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https://www.readbyqxmd.com/read/29231813/evolutionary-transitions-between-beneficial-and-phytopathogenic-rhodococcus-challenge-disease-management
#1
Elizabeth A Savory, Skylar L Fuller, Alexandra J Weisberg, William J Thomas, Michael I Gordon, Danielle M Stevens, Allison L Creason, Michael S Belcher, Maryna Serdani, Michele S Wiseman, Niklaus J Grünwald, Melodie L Putnam, Jeff H Chang
Understanding how bacteria affect plant health is crucial for developing sustainable crop production systems. We coupled ecological sampling and genome sequencing to characterize the population genetic history of Rhodococcus and the distribution patterns of virulence plasmids in isolates from nurseries. Analysis of chromosome sequences shows that plants host multiple lineages of Rhodococcus, and suggested that these bacteria are transmitted due to independent introductions, reservoir populations, and point source outbreaks...
December 12, 2017: ELife
https://www.readbyqxmd.com/read/29228300/dna-synthesis-by-fragment-assembly-using-extra-cellular-dna-delivered-by-artificial-controlled-horizontal-transfer
#2
Shinya Kaneko, Hiromi Fukushima, Misako Nakahama, Satomi Asano, Yasumasa Miyazaki, Yasunori Aizawa, Mitsuhiro Itaya
DNA synthesis in the Bacillus subtilis cells has become possible using extra-cellular DNA. Generally, purified DNAs in a test tube have been required to introduce into the host cells for molecular cloning technology in the laboratory. We have developed a cell lysis technique for natural transformation using stable extra-cellular plasmid DNAs, in which the extra-cellular plasmid DNAs are released from lysed Escherichia coli cells. DNA synthesis then proceeds by fragment assembly using the stable extracellular DNAs, without biochemical purification...
December 7, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29228229/variable-plasmid-fitness-effects-and-mobile-genetic-element-dynamics-across-pseudomonas-species
#3
Anastasia Kottara, James P J Hall, Ellie Harrison, Michael A Brockhurst
Mobile genetic elements (MGE) such as plasmids and transposons mobilise genes within and between species, playing a crucial role in bacterial evolution via horizontal gene transfer (HGT). Currently we lack data on variation in MGE dynamics across bacterial host species. We tracked the dynamics of a large conjugative plasmid, pQBR103, and its Tn5042 mercury resistance transposon, in five diverse Pseudomonas species in environments with and without mercury selection. Plasmid fitness effects and stability varied extensively between host species and environments, as did the propensity for chromosomal capture of the Tn5042 mercury resistance transposon associated with loss of the plasmid...
December 4, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29225610/horizontal-gene-transfer-contributes-to-plant-evolution-the-case-of-agrobacterium-t-dnas
#4
REVIEW
Dora G Quispe-Huamanquispe, Godelieve Gheysen, Jan F Kreuze
Horizontal gene transfer (HGT) can be defined as the acquisition of genetic material from another organism without being its offspring. HGT is common in the microbial world including archaea and bacteria, where HGT mechanisms are widely understood and recognized as an important force in evolution. In eukaryotes, HGT now appears to occur more frequently than originally thought. Many studies are currently detecting novel HGT events among distinct lineages using next-generation sequencing. Most examples to date include gene transfers from bacterial donors to recipient organisms including fungi, plants, and animals...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29225287/lysogenisation-of-shiga-toxin-encoding-bacteriophage-represses-cell-motility
#5
Shoichi Mitsunaka, Naoki Sudo, Yasuhiko Sekine
Bacteriophages are genetic elements that play key roles in the evolution and diversification of bacterial genomes. The Shiga toxin (Stx)-encoding phage plays an important role in the horizontal transfer of the stx gene. However, the influence of the Stx phage integration on the physiological properties and gene expression pattern of the host have not been clearly resolved. In this study, we constructed the Sp5 lysogen through lysogenisation of E. coli K-12 by Sp5, an Stx2 phage in enterohaemorrhagic E. coli (EHEC) O157:H7 Sakai, and examined the effect of the resulting lysogen on cell motility under various growth conditions...
