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Microorganism quality

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https://www.readbyqxmd.com/read/29791443/traceability-reproducibility-and-wiki-exploration-for-%C3%A3-la-carte-reconstructions-of-genome-scale-metabolic-models
#1
Méziane Aite, Marie Chevallier, Clémence Frioux, Camille Trottier, Jeanne Got, María Paz Cortés, Sebastián N Mendoza, Grégory Carrier, Olivier Dameron, Nicolas Guillaudeux, Mauricio Latorre, Nicolás Loira, Gabriel V Markov, Alejandro Maass, Anne Siegel
Genome-scale metabolic models have become the tool of choice for the global analysis of microorganism metabolism, and their reconstruction has attained high standards of quality and reliability. Improvements in this area have been accompanied by the development of some major platforms and databases, and an explosion of individual bioinformatics methods. Consequently, many recent models result from "à la carte" pipelines, combining the use of platforms, individual tools and biological expertise to enhance the quality of the reconstruction...
May 23, 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29787889/diagnosis-of-bloodstream-infections-from-positive-blood-cultures-and-directly-from-blood-samples-recent-developments-in-molecular-approaches
#2
REVIEW
Nilay Peker, Natacha Couto, Bhanu Sinha, John W Rossen
BACKGROUND: Bloodstream infections are a major cause of death with increasing incidence and severity. Blood cultures are still the gold standard for microbiological diagnosis, but are rather slow. Molecular methods can be used as add-on complementary assays. They can be useful to speed up microbial identification and to predict antimicrobial susceptibility, applied to direct blood samples or positive blood cultures. AIM: To review recent developments in molecular based diagnostic platforms used for the identification of bloodstream infections, with a focus on assays performed directly on blood samples and positive blood cultures...
May 19, 2018: Clinical Microbiology and Infection
https://www.readbyqxmd.com/read/29785502/comparative-persistence-of-human-sewage-specific-enterococcal-bacteriophages-in-freshwater-and-seawater
#3
Namfon Booncharoen, Skorn Mongkolsuk, Kwanrawee Sirikanchana
Enterococcus faecalis bacteria have been recently reported for their ability to host bacteriophages that are specifically from human sewage, suggesting their application to track human fecal contamination in water resources. However, little is known about the survivability of sewage-specific enterococcal bacteriophages in various water matrices under ambient and storage conditions. In this study, bacteriophages that were derived from the Thailand-isolated E. faecalis strains AIM06 and SR14 exhibited morphologies consistent with the Siphoviridae, Podoviridae, and Myoviridae families...
May 21, 2018: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29783164/potential-risks-from-uv-h-2-o-2-oxidation-and-uv-photocatalysis-a-review-of-toxic-assimilable-and-sensory-unpleasant-transformation-products
#4
REVIEW
Wen-Long Wang, Qian-Yuan Wu, Nan Huang, Zi-Bin Xu, Min-Yong Lee, Hong-Ying Hu
UV based advanced oxidation processes (UV-AOPs) that efficiently eliminate organic pollutants during water treatment have been the subject of numerous investigations. Most organic pollutants are not completely mineralized during UV-AOPs but are partially oxidized into transformation products (TPs), thereby adding complexity to the treated water and posing risks to humans, ecological systems, and the environment. While the degradation kinetics and mechanisms of pollutants have been widely documented, there is little information about the risks associated with TPs...
May 15, 2018: Water Research
https://www.readbyqxmd.com/read/29778470/genetic-diversity-of-thermoduric-spoilage-microorganisms-of-milk-from-brazilian-dairy-farms
#5
J C Ribeiro Júnior, R Tamanini, A L M de Oliveira, A A Alfieri, V Beloti
When correctly pasteurized, packaged, and stored, milk with low total bacterial counts (TBC) has a longer shelf life. Therefore, microorganisms that resist heat treatments are especially important in the deterioration of pasteurized milk and in its shelf life. The aim of this work was to quantify the thermoduric microorganisms after the pasteurization of refrigerated raw milk samples with low TBC and to identify the diversity of these isolates with proteolytic or lipolytic potential by RFLP analysis. Twenty samples of raw milk were collected in bulk milk tanks shortly after milking in different Brazilian dairy farms and pasteurized...
