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https://www.readbyqxmd.com/read/29051988/starvation-and-xenobiotic-related-transcriptomic-responses-of-the-sulfanilic-acid-degrading-bacterium-novosphingobium-resinovorum-sa1
#1
Botond Hegedüs, Péter B Kós, Gábor Bende, Naila Bounedjoum, Gergely Maróti, Krisztián Laczi, Márk Szuhaj, Katalin Perei, Gábor Rákhely
Novosphingobium resinovorum SA1 was the first single isolate capable of degrading sulfanilic acid, a widely used representative of sulfonated aromatic compounds. The genome of the strain was recently sequenced, and here, we present whole-cell transcriptome analyses of cells exposed to sulfanilic acid as compared to cells grown on glucose. The comparison of the transcript profiles suggested that the primary impact of sulfanilic acid on the cell transcriptome was a starvation-like effect. The genes of the peripheral, central, and common pathways of sulfanilic acid biodegradation had distinct transcript profiles...
October 19, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29050666/the-contribution-of-bacteriophages-to-the-biology-and-virulence-of-pathogenic-clostridia
#2
Louis-Charles Fortier
Bacteriophages are key players in the evolution of most bacteria. Temperate phages have been associated with virulence of some of the deadliest pathogenic bacteria. Among the most notorious cases, the genes encoding the botulinum neurotoxin produced by Clostridium botulinum types C and D and the α-toxin (TcnA) produced by Clostridium novyi are both encoded within prophage genomes. Clostridium difficile is another important human pathogen and the recent identification of a complete binary toxin locus (CdtLoc) carried on a C...
2017: Advances in Applied Microbiology
https://www.readbyqxmd.com/read/29046540/compensatory-mutations-improve-general-permissiveness-to-antibiotic-resistance-plasmids
#3
Wesley Loftie-Eaton, Kelsie Bashford, Hannah Quinn, Kieran Dong, Jack Millstein, Samuel Hunter, Maureen K Thomason, Houra Merrikh, Jose M Ponciano, Eva M Top
Horizontal gene transfer mediated by broad-host-range plasmids is an important mechanism of antibiotic resistance spread. While not all bacteria maintain plasmids equally well, plasmid persistence can improve over time, yet no general evolutionary mechanisms have emerged. Our goal was to identify these mechanisms and to assess if adaptation to one plasmid affects the permissiveness to others. We experimentally evolved Pseudomonas sp. H2 containing multidrug resistance plasmid RP4, determined plasmid persistence and cost using a joint experimental-modelling approach, resequenced evolved clones, and reconstructed key mutations...
September 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/29044211/identification-of-novel-mazef-pemik-family-toxin-antitoxin-loci-and-their-distribution-in-the-staphylococcus-genus
#4
Michal Bukowski, Karolina Hyz, Monika Janczak, Marcin Hydzik, Grzegorz Dubin, Benedykt Wladyka
The versatile roles of toxin-antitoxin (TA) systems in bacterial physiology and pathogenesis have been investigated for more than three decades. Diverse TA loci in Bacteria and Archaea have been identified in genome-wide studies. The advent of massive parallel sequencing has substantially expanded the number of known bacterial genomic sequences over the last 5 years. In staphylococci, this has translated into an impressive increase from a few tens to a several thousands of available genomes, which has allowed us for the re-evalution of prior conclusions...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29042411/a-horizontally-transferred-autonomous-helitron-became-a-full-polydnavirus-segment-in-cotesia-vestalis
#5
Pedro Heringer, Guilherme B Dias, Gustavo C S Kuhn
Bracoviruses associate symbiotically with thousands of parasitoid wasp species in the family Braconidae, working as virulence gene vectors, and allowing the development of wasp larvae within hosts. These viruses are composed by multiple DNA circles that are packaged into infective particles and injected together with wasp's eggs during parasitization. One of the viral segments of Cotesia vestalis bracovirus contains a gene that has been previously described as a helicase of unknown origin. Here we demonstrate that this gene is a Rep/Helicase from an intact Helitron transposable element that covers the viral segment almost entirely...
