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https://www.readbyqxmd.com/read/29792944/enrichment-of-low-density-symbiont-dna-from-minute-insects
#1
Corinne M Stouthamer, Suzanne Kelly, Martha S Hunter
Symbioses between bacteria and insects are often associated with changes in important biological traits that can significantly affect host fitness. To a large extent, studies of these interactions have been based on physiological changes or induced phenotypes in the host, and the genetic mechanisms by which symbionts interact with their hosts have only recently become better understood. Learning about symbionts has been challenging in part due to difficulties such as obtaining enough high quality genomic material for high throughput sequencing technology, especially for symbionts present in low titers, and in small or difficult to rear non-model hosts...
May 21, 2018: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29792377/comparative-analysis-of-probiotic-bacteria-based-on-a-new-definition-of-core-genome
#2
Maria Satti, Yasuhiro Tanizawa, Akihito Endo, Masanori Arita
The commensal genus Bifidobacterium has probiotic properties. We prepared a public library of the gene functions of the genus Bifidobacterium for its online annotation. Orthologous gene cluster analysis showed that the pan genomes of Bifidobacterium and Lactobacillus exhibit striking similarities when mapped to the Clusters of Orthologous Group (COG) database of proteins. When the core genes in each genus were selected based on our statistical definition of "core genome", core genes were present in at least 92% of 52 Bifidobacterium and in 97% of 178 Lactobacillus genomes...
March 26, 2018: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29790926/bathyarchaeota-globally-distributed-metabolic-generalists-in-anoxic-environments
#3
Zhichao Zhou, Jie Pan, Fengping Wang, Ji-Dong Gu, Meng Li
Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundant archaeal communities. Until now, 25 subgroups have been identified in the Bathyarchaeota. The distinct bathyarchaeotal subgroups diverged to adapt to the marine and freshwater environments. Based on the physiological and genomic evidence, acetyl-CoA centralized heterotrophic pathways of energy conservation have been proposed to function in Bathyarchaeota; these microbes are able to anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) and methylated compounds, (v) and/or potentially other organic matter...
May 21, 2018: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/29790651/epitheliocystis-in-fish-an-emerging-aquaculture-disease-with-a-global-impact
#4
REVIEW
Makeely Isabel Blandford, Alyce Taylor-Brown, Thomas A Schlacher, Barbara Nowak, Adam Polkinghorne
Epitheliocystis is a skin and gill disease in fish caused by pathogenic intracellular bacteria. The disease has been reported in at least 90 species of marine and freshwater fish in both the southern and northern hemispheres. It affects a number of commercially important aquaculture species, including salmon, kingfish and bream. In infected fish, cysts typically develop in the gill epithelia, promoting the fusion of gill lamellae. Infections can lead to respiratory distress and death, particularly in cultured and juvenile fish with cases rarely reported in wild fish...
May 23, 2018: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/29789621/taxon-specific-aerosolization-of-bacteria-and-viruses-in-an-experimental-ocean-atmosphere-mesocosm
#5
Jennifer M Michaud, Luke R Thompson, Drishti Kaul, Josh L Espinoza, R Alexander Richter, Zhenjiang Zech Xu, Christopher Lee, Kevin M Pham, Charlotte M Beall, Francesca Malfatti, Farooq Azam, Rob Knight, Michael D Burkart, Christopher L Dupont, Kimberly A Prather
Ocean-derived, airborne microbes play important roles in Earth's climate system and human health, yet little is known about factors controlling their transfer from the ocean to the atmosphere. Here, we study microbiomes of isolated sea spray aerosol (SSA) collected in a unique ocean-atmosphere facility and demonstrate taxon-specific aerosolization of bacteria and viruses. These trends are conserved within taxonomic orders and classes, and temporal variation in aerosolization is similarly shared by related taxa...
May 22, 2018: Nature Communications
https://www.readbyqxmd.com/read/29789467/the-present-and-future-of-whole-genome-sequencing-wgs-and-whole-metagenome-sequencing-wms-for-surveillance-of-antimicrobial-resistant-microorganisms-and-antimicrobial-resistance-genes-across-the-food-chain
#6
REVIEW
Elena A Oniciuc, Eleni Likotrafiti, Adrián Alvarez-Molina, Miguel Prieto, Jesús A Santos, Avelino Alvarez-Ordóñez
Antimicrobial resistance (AMR) surveillance is a critical step within risk assessment schemes, as it is the basis for informing global strategies, monitoring the effectiveness of public health interventions, and detecting new trends and emerging threats linked to food. Surveillance of AMR is currently based on the isolation of indicator microorganisms and the phenotypic characterization of clinical, environmental and food strains isolated. However, this approach provides very limited information on the mechanisms driving AMR or on the presence or spread of AMR genes throughout the food chain...