December 8, 2017: Journal of General and Applied Microbiology
https://www.readbyqxmd.com/read/29223450/pesticide-degrading-natural-multidrug-resistance-bacterial-flora
#6
REVIEW
Kirubakaran Rangasamy, Murugan Athiappan, Natarajan Devarajan, Gopinath Samykannu, Javid A Parray, K N Aruljothi, Nowsheen Shameem, Abdulaziz A Alqarawi, Abeer Hashem, Elsayed Fathi Abd Allah
Multidrug-resistant (MDR) bacteria are a growing threat to humans across the world. Antibiotic resistance is a global problem that has developed through continuous antibiotic use, combinatorial antibiotic use, pesticide-antibiotic cross-resistance, and horizontal gene transfer, as well as various other modes. Pesticide-antibiotic cross-resistance and the subsequent expansion of drug-resistant bacteria are critically documented in this review, the primary focus of which is to assess the impact of indiscriminate pesticide use on the development of microbial communities with parallel pesticide and multidrug resistance...
December 6, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/29221804/the-impact-of-the-cd9-tetraspanin-on-lentivirus-infectivity-and-exosome-secretion
#7
Kai O Böker, Nicolas Lemus-Diaz, Rafael Rinaldi Ferreira, Lara Schiller, Stefan Schneider, Jens Gruber
Efficient transduction tools are a hallmark for both research and therapy development. Here, we introduce new insights into the generation of lentiviral vectors with improved performance by utilizing producer cells with increased production rates of extracellular vesicles through CD9 overexpression. Most human cells secrete small vesicles from their surface (microvesicles) or intraluminal endosome-derived membranes (exosomes). In particular, enhanced levels of the tetraspanin CD9 result in significantly increased numbers of extracellular vesicles with exosome-like features that were secreted from four different human cell lines...
November 16, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/29220487/ancestral-genome-estimation-reveals-the-history-of-ecological-diversification-in-agrobacterium
#8
Florent Lassalle, Rémi Planel, Simon Penel, David Chapulliot, Valérie Barbe, Audrey Dubost, Alexandra Calteau, David Vallenet, Damien Mornico, Thomas Bigot, Laurent Guéguen, Ludovic Vial, Daniel Muller, Vincent Daubin, Xavier Nesme
Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species...
December 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29218031/crispr-cas-systems-in-bacteroides-fragilis-an-important-pathobiont-in-the-human-gut-microbiome
#9
Mehrdad Tajkarimi, Hannah M Wexler
Background: While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in Bacteroides species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus Bacteroides make up ~25% of the total gut microbiome. Bacteroides fragilis comprises only 2% of the total Bacteroides in the gut, yet causes of >70% of Bacteroides infections. The factors causing it to transition from benign resident of the gut microbiome to virulent pathogen are not well understood, but a combination of horizontal gene transfer (HGT) of virulence genes and differential transcription of endogenous genes are clearly involved...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29217794/draft-genome-sequence-of-lactobacillus-salivarius-sgl-03-a-novel-potential-probiotic-strain
#10
Federica Federici, Laura Manna, Eleonora Rizzi, Elena Galantini, Umberto Marini
In this work, we report the draft genome sequence of Lactobacillus salivarius SGL 03, a novel potential probiotic strain isolated from healthy infant stools. Antibiotic resistance analysis revealed the presence of a tetracycline resistance gene without elements potentially responsible for interspecific horizontal gene transfer.
December 7, 2017: Genome Announcements
https://www.readbyqxmd.com/read/29216827/comparative-genomic-analysis-of-brevibacterium-strains-insights-into-key-genetic-determinants-involved-in-adaptation-to-the-cheese-habitat
#11
Nguyen-Phuong Pham, Séverine Layec, Eric Dugat-Bony, Marie Vidal, Françoise Irlinger, Christophe Monnet
BACKGROUND: Brevibacterium strains are widely used for the manufacturing of surface-ripened cheeses, contributing to the breakdown of lipids and proteins and producing volatile sulfur compounds and red-orange pigments. The objective of the present study was to perform comparative genomic analyses in order to better understand the mechanisms involved in their ability to grow on the cheese surface and the differences between the strains. RESULTS: The genomes of 23 Brevibacterium strains, including twelve strains isolated from cheeses, were compared for their gene repertoire involved in salt tolerance, iron acquisition, bacteriocin production and the ability to use the energy compounds present in cheeses...
