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https://www.readbyqxmd.com/read/29793117/metagenomic-insights-into-the-microbiota-profiles-and-bioaugmentation-mechanism-of-organics-removal-in-coal-gasification-wastewater-in-an-anaerobic-anoxic-oxic-system-by-methanol
#1
Weichao Xu, Yuxiu Zhang, Hongbin Cao, Yuxing Sheng, Haibo Li, Yuping Li, He Zhao, Xuefei Gui
Coal gasification wastewater is a typical high phenol-containing, toxic and refractory industrial wastewater. Here, lab-scale anaerobic-anoxic-oxic system was employed to treat real coal gasification wastewater, and methanol was added to oxic tank as the co-substrate to enhance the removal of refractory organic pollutants. The results showed that the average COD removal in oxic effluent increased from 24.9% to 36.0% by adding methanol, the total phenols concentration decreased from 54.4 to 44.9 mg/L. GC-MS analysis revealed that contents of phenolic components and polycyclic aromatic hydrocarbons (PAHs) were decreased compared to the control and their degradation intermediates were observed...
May 18, 2018: Bioresource Technology
https://www.readbyqxmd.com/read/29792207/metagenomic-analysis-of-viruses-associated-with-maize-lethal-necrosis-in-kenya
#2
Mwathi Jane Wamaitha, Deepti Nigam, Solomon Maina, Francesca Stomeo, Anne Wangai, Joyce Njoki Njuguna, Timothy A Holton, Bramwel W Wanjala, Mark Wamalwa, Tanui Lucas, Appolinaire Djikeng, Hernan Garcia-Ruiz
BACKGROUND: Maize lethal necrosis is caused by a synergistic co-infection of Maize chlorotic mottle virus (MCMV) and a specific member of the Potyviridae, such as Sugarcane mosaic virus (SCMV), Wheat streak mosaic virus (WSMV) or Johnson grass mosaic virus (JGMV). Typical maize lethal necrosis symptoms include severe yellowing and leaf drying from the edges. In Kenya, we detected plants showing typical and atypical symptoms. Both groups of plants often tested negative for SCMV by ELISA...
May 23, 2018: Virology Journal
https://www.readbyqxmd.com/read/29792119/maple-2-3-0-an-improved-system-for-evaluating-the-functionomes-of-genomes-and-metagenomes
#3
Wataru Arai, Takeaki Taniguchi, Susumu Goto, Yuki Moriya, Hideya Uehara, Kazuhiro Takemoto, Hiroyuki Ogata, Hideto Takami
MAPLE is an automated system for inferring the potential comprehensive functions harbored by genomes and metagenomes. To reduce runtime in MAPLE analyzing the massive amino acid datasets of over 1 million sequences, we improved it by adapting the KEGG automatic annotation server to use GHOSTX and verified no substantial difference in the MAPLE results between the original and new implementations.
May 24, 2018: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/29791446/nitrogen-limitation-toxin-synthesis-potential-and-toxicity-of-cyanobacterial-populations-in-lake-okeechobee-and-the-st-lucie-river-estuary-florida-during-the-2016-state-of-emergency-event
#4
Benjamin J Kramer, Timothy W Davis, Kevin A Meyer, Barry H Rosen, Jennifer A Goleski, Gregory J Dick, Genesok Oh, Christopher J Gobler
Lake Okeechobee, FL, USA, has been subjected to intensifying cyanobacterial blooms that can spread to the adjacent St. Lucie River and Estuary via natural and anthropogenically-induced flooding events. In July 2016, a large, toxic cyanobacterial bloom occurred in Lake Okeechobee and throughout the St. Lucie River and Estuary, leading Florida to declare a state of emergency. This study reports on measurements and nutrient amendment experiments performed in this freshwater-estuarine ecosystem (salinity 0-25 PSU) during and after the bloom...
2018: PloS One
https://www.readbyqxmd.com/read/29790949/fecal-microbiota-composition-changes-after-a-body-weight-loss-diet-in-beagle-dogs
#5
A Salas, I Jeusette, I Castillo, C L Manuelian, C Lionnet, N Iraculis, N Sanchez, S Fernández, L L Vilaseca, C Torre
In developed countries, dogs and cats frequently suffer from obesity. Recently, gut microbiota composition in humans has been related to obesity and metabolic diseases. This study aimed to evaluate changes in body composition, and gut microbiota composition in obese Beagle dogs after a 17-week body weight (BW) loss program. A total of six neutered adult Beagle dogs with an average initial BW of 16.34 ± 1.52 kg and BCS of 7.8 ± 0.1 points (9-point scale) were restrictedly fed with a hypocaloric, low-fat and high-fiber dry-type diet...
