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https://www.readbyqxmd.com/read/28637301/eden-evolutionary-dynamics-within-environments
#1
Philipp C Münch, Bärbel Stecher, Alice C McHardy
Summary: Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data...
June 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28625995/novel-antibiotic-resistance-determinants-from-agricultural-soil-exposed-to-antibiotics-widely-used-in-human-medicine-and-animal-farming
#2
Calvin Ho-Fung Lau, Kalene van Engelen, Stephen Gordon, Justin Renaud, Edward Topp
Antibiotic resistance has emerged globally as one of the biggest threats to human and animal health. Although the excessive use of antibiotics is recognized for accelerating the selection for resistance, there is a growing body of evidence suggesting that natural environments are "hotspots" for the development of both ancient and contemporary resistance mechanisms. Given that pharmaceuticals can be entrained onto agricultural land through anthropogenic activities, this could be a potential driver for the emergence and dissemination of resistance in soil bacteria...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28611758/genome-wide-analyses-reveal-genes-subject-to-positive-selection-in-pasteurella-multocida
#3
Peili Cao, Dongchun Guo, Jiasen Liu, Qian Jiang, Zhuofei Xu, Liandong Qu
Pasteurella multocida, a Gram-negative opportunistic pathogen, has led to a broad range of diseases in mammals and birds, including fowl cholera in poultry, pneumonia and atrophic rhinitis in swine and rabbit, hemorrhagic septicemia in cattle, and bite infections in humans. In order to better interpret the genetic diversity and adaptation evolution of this pathogen, seven genomes of P. multocida strains isolated from fowls, rabbit and pigs were determined by using high-throughput sequencing approach. Together with publicly available P...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28594829/mendel-md-a-user-friendly-open-source-web-tool-for-analyzing-wes-and-wgs-in-the-diagnosis-of-patients-with-mendelian-disorders
#4
Raony G C C L Cardenas, Natália D Linhares, Raquel L Ferreira, Sérgio D J Pena
Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human Mendelian disorders. As pangenomic agnostic tests, they are capable of more accurate and agile diagnosis compared to traditional sequencing methods. This article describes new software called Mendel,MD, which combines multiple types of filter options and makes use of regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants for experimental validation and possible diagnosis...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28593194/fine-scale-structure-analysis-shows-epidemic-patterns-of-clonal-complex-95-a-cosmopolitan-escherichia-coli-lineage-responsible-for-extraintestinal-infection
#5
David M Gordon, Sarah Geyik, Olivier Clermont, Claire L O'Brien, Shiwei Huang, Charmalie Abayasekara, Ashwin Rajesh, Karina Kennedy, Peter Collignon, Paul Pavli, Christophe Rodriguez, Brian D Johnston, James R Johnson, Jean-Winoc Decousser, Erick Denamur
The Escherichia coli lineage known as clonal complex 95 (CC95) is a cosmopolitan human-associated lineage responsible for a significant fraction of extraintestinal infections of humans. Whole-genome sequence data of 200 CC95 strains from various origins enabled determination of the CC95 pangenome. The pangenome analysis revealed that strains of the complex could be assigned to one of five subgroups that vary in their serotype, extraintestinal virulence, virulence gene content, and antibiotic resistance gene profile...
May 2017: MSphere
https://www.readbyqxmd.com/read/28560114/differentiation-of-bifidobacterium-longum-subspecies-longum-and-infantis-by-quantitative-pcr-using-functional-gene-targets
#6
Blair Lawley, Karen Munro, Alan Hughes, Alison J Hodgkinson, Colin G Prosser, Dianne Lowry, Shao J Zhou, Maria Makrides, Robert A Gibson, Christophe Lay, Charmaine Chew, Pheng Soon Lee, Khai Hong Wong, Gerald W Tannock
BACKGROUND: Members of the genus Bifidobacterium are abundant in the feces of babies during the exclusively-milk-diet period of life. Bifidobacterium longum is reported to be a common member of the infant fecal microbiota. However, B. longum is composed of three subspecies, two of which are represented in the bowel microbiota (B. longum subsp. longum; B. longum subsp. infantis). B. longum subspecies are not differentiated in many studies, so that their prevalence and relative abundances are not accurately known...
