-frankia-sp-nrrl-b-16219-reveals-the-presence-of-canonical-nod-genes-which-are-highly-homologous-to-those-detected-in-candidatus-frankia-dg1-genome
#16
Amir Ktari, Imen Nouioui, Teal Furnholm, Erik Swanson, Faten Ghodhbane-Gtari, Louis S Tisa, Maher Gtari
Frankia sp. NRRL B-16219 was directly isolated from a soil sample obtained from the rhizosphere of Ceanothus jepsonii growing in the USA. Its host plant range includes members of Elaeagnaceae species. Phylogenetically, strain NRRL B-16219 is closely related to "Frankia discariae" with a 16S rRNA gene similarity of 99.78%. Because of the lack of genetic tools for Frankia, our understanding of the bacterial signals involved during the plant infection process and the development of actinorhizal root nodules is very limited...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28826610/calling-chromosome-alterations-dna-methylation-statuses-and-mutations-in-tumors-by-simple-targeted-next-generation-sequencing-a-solution-for-transferring-integrated-pangenomic-studies-into-routine-practice
#17
Simon Garinet, Mario Néou, Bruno de La Villéon, Simon Faillot, Julien Sakat, Juliana P Da Fonseca, Anne Jouinot, Christophe Le Tourneau, Maud Kamal, Windy Luscap-Rondof, Valentina Boeva, Sebastien Gaujoux, Michel Vidaud, Eric Pasmant, Franck Letourneur, Jérôme Bertherat, Guillaume Assié
Pangenomic studies identified distinct molecular classes for many cancers, with major clinical applications. However, routine use requires cost-effective assays. We assessed whether targeted next-generation sequencing (NGS) could call chromosomal alterations and DNA methylation status. A training set of 77 tumors and a validation set of 449 (43 tumor types) were analyzed by targeted NGS and single-nucleotide polymorphism (SNP) arrays. Thirty-two tumors were analyzed by NGS after bisulfite conversion, and compared to methylation array or methylation-specific multiplex ligation-dependent probe amplification...
September 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28821232/genomic-transcriptomic-and-proteomic-approaches-towards-understanding-the-molecular-mechanisms-of-salt-tolerance-in-frankia-strains-isolated-from-casuarina-trees
#18
Rediet Oshone, Mariama Ngom, Feixia Chu, Samira Mansour, Mame Ourèye Sy, Antony Champion, Louis S Tisa
BACKGROUND: Soil salinization is a worldwide problem that is intensifying because of the effects of climate change. An effective method for the reclamation of salt-affected soils involves initiating plant succession using fast growing, nitrogen fixing actinorhizal trees such as the Casuarina. The salt tolerance of Casuarina is enhanced by the nitrogen-fixing symbiosis that they form with the actinobacterium Frankia. Identification and molecular characterization of salt-tolerant Casuarina species and associated Frankia is imperative for the successful utilization of Casuarina trees in saline soil reclamation efforts...
August 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28756981/congenital-undifferentiated-sarcoma-associated-to-bcor-ccnb3-gene-fusion
#19
Clara Alfaro-Cervello, Verónica Andrade-Gamarra, Gema Nieto, Lara Navarro, Susana Martín-Vañó, Juan Pablo García de la Torre, María Bengoa Caamaño, Mª Luisa García Mauriño, Rosa Noguera, Samuel Navarro
Small round cell sarcomas are aggressive bone and soft tissue tumors that predominantly affect children and young adults. A new group of sarcomas with a recurrent BCOR-CCNB3 gene fusion has been recently identified in previously unclassifiable small round cell sarcomas. BCOR-CCNB3 sarcomas share clinical and pathologic similarities with Ewing sarcoma, but show a stronger male predilection and less aggressiveness, as well as distinct gene expression profiling and pangenomic SNP array analyses. We report the unusual case of a congenital BCOR-CCNB3 retroperitoneal sarcoma in a female born at 34th gestational week, which was diagnosed in necropsy after 21hours of life...
July 14, 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28705964/draft-genome-sequences-of-seven-streptococcus-agalactiae-strains-isolated-from-camelus-dromedarius-at-the-horn-of-africa
#20
Julian Rothen, Tobias Schindler, Joël F Pothier, Mario Younan, Ulrich Certa, Claudia Daubenberger, Valentin Pflüger, Joerg Jores
We present draft whole-genome sequences of seven Streptococcus agalactiae strains isolated from Camelus dromedarius in Kenya and Somalia. These data are an extension to the group B Streptococcus (GBS) pangenome and might provide more insight into the underlying mechanisms of pathogenicity and antibiotic resistance of camel GBS.
July 13, 2017: Genome Announcements
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