December 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29214000/role-of-antigen-43-on-biofilm-formation-and-horizontal-antibiotic-resistance-gene-transfer-in-non-o157-shiga-toxin-producing-escherichia-coli-strains
#12
Roholla Taghadosi, Mohammad Reza Shakibaie, Reza Ghanbarpour, Hossein Hosseini-Nave
Background and Objectives: The objectives of this study were to evaluate the antibiotic resistance profiles, biofilm formation, presence of antigen 43 (Ag43) gene, and transfer of antibiotic resistance phenotype among non-O157 Shiga toxin producing Escherichia coli (STEC). Materials and Methods: From October 2014 to November 2015 a total of 276 stool samples were collected from healthy calves, goats and 395 patients with the sign of nonbloody diarrhea and screened for presence of stx and serotype O157 genes by polymerase chain reaction (PCR) technique...
April 2017: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/29207350/mobile-genetic-elements-and-antibiotic-resistance-in-mine-soil-amended-with-organic-wastes
#13
Carlos Garbisu, Olatz Garaiyurrebaso, Anders Lanzén, Itxaso Álvarez-Rodríguez, Lide Arana, Fernando Blanco, Kornelia Smalla, Elisabeth Grohmann, Itziar Alkorta
Metal resistance has been associated with antibiotic resistance due to co- or cross-resistance mechanisms. Here, metal contaminated mine soil treated with organic wastes was screened for the presence of mobile genetic elements (MGEs). The occurrence of conjugative IncP-1 and mobilizable IncQ plasmids, as well as of class 1 integrons, was confirmed by PCR and Southern blot hybridization, suggesting that bacteria from these soils have gene-mobilizing capacity with implications for the dissemination of resistance factors...
December 2, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/29205228/repression-of-ydas-toxin-is-mediated-by-transcriptional-repressor-racr-in-the-cryptic-rac-prophage-of-escherichia-coli-k-12
#14
Revathy Krishnamurthi, Swagatha Ghosh, Supriya Khedkar, Aswin Sai Narain Seshasayee
Horizontal gene transfer is a major driving force behind the genomic diversity seen in prokaryotes. The cryptic rac prophage in Escherichia coli K-12 carries the gene for a putative transcription factor RacR, whose deletion is lethal. We have shown that the essentiality of racR in E. coli K-12 is attributed to its role in transcriptionally repressing toxin gene(s) called ydaS and ydaT, which are adjacent to and coded divergently to racR. IMPORTANCE Transcription factors in the bacterium E. coli are rarely essential, and when they are essential, they are largely toxin-antitoxin systems...
November 2017: MSphere
https://www.readbyqxmd.com/read/29195994/identification-of-variable-genomic-regions-related-to-stress-response-in-oenococcus-oeni
#15
Mar Margalef-Català, Giovanna E Felis, Cristina Reguant, Elena Stefanelli, Sandra Torriani, Albert Bordons
The lactic acid bacterium Oenococcus oeni is the most important species involved in malolactic fermentation due to its capability to survive in presence of ethanol and in the acidic environment of wine. In order to identify novel genes involved in adaptation to wine, a new approach using genome-wide analysis based on stress-related genes was performed in strain O. oeni PSU-1, and 106 annotated stress genes were identified. The in silico analysis revealed the high similarity of all those genes through 57 O. oeni genomes; however, seven variable regions of genomic plasticity could be determined for their different presence observed among these strains...