2017: PeerJ
https://www.readbyqxmd.com/read/28475226/molecular-cytogenetic-characterization-of-five-f8-complex-rearrangements-utility-for-haemophilia-a-genetic-counselling
#7
Y Jourdy, N Chatron, M Fretigny, M L Carage, H Chambost, S Claeyssens-Donadel, V Roussel-Robert, C Negrier, D Sanlaville, C Vinciguerra
BACKGROUND: Genomic inversions are usually balanced, but unusual patterns have been described in haemophilia A (HA) patients for intron 22 (Inv22) and intron 1 (Inv1) inversions leading to the hypothesis of more complex rearrangements involving deletions or duplications. AIM: To characterize five abnormal patterns either in Southern blot and long-range PCR for Inv22 or in PCR for Inv1. MATERIALS AND METHODS: All patients were studied using cytogenetic microarray analysis (CMA)...
May 5, 2017: Haemophilia: the Official Journal of the World Federation of Hemophilia
https://www.readbyqxmd.com/read/28403535/assembly-and-comparison-of-two-closely-related-brassica-napus-genomes
#8
Philipp E Bayer, Bhavna Hurgobin, Agnieszka A Golicz, Chon-Kit Kenneth Chan, Yuxuan Yuan, HueyTyng Lee, Michael Renton, Jinling Meng, Ruiyuan Li, Yan Long, Jun Zou, Ian Bancroft, Boulos Chalhoub, Graham J King, Jacqueline Batley, David Edwards
As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the B...
April 12, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28369330/comparative-genomics-of-rhodococcus-equi-virulence-plasmids-indicates-host-driven-evolution-of-the-vap-pathogenicity-island
#9
Iain MacArthur, Elisa Anastasi, Sonsiray Alvarez, Mariela Scortti, José A Vázquez-Boland
The conjugative virulence plasmid is a key component of the Rhodococcus equi accessory genome essential for pathogenesis. Three host-associated virulence plasmid types have been identified the equine pVAPA and porcine pVAPB circular variants, and the linear pVAPN found in bovine (ruminant) isolates. We recently characterized the R. equi pangenome (Anastasi E, et al. 2016. Pangenome and phylogenomic analysis of the pathogenic actinobacterium Rhodococcus equi. Genome Biol Evol. 8:3140-3148.) and we report here the comparative analysis of the virulence plasmid genomes...
May 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28350002/why-prokaryotes-have-pangenomes
#10
James O McInerney, Alan McNally, Mary J O'Connell
No abstract text is available yet for this article.
March 28, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28337203/a-universal-vaccine-against-leptospirosis-are-we-going-in-the-right-direction
#11
André Alex Grassmann, Jéssica Dias Souza, Alan John Alexander McBride
Leptospirosis is the most widespread zoonosis in the world and a neglected tropical disease estimated to cause severe infection in more than one million people worldwide every year that can be combated by effective immunization. However, no significant progress has been made on the leptospirosis vaccine since the advent of bacterins over 100 years. Although protective against lethal infection, particularly in animals, bacterin-induced immunity is considered short term, serovar restricted, and the vaccine can cause serious side effects...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28321969/the-pangenome-of-the-genus-clostridium
#12
Zulema Udaondo, Estrella Duque, Juan Luis Ramos
We present the pangenome for the genus Clostridium sensu stricto, which was obtained using highly curated and annotated genomes from 16 species, some of these cause disease, while others are used for the production of added-value chemicals. Multilocus sequencing analysis revealed that species of this genus group into at least two clades that include non-pathogenic and pathogenic strains, suggesting that pathogenicity is dispersed across the phylogenetic tree. The core genome of the genus includes 546 protein families, which mainly comprise those involved in protein translation and DNA repair...
March 21, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28314726/global-distribution-patterns-and-pangenomic-diversity-of-the-candidate-phylum-latescibacteria-ws3
#13
Ibrahim F Farag, Noha H Youssef, Mostafa S Elshahed
We investigated the global distribution patterns and pangenomic diversity of the candidate phylum "Latescibacteria" (WS3) in 16S rRNA gene as well as metagenomic data sets. We document distinct distribution patterns for various "Latescibacteria" orders in 16S rRNA gene data sets, with prevalence of orders sediment_1 in terrestrial, PBSIII_9 in groundwater and temperate freshwater, and GN03 in pelagic marine, saline-hypersaline, and wastewater habitats. Using a fragment recruitment approach, we identified 68...
May 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28287462/snp-discovery-using-a-pangenome-has-the-single-reference-approach-become-obsolete
#14
REVIEW
Bhavna Hurgobin, David Edwards
Increasing evidence suggests that a single individual is insufficient to capture the genetic diversity within a species due to gene presence absence variation. In order to understand the extent to which genomic variation occurs in a species, the construction of its pangenome is necessary. The pangenome represents the complete set of genes of a species; it is composed of core genes, which are present in all individuals, and variable genes, which are present only in some individuals. Aside from variations at the gene level, single nucleotide polymorphisms (SNPs) are also an important form of genetic variation...