May 22, 2018: Genes
https://www.readbyqxmd.com/read/29789313/blast-xyplot-viewer-a-tool-for-performing-blast-in-whole-genome-sequenced-bacteria-archaea-and-visualize-whole-results-simultaneously
#7
Yagul Pedraza-Pérez, Rodrigo Alberto Cuevas-Vede, Ángel Bernardo Canto-Gómez, Liliana López-Pliego, Rosa María Gutiérrez-Ríos, Ismael Hernández-Lucas, Gustavo Rubín-Linares, Ygnacio Martínez-Laguna, Jesús Francisco López-Olguín, Luis Ernesto Fuentes-Ramírez
One of the most commonly used tools to compare protein or DNA sequences against databases is BLAST. We introduce a web tool that allows the performance of BLAST-searches of protein/DNA sequences in whole-genome sequenced bacteria/archaea, and displays a large amount of BLAST-results simultaneously. The circular bacterial replicons are projected as horizontal lines with fixed length of 360, representing the degrees of a circle. A coordinate system is created with length of the replicon along the x -axis and the number of replicon used on the y -axis...
May 22, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29788916/in-silico-exploration-of-red-sea-bacillus-genomes-for-natural-product-biosynthetic-gene-clusters
#8
Ghofran Othoum, Salim Bougouffa, Rozaimi Razali, Ameerah Bokhari, Soha Alamoudi, André Antunes, Xin Gao, Robert Hoehndorf, Stefan T Arold, Takashi Gojobori, Heribert Hirt, Ivan Mijakovic, Vladimir B Bajic, Feras F Lafi, Magbubah Essack
BACKGROUND: The increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29786865/infection-with-phytopathogenic-bacterium-inhibits-melatonin-biosynthesis-decreases-longevity-of-its-vector-and-suppresses-the-free-radical-defense
#9
Yasser Nehela, Nabil Killiny
Vector-borne phytopathogenic bacteria may alter the reproductive fitness, survival, behavior, and metabolism of their vectors. Candidatus Liberibacter asiaticus (CLas) is associated with the Huanglongbing (HLB; also known as citrus greening disease), one of the most destructive citrus diseases worldwide, and transmitted by Asian citrus psyllid, Diaphorina citri (Insecta, Hemiptera, Liviidae). The genome sequencing of CLas revealed that it does not have the ability to synthesize tryptophan, the precursor of melatonin, and it must acquire it from its host plant or insect vector to achieve its biological processes, such as growth and multiplication...
May 22, 2018: Journal of Pineal Research
https://www.readbyqxmd.com/read/29786171/root-bacterial-endophytes-confer-drought-resistance-and-enhance-expression-and-activity-of-a-vacuolar-h-pumping-pyrophosphatase-in-pepper-plants
#10
Gianpiero Vigani, Eleonora Rolli, Ramona Marasco, Marta Dell'Orto, Grégoire Michoud, Asma Soussi, Noura Raddadi, Sara Borin, Claudia Sorlini, Graziano Zocchi, Daniele Daffonchio
It has been previously shown that the transgenic overexpression of the plant root vacuolar proton pumps H+ -ATPase (V-ATPase) and H+ -PPase (V-PPase) confer tolerance to drought. Since plant-root endophytic bacteria can also promote drought tolerance, we hypothesize that such promotion can be associated to the enhancement of the host vacuolar proton pumps expression and activity. To test this hypothesis, we selected two endophytic bacteria endowed with an array of in vitro plant growth promoting traits. Their genome sequences confirmed the presence of traits previously shown to confer drought resistance to plants, such as the synthesis of nitric oxide and of organic volatile organic compounds...