May 16, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29778225/identification-growth-and-toxicity-assessment-of-coolia-meunier-dinophyceae-from-nova-scotia-canada
#6
Nancy I Lewis, Jennifer L Wolny, John Claude Achenbach, Lee Ellis, Joseph S Pitula, Cheryl Rafuse, Detbra S Rosales, Pearse McCarron
Benthic dinoflagellates of the toxigenic genus Coolia Meunier (Dinophyceae) are known to have a global distribution in both tropical and temperate waters. The type species, C. monotis, has been reported from the Mediterranean Sea, the NE Atlantic and from Rhode Island, USA in the NW Atlantic, whereas other species in the genus have been reported from tropical locations. Coolia cells were observed in algal drift samples collected at seven sites in Nova Scotia, Canada. Clonal isolates were established from four of these locations and identified with light and scanning electron microscopy, then confirmed with genetic sequencing to be C...
May 2018: Harmful Algae
https://www.readbyqxmd.com/read/29777739/alkaline-treatment-of-resting-spores-prior-to-dna-extraction-improves-the-purity-of-plasmodiophora-brassicae-dna
#7
Yalong Yang, Kher Zahr, Michael W Harding, Stephen E Strelkov, Krista Zuzak, David Feindel, Jie Feng
A commonly used protocol for DNA extraction from Plasmodiophora brassicae was modified by adding an alkaline treatment step to increase the purity of resting spores. The quality of DNA extracted by the modified protocol was improved due to the removal of DNA contamination from host plant cells and other microorganisms.
May 16, 2018: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29767710/relationship-between-dissolved-organic-matter-quality-and-microbial-community-composition-across-polar-glacial-environments
#8
H J Smith, M Dieser, D M McKnight, M D SanClements, C M Foreman
Vast expanses of Earth's surface are covered by ice, with microorganisms in these systems affecting local and global biogeochemical cycles. We examined microbial assemblages from habitats fed by glacial meltwater within the McMurdo Dry Valleys, Antarctica, and on the west Greenland Ice Sheet, (GrIS) evaluating potential physicochemical factors explaining trends in community structure. Microbial assemblages present in the different Antarctic dry valley habitats were dominated by Sphingobacteria and Flavobacteria, while Gammaproteobacteria and Sphingobacteria prevailed in west GrIS supraglacial environments...
May 14, 2018: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29762695/development-and-validation-of-an-extended-database-for-yeast-identification-by-maldi-tof-ms-in-argentina
#9
Constanza Giselle Taverna, Mariana Mazza, Nadia Soledad Bueno, Christian Alvarez, Susana Amigot, Mariana Andreani, Natalia Azula, Rubén Barrios, Norma Fernández, Barbara Fox, Liliana Guelfand, Ivana Maldonado, Omar Alejandro Murisengo, Silvia Relloso, Matias Vivot, Graciela Davel
Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) has revolutionized the identification of microorganisms in clinical laboratories because it is rapid, relatively simple to use, accurate, and can be used for a wide number of microorganisms. Several studies have demonstrated the utility of this technique in the identification of yeasts; however, its performance is usually improved by the extension of the database. Here we developed an in-house database of 143 strains belonging to 42 yeast species in the MALDI Biotyper platform, and we validated the extended database with 388 regional strains and 15 reference strains belonging to 55 yeast species...
May 11, 2018: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29759899/integrated-diversity-analysis-of-the-microbial-community-in-a-reverse-osmosis-system-from-a-brazilian-oil-refinery
#10
Daiane R B Belgini, Virgínia M Siqueira, Douglas M Oliveira, Samantha G Fonseca, Viviane Piccin-Santos, Roberto S Dias, Larissa Quartaroli, Rodrigo S Souza, Ana Paula R Torres, Maíra P Sousa, Cláudio M Silva, Cynthia C Silva, Sérgio O De Paula, Valéria M Oliveira
Oil refineries are known for the large volume of water used in their processes, as well as the amount of wastewater generated at the end of the production chain. Due to strict environmental regulations, the recycling of water has now become a viable alternative for refineries. Among the many methods available to treat wastewater for reuse, the use of membranes in reverse osmosis systems stands out due to several economic and environmental benefits. However, these systems are vulnerable to contamination and deposition of microorganisms, mainly because of the feedwater quality...