March 11, 2017: Biology
https://www.readbyqxmd.com/read/28231383/the-pangenome-of-hexaploid-bread-wheat
#15
Juan D Montenegro, Agnieszka A Golicz, Philipp E Bayer, Bhavna Hurgobin, HueyTyng Lee, Chon-Kit Kenneth Chan, Paul Visendi, Kaitao Lai, Jaroslav Doležel, Jacqueline Batley, David Edwards
There is an increasing understanding that variation in gene presence-absence plays an important role in the heritability of agronomic traits; however, there have been relatively few studies on variation in gene presence-absence in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic diversity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome diversity found in current modern elite cultivars...
June 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28194158/role-and-regulation-of-acc-deaminase-gene-in-sinorhizobium-meliloti-is-it-a-symbiotic-rhizospheric-or-endophytic-gene
#16
Alice Checcucci, Elisa Azzarello, Marco Bazzicalupo, Anna De Carlo, Giovanni Emiliani, Stefano Mancuso, Giulia Spini, Carlo Viti, Alessio Mengoni
Plant-associated bacteria exhibit a number of different strategies and specific genes allow bacteria to communicate and metabolically interact with plant tissues. Among the genes found in the genomes of plant-associated bacteria, the gene encoding the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) is one of the most diffused. This gene is supposed to be involved in the cleaving of plant-produced ACC, the precursor of the plant stress-hormone ethylene toning down the plant response to infection...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28187427/genomic-islands-an-overview-of-current-software-and-future-improvements
#17
Siomar de Castro Soares, Letícia de Castro Oliveira, Arun Kumar Jaiswal, Vasco Azevedo
Microbes are highly diverse and widely distributed organisms. They account for ~60% of Earth’s biomass and new predictions point for the existence of 1011 to 1012 species, which are constantly sharing genes through several different mechanisms. Genomic Islands (GI) are critical in this context, as they are large regions acquired through horizontal gene transfer. Also, they present common features like genomic signature deviation, transposase genes, flanking tRNAs and insertion sequences. GIs carry large numbers of genes related to specific lifestyle and are commonly classified in Pathogenicity, Resistance, Metabolic or Symbiotic Islands...
December 22, 2016: Journal of Integrative Bioinformatics
https://www.readbyqxmd.com/read/28130242/hierarchical-sets-analyzing-pangenome-structure-through-scalable-set-visualizations
#18
Thomas Lin Pedersen
Motivation: The increase in available microbial genome sequences has resulted in an increase in the size of the pangenomes being analyzed. Current pangenome visualizations are not intended for the pangenome sizes possible today and new approaches are necessary in order to convert the increase in available information to increase in knowledge. As the pangenome data structure is essentially a collection of sets we explore the potential for scalable set visualization as a tool for pangenome analysis...
June 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28125655/assessing-the-genotypic-differences-between-strains-of-corynebacterium-pseudotuberculosis-biovar-equi-through-comparative-genomics
#19
Rafael A Baraúna, Rommel T J Ramos, Adonney A O Veras, Kenny C Pinheiro, Leandro J Benevides, Marcus V C Viana, Luís C Guimarães, Judy M Edman, Sharon J Spier, Vasco Azevedo, Artur Silva
Seven genomes of Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, generating high-quality scaffolds over 2.35 Mbp. This bacterium is the causative agent of disease known as "pigeon fever" which commonly affects horses worldwide. The pangenome of biovar equi was calculated and two phylogenomic approaches were used to identify clustering patterns within Corynebacterium genus. Furthermore, other comparative analyses were performed including the prediction of genomic islands and prophages, and SNP-based phylogeny...
2017: PloS One
https://www.readbyqxmd.com/read/28117406/insights-into-the-planktothrix-genus-genomic-and-metabolic-comparison-of-benthic-and-planktic-strains
#20
Claire Pancrace, Marie-Anne Barny, Reiko Ueoka, Alexandra Calteau, Thibault Scalvenzi, Jacques Pédron, Valérie Barbe, Joern Piel, Jean-François Humbert, Muriel Gugger
Planktothrix is a dominant cyanobacterial genus forming toxic blooms in temperate freshwater ecosystems. We sequenced the genome of planktic and non planktic Planktothrix strains to better represent this genus diversity and life style at the genomic level. Benthic and biphasic strains are rooting the Planktothrix phylogenetic tree and widely expand the pangenome of this genus. We further investigated in silico the genetic potential dedicated to gas vesicles production, nitrogen fixation as well as natural product synthesis and conducted complementary experimental tests by cell culture, microscopy and mass spectrometry...
January 24, 2017: Scientific Reports
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