December 2017: Food Research International
https://www.readbyqxmd.com/read/29194520/trajectories-and-drivers-of-genome-evolution-in-surface-associated-marine-phaeobacter
#16
Heike M Freese, Johannes Sikorski, Boyke Bunk, Carmen Scheuner, Jan P Meier-Kolthoff, Cathrin Spröer, Lone Gram, Jörg Overmann
The extent of genome divergence and the evolutionary events leading to speciation of marine bacteria have mostly been studied for (locally) abundant, free-living groups. The genus Phaeobacter is found on different marine surfaces, seems to occupy geographically disjunct habitats, and is involved in different biotic interactions, and was therefore targeted in the present study. The analysis of the chromosomes of 32 closely related but geographically spread Phaeobacter strains revealed an exceptionally large, highly syntenic core genome...
November 27, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29193598/pseudomonas-fluorescens-strain-r124-encodes-three-different-mio-enzymes
#17
Pál Csuka, Vivienn Juhász, Szabolcs Kohári, Alina Filip, Andrea Varga, Péter Sátorhelyi, László Csaba Bencze, Hazel A Barton, Csaba Paizs, Laszlo Poppe
A number of class I lyase-like enzymes including aromatic ammonia-lyases and aromatic 2,3-aminomutases containing the electrophilic 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) catalytic moiety. This study reveals that Pseudomonas fluorescens R124 strain isolated from a nutrient limited cave encodes a histidine ammonia-lyase (HAL), a tyrosine/phenylalanine/histidine ammonia-lyase (XAL) and a phenylalanine 2,3-aminomutase (PAM), and demonstrates that an organism under nitrogen-limited conditions can develop novel nitrogen fixation and transformation pathways to enrich the possibility of the nitrogen metabolism by gaining a PAM via horizontal gene transfer...
November 28, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29191398/the-search-for-evolution-proof-antibiotics
#18
REVIEW
Graham Bell, Craig MacLean
The effectiveness of antibiotics has been widely compromised by the evolution of resistance among pathogenic bacteria. It would be restored by the development of antibiotics to which bacteria cannot evolve resistance. We first discuss two kinds of 'evolution-proof' antibiotic. The first comprises literally evolution-proof antibiotics to which bacteria cannot become resistant by mutation or horizontal gene transfer. The second category comprises agents to which resistance may arise, but so rarely that it does not become epidemic...
November 27, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/29191308/amoxicillin-effects-on-functional-microbial-community-and-spread-of-antibiotic-resistance-genes-in-amoxicillin-manufacture-wastewater-treatment-system
#19
Lingwei Meng, Xiangkun Li, Xinran Wang, Kaili Ma, Gaige Liu, Jie Zhang
This study aimed to reveal how amoxicillin (AMX) affected the microbial community and the spread mechanism of antibiotic resistance genes (ARGs) in the AMX manufacture wastewater treatment system. For this purpose, a 1.47 L expanded granular sludge bed (EGSB) reactor was designed and run for 241days treating artificial AMX manufacture wastewater. 454 pyrosequencing was applied to analyze functional microorganisms in the system. The antibiotic genes OXA-1, OXA-2, OXA-10, TEM-1, CTX-M-1, class I integrons (intI1) and 16S rRNA genes were also examined in sludge samples...
November 2017: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/29187976/genome-comparisons-indicate-recent-transfer-of-wri-like-wolbachia-between-sister-species-drosophila-suzukii-and-d-%C3%A2-subpulchrella
#20
William R Conner, Mark L Blaxter, Gianfranco Anfora, Lino Ometto, Omar Rota-Stabelli, Michael Turelli
Wolbachia endosymbionts may be acquired by horizontal transfer, by introgression through hybridization between closely related species, or by cladogenic retention during speciation. All three modes of acquisition have been demonstrated, but their relative frequency is largely unknown. Drosophila suzukii and its sister species D. subpulchrella harbor Wolbachia, denoted wSuz and wSpc, very closely related to wRi, identified in California populations of D. simulans. However, these variants differ in their induced phenotypes: wRi causes significant cytoplasmic incompatibility (CI) in D...
November 2017: Ecology and Evolution
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