April 13, 2018: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/29754988/bioremediation-of-petroleum-contaminated-soil-using-aged-refuse-from-landfills
#11
Qingmei Liu, Qibin Li, Ning Wang, Dan Liu, Li Zan, Le Chang, Xuemei Gou, Peijin Wang
This study explored the effects and mechanisms of petroleum-contaminated soil bioremediation using aged refuse (AR) from landfills. Three treatments of petroleum-contaminated soil (47.28 mg·g-1 ) amended with AR, sterilized aged refuse (SAR) and petroleum-contaminated soil only (as a control) were tested. During 98 days of incubation, changes in soil physicochemical properties, residual total petroleum hydrocarbon (TPH), biodegradation kinetics, enzyme activities and the microbial community were investigated...
May 10, 2018: Waste Management
https://www.readbyqxmd.com/read/29754079/urban-stormwater-treatment-by-a-constructed-wetland-seasonality-impacts-on-hydraulic-efficiency-physico-chemical-behavior-and-heavy-metal-occurrence
#12
M Walaszek, P Bois, J Laurent, E Lenormand, A Wanko
Urban stormwater affects the general quality of water bodies because of their hydraulic and pollution impacts. Stormwater discharges modify stream water flow and are reported as major source of heavy metals (HMs) in urban streams. Stormwater Constructed Wetlands (SCWs) have been built worldwide to manage stormwater before it is released into hydrosystems. In SCWs, stormwater is stored, evaporated and sometimes infiltrated. Subsequently, the HMs in stormwater can be settled, filtered and bioassimilated by microorganisms...
May 9, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29735106/chitosan-active-films-containing-agro-industrial-residue-extracts-for-shelf-life-extension-of-chicken-restructured-product
#13
Juan S Serrano-León, Keityane B Bergamaschi, Cristiana M P Yoshida, Erick Saldaña, Miriam M Selani, Juan D Rios-Mera, Severino M Alencar, Carmen J Contreras-Castillo
This study aimed to develop chitosan films incorporating natural antioxidants from peanut skin (EPS) and pink pepper residue (EPP) extracts, as well as to evaluate their effects on lipid oxidation, pH, color, and microbial counts of a restructured chicken product. EPS had higher phenolic content and antioxidant activity compared to EPP. When both extracts were applied to chicken meat and the chitosan films, there were no differences for color, pH and total mesophilic counts compared to control at the end of the storage period...
June 2018: Food Research International
https://www.readbyqxmd.com/read/29734583/combining-sun-based-technologies-microalgae-and-solar-disinfection-for-urban-wastewater-regeneration
#14
Sergio Gutiérrez-Alfaro, Juan J Rueda-Márquez, José A Perales, Manuel A Manzano
Solar disinfection (SODIS) of urban wastewater can be a suitable technology for improving the microbiological quality of reclaimed water as a complement to other extensive and environmentally friendly technologies such as microalgae biotreatment. The objective of this work is to evaluate the feasibility of incorporating the SODIS technology at the end of a pilot scale urban wastewater treatment plant (WWTP) where the processes are based on microalgae biotechnology and comprising three Upflow Anaerobic Sludge Blanket (UASB, 20m3 each one) reactor, six High Rate Algal Ponds (HRAP, 32m2 each one), and a Dissolved Air Flotation (DAF, 1m3 ) unit...
April 1, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29732916/inactivation-of-the-microbiota-and-effect-on-the-quality-attributes-of-pineapple-juice-using-a-continuous-flow-ultrasound-assisted-supercritical-carbon-dioxide-system
#15
I Paniagua-Martínez, A Mulet, M A García-Alvarado, J Benedito
Supercritical carbon dioxide inactivation technology represents a promising nonthermal processing method, as it causes minimum impact on the nutritional food properties. The aim of this study was to analyze the combined effect of supercritical carbon dioxide and high-power ultrasound on the inactivation of natural microbiota and the quality attributes of pineapple juice treated in a continuous flow system. Different juice residence times (3.06-4.6 min), at 100 bar and 31.5 ℃, were used. The results indicated that the microbiota inactivation was complete and the differences obtained in the quality attributes (2...