October 17, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29041914/analysis-of-the-genome-of-the-new-zealand-giant-collembolan-holacanthella-duospinosa-sheds-light-on-hexapod-evolution
#6
Chen Wu, Melissa D Jordan, Richard D Newcomb, Neil J Gemmell, Sarah Bank, Karen Meusemann, Peter K Dearden, Elizabeth J Duncan, Sefanie Grosser, Kim Rutherford, Paul P Gardner, Ross N Crowhurst, Bernd Steinwender, Leah K Tooman, Mark I Stevens, Thomas R Buckley
BACKGROUND: The New Zealand collembolan genus Holacanthella contains the largest species of springtails (Collembola) in the world. Using Illumina technology we have sequenced and assembled a draft genome and transcriptome from Holacanthella duospinosa (Salmon). We have used this annotated assembly to investigate the genetic basis of a range of traits critical to the evolution of the Hexapoda, the phylogenetic position of H. duospinosa and potential horizontal gene transfer events. RESULTS: Our genome assembly was ~375 Mbp in size with a scaffold N50 of ~230 Kbp and sequencing coverage of ~180×...
October 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29038487/the-microbiome-beyond-the-horizon-of-ecological-and-evolutionary-theory
#7
REVIEW
Britt Koskella, Lindsay J Hall, C Jessica E Metcalf
The ecological and evolutionary study of community formation, diversity, and stability is rooted in general theory and reinforced by decades of system-specific empirical work. Deploying these ideas to study the assembly, complexity, and dynamics of microbial communities living in and on eukaryotes has proved seductive, but challenging. The success of this research endeavour depends on our capacity to observe and characterize the distributions, abundances, and functional traits of microbiota, representing an array of technical and analytical challenges...
October 16, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/29033338/antibiotic-resistance-genes-in-waste-water
#8
REVIEW
Antti Karkman, Thi Thuy Do, Fiona Walsh, Marko P J Virta
Waste water and waste water treatment plants can act as reservoirs and environmental suppliers of antibiotic resistance. They have also been proposed to be hotspots for horizontal gene transfer, enabling the spread of antibiotic resistance genes between different bacterial species. Waste water contains antibiotics, disinfectants, and metals which can form a selection pressure for antibiotic resistance, even in low concentrations. Our knowledge of antibiotic resistance in waste water has increased tremendously in the past few years with advances in the molecular methods available...
October 12, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/29030446/comparative-genomics-based-markers-discrimination-of-host-specificity-in-fusarium-oxysporum
#9
Peter van Dam, Mara de Sain, Anneliek Ter Horst, Michelle van der Gragt, Martijn Rep
The polyphyletic nature of many formae speciales of Fusarium oxysporum (Fo) prevents molecular identification of newly encountered strains based on conserved, vertically inherited genes. Alternative molecular detection methods that could replace labour- and time-intensive disease assays are therefore highly desired. Effectors are functional elements in the pathogen-host interaction and have been found to show very limited sequence diversity between strains of the same forma specialis, which makes them potential markers for host-specific pathogenicty...
October 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29030439/conjugation-mediated-horizontal-gene-transfer-of-clostridium-perfringens-plasmids-in-the-chicken-gastrointestinal-tract-results-in-the-formation-of-new-virulent-strains
#10
Jake A Lacey, Anthony L Keyburn, Mark E Ford, Ricardo W Portela, Priscilla A Johanesen, Dena Lyras, Robert J Moore
Clostridium perfringens is a gastrointestinal pathogen capable of causing disease in a variety of hosts. Necrotic enteritis in chickens is caused by C. perfringens strains that produce the pore-forming toxin NetB, the major virulence factor for this disease. Like many other C. perfringens toxins and antibiotic resistance genes, NetB is encoded on a conjugative plasmid. Conjugative transfer of the netB-containing plasmid pJIR3535 has been demonstrated in vitro with a netB null mutant. This study has investigated the effect of plasmid transfer on disease pathogenesis, with two genetically distinct transconjugants constructed under in vitro conditions, within the intestinal tract of chickens...
October 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29030023/on-universal-coding-events-in-protein-biogenesis
#11
REVIEW
Vladimir Kubyshkin, Carlos G Acevedo-Rocha, Nediljko Budisa
The complete ribosomal protein synthesis cycle and codon-amino acids associations are universally preserved in all life taxa on Earth. This process is accompanied by a set of hierarchically organized recognition and controlling events at different complexity levels. It starts with amino acid activation by aminoacyl tRNA synthetases (aaRS) followed by cellular matching with the acceptor units of their cognitive tRNAs ("operational RNA code") and ribosomal codon-anticodon pairing of messenger RNA ("triplet code")...