May 22, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29786121/genome-sequence-of-the-novel-virulent-bacteriophage-pmbt14-with-lytic-activity-against-pseudomonas-fluorescens-dsm-50090-r
#11
Sabrina Koberg, Stefanie Gieschler, Erik Brinks, Mareike Wenning, Horst Neve, Charles M A P Franz
Psychrotrophic gram-negative Pseudomonas spp. represent a serious problem in the dairy industry as they can cause spoilage of milk and dairy products. Bacteriophages have moved into focus as promising biocontrol agents for such food spoilage bacteria. The virulent Siphoviridae phage PMBT14 was isolated on a mutant variant of P. fluorescens DSM 50090 challenged with an unrelated virulent P. fluorescens DSM 50090 Podoviridae phage (i.e., mutant strain DSM 50090R ). PMBT14 has a 47,820-bp dsDNA genome with 76 predicted open reading frames (ORFs)...
May 21, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29785529/isolation-and-characterization-of-bacillus-sp-gfp-2-a-novel-bacillus-strain-with-antimicrobial-activities-from-whitespotted-bamboo-shark-intestine
#12
Jia Wu, Guoqiang Xu, Yangyang Jin, Cong Sun, Li Zhou, Guodong Lin, Rong Xu, Ling Wei, Hui Fei, Dan Wang, Jianqing Chen, Zhengbing Lv, Kuancheng Liu
The abuse of antibiotics and following rapidly increasing of antibiotic-resistant pathogens is the serious threat to our society. Natural products from microorganism are regarded as the important substitution antimicrobial agents of antibiotics. We isolated a new strain, Bacillus sp. GFP-2, from the Chiloscyllium plagiosum (Whitespotted bamboo shark) intestine, which showed great inhibitory effects on the growth of both Gram-positive and Gram-negative bacteria. Additionally, the growth of salmon was effectively promoted when fed with inactivated strain GFP-2 as the inhibition agent of pathogenic bacteria...
May 22, 2018: AMB Express
https://www.readbyqxmd.com/read/29785517/optimization-and-enhancement-of-textile-reactive-remazol-black-b-decolorization-and-detoxification-by-environmentally-isolated-ph-tolerant-pseudomonas-aeruginosa-ky284155
#13
Rasha A Hashem, Reham Samir, Tamer M Essam, Amal E Ali, Magdy A Amin
Azo dyes are complex derivatives of diazene used in food and textile manufacture. They are highly recalcitrant compounds, and account for severe environmental and health problems. Different strains of Pseudomonas species were isolated from textile wastewater effluents. The bioconversion of Remazol black B (a commonly used water soluble dye) by Pseudomonas aeruginosa was observed in static conditions. The bio-decolorization process was optimized by a multi factorial Plackett-Burman experimental design. Decolorization of 200 mg L-1 reached 100% in 32 h...
May 21, 2018: AMB Express
https://www.readbyqxmd.com/read/29785501/improving-the-acetic-acid-tolerance-and-fermentation-of-acetobacter-pasteurianus-by-nucleotide-excision-repair-protein-uvra
#14
Yu Zheng, Jing Wang, Xiaolei Bai, Yangang Chang, Jun Mou, Jia Song, Min Wang
Acetic acid bacteria (AAB) are widely used in acetic acid fermentation due to their remarkable ability to oxidize ethanol and high tolerance against acetic acid. In Acetobacter pasteurianus, nucleotide excision repair protein UvrA was up-regulated 2.1 times by acetic acid when compared with that without acetic acid. To study the effects of UvrA on A. pasteurianus acetic acid tolerance, uvrA knockout strain AC2005-ΔuvrA, uvrA overexpression strain AC2005 (pMV24-uvrA), and the control strain AC2005 (pMV24), were constructed...
May 21, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29784887/identification-of-the-thioredoxin-partner-of-vkor-in-mycobacterial-disulfide-bond-formation
#15
Na Ke, Cristina Landeta, Xiaoyun Wang, Dana Boyd, Markus Eser, Jon Beckwith
Disulfide bonds influence stability and activity of many proteins. In Escherichia coli the DsbA and DsbB enzymes promote disulfide bond formation. Other bacteria, including the Actinobacteria, use instead of DsbB the enzyme VKOR (Vitamin K Epoxide Reductase), which is found either fused to or encoded in the same operon as a dsbA -like protein. Mycobacterium tuberculosis and other gram-positive Actinobacteria secrete to the cell envelope many proteins with even numbers of cysteines. These organisms have predicted oxidoreductases and VKOR orthologs...