January 1, 2018: Food Science and Technology International, Ciencia y Tecnología de Los Alimentos Internacional
https://www.readbyqxmd.com/read/29732324/retrospective-study-on-the-hygienic-quality-of-fresh-ricotta-cheeses-produced-in-sicily-italy
#16
Maria Luisa Scatassa, Isabella Mancuso, Sonia Sciortino, Giusi Macaluso, Marisa Palmeri, Luigi Arcuri, Massimo Todaro, Cinzia Cardamone
The present work was carried out to investigate the microbiological profile of Sicilian ewes' ricotta cheeses during fifteen years of investigations (2002-2016). The samples were collected between those conferred to the Istituto Zooprofilattico Sperimentale della Sicilia (IZSSi) Adelmo Mirri , Palermo (Italy), by the competent authority during official control, by food business operator in HACCP systems and in research projects. Enterobacteriaceae, Escherichia coli and coagulase - positive staphylococci (CPS) were found only in some samples...
March 31, 2018: Italian Journal of Food Safety
https://www.readbyqxmd.com/read/29730283/photodynamic-therapy-as-an-alternative-to-antibiotic-therapy-for-the-treatment-of-infected-leg-ulcers
#17
REVIEW
Aleksandra Kawczyk-Krupka, Barbara Pucelik, Anna Międzybrodzka, Aleksander Sieroń, Janusz M Dąbrowski
Infected leg ulcers are painful, debilitating and immensely reducing patient's quality of life, therefore they are becoming a more and more significant clinical and socioeconomic problems nowadays. Increasing resistance to antibiotics, drugs and therapies is one of the most urgent challenge in medicine worldwide and requires searching for a new, innovative and more efficient medical strategies. One of the opportunities for the cure of leg ulcers is photodynamic inactivation (PDI), that has been widely used in the treatment of various bacterial, fungal and viral infections...
May 3, 2018: Photodiagnosis and Photodynamic Therapy
https://www.readbyqxmd.com/read/29727857/unravelling-the-contribution-of-lactic-acid-bacteria-and-acetic-acid-bacteria-to-cocoa-fermentation-using-inoculated-organisms
#18
Van Thi Thuy Ho, Graham H Fleet, Jian Zhao
Cocoa beans (Theobroma cacao L.) are the raw material for chocolate production. Fermentation of the bean pulp by microorganisms is essential for developing the precursors of chocolate flavour. Currently, the cocoa fermentation is still conducted by an uncontrolled traditional process via a consortium of indigenous species of yeasts, lactic acid bacteria and acetic acid bacteria. Although the essential contribution of yeasts to the production of good quality beans and, typical chocolate character is generally agreed, the roles of lactic acid bacteria and acetic acid bacteria are less certain...
April 27, 2018: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29727839/impact-of-nutrient-addition-on-diversity-and-fate-of-fecal-bacteria
#19
Yang Zhang, Renren Wu, Yimin Zhang, Guang Wang, Kaiming Li
Understanding the variations in the microorganisms associated with human fecal pollution in different types of water is necessary to manage water quality and predict human health risks. Using an Illumina sequencing method, we investigated variations in the fecal bacteria originating from fresh human feces and their decay trends in nutrient-supplemented water and natural river water. Nutrient addition contributed to the growth of heterotrophic bacteria like Comamonadaceae, Cytophagaceae, and Sphingobacteriaceae, but led to lower concentrations for Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae...
May 1, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29722232/-effects-of-exogenous-spermidine-and-arbuscular-mycorrhizal-fungi-on-plant-growth-of-cucumber
#20
Ya Sheng Wu, Shi Rong Guo, Jie Zhang, Nan Shan Du, Jin Sun
Effects of spermidine (Spd) and arbuscular mycorrhizal fungi (AMF) on the growth and photosynthesis of cucumber (Cucumis sativus L., cv. Jinchun 2) seedlings, fruit yield and quality, microorganism and enzymatic activity in rhizosphere were investigated. The results showed that combined Spd and AMF addition significantly promoted the growth of cucumber seedlings, increased the root activity, fruit production and quality, enhanced nutrients absorption of seedlings. Net photosynthetic rate, actual photochemical efficiency, light quantum efficiency, carboxylation efficiency and light respiration rate of cucumber seedlings were increased by combined addition of Spd and AMF...
March 2018: Ying Yong Sheng Tai Xue Bao, the Journal of Applied Ecology
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