October 10, 2017: Bio Systems
https://www.readbyqxmd.com/read/29029703/comparative-genomics-of-maize-ear-rot-pathogens-reveals-expansion-of-carbohydrate-active-enzymes-and-secondary-metabolism-backbone-genes-in-stenocarpella-maydis
#12
Alex Z Zaccaron, Charles P Woloshuk, Burton H Bluhm
Stenocarpella maydis is a plant pathogenic fungus that causes Diplodia ear rot, one of the most destructive diseases of maize. To date, little information is available regarding the molecular basis of pathogenesis in this organism, in part due to limited genomic resources. In this study, a 54.8 Mb draft genome assembly of S. maydis was obtained with Illumina and PacBio sequencing technologies, and analyzed. Comparative genomic analyses with the predominant maize ear rot pathogens Aspergillus flavus, Fusarium verticillioides, and Fusarium graminearum revealed an expanded set of carbohydrate-active enzymes for cellulose and hemicellulose degradation in S...
November 2017: Fungal Biology
https://www.readbyqxmd.com/read/29028004/geobiological-feedbacks-and-the-evolution-of-thermoacidophiles
#13
Daniel R Colman, Saroj Poudel, Trinity L Hamilton, Jeff R Havig, Matthew J Selensky, Everett L Shock, Eric S Boyd
Oxygen-dependent microbial oxidation of sulfur compounds leads to the acidification of natural waters. How acidophiles and their acidic habitats evolved, however, is largely unknown. Using 16S rRNA gene abundance and composition data from 72 hot springs in Yellowstone National Park, Wyoming, we show that hyperacidic (pH<3.0) hydrothermal ecosystems are dominated by a limited number of archaeal lineages with an inferred ability to respire O2. Phylogenomic analyses of 584 existing archaeal genomes revealed that hyperacidophiles evolved independently multiple times within the Archaea, each coincident with the emergence of the ability to respire O2, and that these events likely occurred in the recent evolutionary past...
October 13, 2017: ISME Journal
https://www.readbyqxmd.com/read/29027482/structural-genomics-of-pndm-btr-harboring-in191-and-tn6360-and-other-bla-ndm-carrying-incn1-plasmids
#14
Yachao Zhao, Lijun Wang, Zhiyi Zhang, Jiao Feng, Huaixing Kang, Liqun Fang, Xiaoyuan Jiang, Defu Zhang, Zhe Zhan, Dongsheng Zhou, Yigang Tong
AIM: To characterize a conjugative bla NDM-1-carrying plasmid pNDM-BTR from a clinical Escherichia coli isolate. MATERIALS & METHODS: The complete nucleotide sequence of pNDM-BTR was determined using next-generation sequencing technology. Comparative genomic analysis of bla NDM-carrying IncN1 plasmids, including pNDM-BTR, was performed, and the antimicrobial resistance phenotypes were determined. RESULTS: pNDM-BTR contained three accessory modules, namely IS26, a novel Tn3-family transposon Tn6360 and the dfrA14 region composed of In191, ecoRII-ecoRIImet and ΔIS1X2...
October 13, 2017: Future Microbiology
https://www.readbyqxmd.com/read/29026795/the-prevalence-of-plasmid-mediated-quinolone-resistance-genes-in-escherichia-coli-isolated-from-hospital-wastewater-sources-in-tehran-iran
#15
Reza Ranjbar, Omid Farahani
BACKGROUND: Considering the importance of hospital wastewaters as potential reservoirs for the dissemination of bacterial pathogens such as Escherichia coli and antibiotic resistance genes in the environment, the need for such information becomes imperative. METHODS: E. coli strains were isolated from hospital wastewater sources in Tehran, Iran, over a 24-month sampling period (Jun 2014- Jun 2016) and identified using standard bacteriological methods. Quinolone resistance among the strains was determined using Kirby-Bauer method and the frequency of plasmid-mediated quinolone resistance genes (qnrA, qnrB, qnrS) was investigated by PCR...