May 21, 2018: Journal of Bacteriology
https://www.readbyqxmd.com/read/29784781/c-4-sterol-demethylation-enzymes-distinguish-bacterial-and-eukaryotic-sterol-synthesis
#16
Alysha K Lee, Amy B Banta, Jeremy H Wei, David J Kiemle, Ju Feng, José-Luis Giner, Paula V Welander
Sterols are essential eukaryotic lipids that are required for a variety of physiological roles. The diagenetic products of sterol lipids, sterane hydrocarbons, are preserved in ancient sedimentary rocks and are utilized as geological biomarkers, indicating the presence of both eukaryotes and oxic environments throughout Earth's history. However, a few bacterial species are also known to produce sterols, bringing into question the significance of bacterial sterol synthesis for our interpretation of sterane biomarkers...
May 21, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29784711/quantitative-proteome-and-phosphoproteome-analyses-of-streptomyces-coelicolor-reveal-proteins-and-phosphoproteins-modulating-differentiation-and-secondary-metabolism
#17
Beatriz Rioseras, Pavel V Sliaha, Vladimir Gorshkov, Paula Yagüe, Maria T López-García, Nathaly González-Quiñónez, Sergey Kovalchuk, Adelina Rogowska-Wrzesinska, Ole N Jensen, Angel Manteca
Streptomycetes are multicellular bacteria with complex developmental cycles. They are of biotechnological importance as they produce most bioactive compounds used in biomedicine, e.g. antibiotic, antitumoral and immunosupressor compounds. Streptomyces genomes encode a large number of Ser/Thr/Tyr kinases, making this genus an outstanding model for the study of bacterial protein phosphorylation events. We used mass spectrometry based quantitative proteomics and phosphoproteomics to characterize bacterial differentiation and activation of secondary metabolism of Streptomyces coelicolor...
May 21, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29784342/rapid-and-sensitive-detection-of-staphylococcus-aureus-assisted-by-polydopamine-modified-magnetic-nanoparticles
#18
Xiaomei Gao, Xin Yao, Zitao Zhong, Li Jia
Pathogens cause significant morbidity and mortality to humans. Thus, development of fast and reliable methods for detection and identification of pathogens is urgently needed to increase protection level of public health and ensure the safety of consumers. Herein, a rapid and sensitive method has been developed for Staphylococcus aureus (S. aureus) detection based on the dual role of polydopamine modified magnetic nanoparticles (PDA@Fe3 O4 NPs) combined with polymerase chain reaction (PCR) and capillary electrophoresis (CE)...
August 15, 2018: Talanta
https://www.readbyqxmd.com/read/29783045/factors-affecting-gene-expression-and-activity-of-heme-and-manganese-dependent-catalases-in-lactobacillus-casei-strains
#19
Annamaria Ricciardi, Rocco Gerardo Ianniello, Eugenio Parente, Teresa Zotta
Catalases reduce oxidative stress by degrading hydrogen peroxide to molecular oxygen and water. The presence of heme-dependent or manganese-dependent catalases was observed for a long time in lactic acid bacteria (LAB) but, to date, knowledge on the factors affecting gene expression and enzymatic functionality are limited to a very few strains. In this study, the effect of atmosphere of incubation (not aerated static growth vs aerated shaken growth) and supplementation with Fe2+ , hemin, Mn2+ or their combinations on the catalase production of respiration-competent strain Lactobacillus casei N87 was evaluated using a 24 factorial design...
May 8, 2018: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29782030/the-genomes-of-three-bradyrhizobium-sp-isolated-from-root-nodules-of-lupinus-albescens-grown-in-extremely-poor-soils-display-important-genes-for-resistance-to-environmental-stress
#20
Camille E Granada, Luciano K Vargas, Fernando Hayashi Sant'Anna, Eduardo Balsanelli, Valter Antonio de Baura, Fábio de Oliveira Pedrosa, Emanuel Maltempi de Souza, Tiago Falcon, Luciane M P Passaglia
Lupinus albescens is a resistant cover plant that establishes symbiotic relationships with bacteria belonging to the Bradyrhizobium genus. This symbiosis helps the development of these plants in adverse environmental conditions, such as the ones found in arenized areas of Southern Brazil. This work studied three Bradyrhizobium sp. (AS23, NAS80 and NAS96) isolated from L. albescens plants that grow in extremely poor soils (arenized areas and adjacent grasslands). The genomes of these three strains were sequenced in the Ion Torrent platform using the IonXpress library preparation kit, and presented a total number of bases of 1,230,460,823 for AS23, 1,320,104,022 for NAS80, and 1,236,105,093 for NAS96...
May 17, 2018: Genetics and Molecular Biology
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