September 2017: Iranian Journal of Public Health
https://www.readbyqxmd.com/read/29026659/emergence-and-genomic-diversification-of-a-virulent-serogroup-w-st-2881-cc175-neisseria-meningitidis-clone-in-the-african-meningitis-belt
#16
Araceli Lamelas, Julia Hauser, Jean-Pierre Dangy, Abdul-Wahab M Hamid, Katharina Röltgen, Mohamad R Abdul Sater, Abraham Hodgson, Ali Sie, Thomas Junghanss, Simon R Harris, Julian Parkhill, Stephen D Bentley, Gerd Pluschke
Countries of the African 'meningitis belt' are susceptible to meningococcal meningitis outbreaks. While in the past major epidemics have been primarily caused by serogroup A meningococci, W strains are currently responsible for most of the cases. After an epidemic in Mecca in 2000, W:ST-11 strains have caused many outbreaks worldwide. An unrelated W:ST-2881 clone was described for the first time in 2002, with the first meningitis cases caused by these bacteria reported in 2003. Here we describe results of a comparative whole-genome analysis of 74 W:ST-2881 strains isolated within the framework of two longitudinal colonization and disease studies conducted in Ghana and Burkina Faso...
August 2017: Microbial Genomics
https://www.readbyqxmd.com/read/29018426/transfer-and-persistence-of-a-multi-drug-resistance-plasmid-in-situ-of-the-infant-gut-microbiota-in-the-absence-of-antibiotic-treatment
#17
Heidi Gumpert, Jessica Z Kubicek-Sutherland, Andreas Porse, Nahid Karami, Christian Munck, Marius Linkevicius, Ingegerd Adlerberth, Agnes E Wold, Dan I Andersson, Morten O A Sommer
The microbial ecosystem residing in the human gut is believed to play an important role in horizontal exchange of virulence and antibiotic resistance genes that threatens human health. While the diversity of gut-microorganisms and their genetic content has been studied extensively, high-resolution insight into the plasticity, and selective forces shaping individual genomes is scarce. In a longitudinal study, we followed the dynamics of co-existing Escherichia coli lineages in an infant not receiving antibiotics...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29018417/molecular-mechanisms-that-contribute-to-horizontal-transfer-of-plasmids-by-the-bacteriophage-spp1
#18
Ana Valero-Rello, María López-Sanz, Alvaro Quevedo-Olmos, Alexei Sorokin, Silvia Ayora
Natural transformation and viral-mediated transduction are the main avenues of horizontal gene transfer in Firmicutes. Bacillus subtilis SPP1 is a generalized transducing bacteriophage. Using this lytic phage as a model, we have analyzed how viral replication and recombination systems contribute to the transfer of plasmid-borne antibiotic resistances. Phage SPP1 DNA replication relies on essential phage-encoded replisome organizer (G38P), helicase loader (G39P), hexameric replicative helicase (G40P), recombinase (G35P) and in less extent on the partially dispensable 5'→3' exonuclease (G34...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29018197/the-chromosomal-organization-of-horizontal-gene-transfer-in-bacteria
#19
Pedro H Oliveira, Marie Touchon, Jean Cury, Eduardo P C Rocha
Bacterial adaptation is accelerated by the acquisition of novel traits through horizontal gene transfer, but the integration of these genes affects genome organization. We found that transferred genes are concentrated in only ~1% of the chromosomal regions (hotspots) in 80 bacterial species. This concentration increases with genome size and with the rate of transfer. Hotspots diversify by rapid gene turnover; their chromosomal distribution depends on local contexts (neighboring core genes), and content in mobile genetic elements...
October 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28993659/comparative-genomics-of-lactobacillus-kefiranofaciens-zw3-and-related-members-of-lactobacillus-spp-reveal-adaptations-to-dairy-and-gut-environments
#20
Zhuqing Xing, Weitao Geng, Chao Li, Ye Sun, Yanping Wang
It is important for probiotics that are currently utilized in the dairy industry to have clear genetic backgrounds. In this study, the genetic characteristics of Lactobacillus kefiranofaciens ZW3 were studied by undertaking a comparative genomics study, and key genes for adaptation to different environments were investigated and validated in vitro. Evidence for horizontal gene transfer resulting in strong self-defense mechanisms was detected in the ZW3 genome. We identified a series of genes relevant for dairy environments and the intestinal tract, particularly for extracellular polysaccharide (EPS) production...
October 9, 2017: Scientific Reports
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