May 22, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29790941/asaim-a-galaxy-based-framework-to-analyze-microbiota-data
#6
Bérénice Batut, Kévin Gravouil, Clémence Defois, Saskia Hiltemann, Jean-François Brugère, Eric Peyretaillade, Pierre Peyret
Background: New generations of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. Findings: We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses...
May 22, 2018: GigaScience
https://www.readbyqxmd.com/read/29789681/genomic-and-ecological-study-of-two-distinctive-freshwater-bacteriophages-infecting-a-comamonadaceae-bacterium
#7
Kira Moon, Ilnam Kang, Suhyun Kim, Sang-Jong Kim, Jang-Cheon Cho
Bacteriophages of freshwater environments have not been well studied despite their numerical dominance and ecological importance. Currently, very few phages have been isolated for many abundant freshwater bacterial groups, especially for the family Comamonadaceae that is found ubiquitously in freshwater habitats. In this study, we report two novel phages, P26059A and P26059B, that were isolated from Lake Soyang in South Korea, and lytically infected bacterial strain IMCC26059, a member of the family Comamonadaceae...
May 22, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29789624/interplay-between-gut-microbiota-metabolism-and-inflammation-in-hiv-infection
#8
EDITORIAL
Jorge F Vázquez-Castellanos, Sergio Serrano-Villar, Nuria Jiménez-Hernández, María Dolores Soto Del Rio, Sara Gayo, David Rojo, Manuel Ferrer, Coral Barbas, Santiago Moreno, Vicente Estrada, Tomas Rattei, Amparo Latorre, Andrés Moya, María José Gosalbes
HIV infection causes a disruption of gut-associated lymphoid tissue, driving a shift in the composition of gut microbiota. A deeper understanding of the metabolic changes and how they affect the interplay with the host is needed. Here, we assessed functional modifications of HIV-associated microbiota by combining metagenomic and metatranscriptomic analyses. The transcriptionally active microbiota was well-adapted to the inflamed environment, overexpressing pathways related to resistance to oxidative stress...
May 23, 2018: ISME Journal
https://www.readbyqxmd.com/read/29789574/helicobacter-pylori-infected-c57bl-6-mice-with-different-gastrointestinal-microbiota-have-contrasting-gastric-pathology-microbial-and-host-immune-responses
#9
Zhongming Ge, Alexander Sheh, Yan Feng, Sureshkumar Muthupalani, Lili Ge, Chuanwu Wang, Susanna Kurnick, Anthony Mannion, Mark T Whary, James G Fox
C57BL/6 (B6) mice from Taconic Sciences (Tac) and the Jackson Laboratory (Jax) were infected with H. pylori PMSS1 (Hp) for 16 week; there was no significant difference in the gastric histologic activity index between Hp infected Tac and Jax B6. However, the degree of gastric mucous metaplasia and Th1-associated IgG2c levels in response to Hp infection were increased in Tac mice over Jax mice, whereas the colonization levels of gastric Hp were higher by 8-fold in Jax B6 compared with Tac B6. Additionally, mRNA expression of gastric Il-1β, Il-17A and RegIIIγ were significantly lower in the infected Tac compared to the infected Jax mice...
May 22, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29789481/concepts-and-methods-to-access-novel-antibiotics-from-actinomycetes
#10
REVIEW
Joachim J Hug, Chantal D Bader, Maja Remškar, Katarina Cirnski, Rolf Müller
Actinomycetes have been proven to be an excellent source of secondary metabolites for more than half a century. Exhibiting various bioactivities, they provide valuable approved drugs in clinical use. Most microorganisms are still untapped in terms of their capacity to produce secondary metabolites, since only a small fraction can be cultured in the laboratory. Thus, improving cultivation techniques to extend the range of secondary metabolite producers accessible under laboratory conditions is an important first step in prospecting underexplored sources for the isolation of novel antibiotics...
May 22, 2018: Antibiotics
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
#11
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/29789360/bat-caliciviruses-and-human-noroviruses-are-antigenically-similar-and-have-overlapping-histo-blood-group-antigen-binding-profiles
#12
Jacob F Kocher, Lisa C Lindesmith, Kari Debbink, Anne Beall, Michael L Mallory, Boyd L Yount, Rachel L Graham, Jeremy Huynh, J Edward Gates, Eric F Donaldson, Ralph S Baric
Emerging zoonotic viral diseases remain a challenge to global public health. Recent surveillance studies have implicated bats as potential reservoirs for a number of viral pathogens, including coronaviruses and Ebola viruses. Caliciviridae represent a major viral family contributing to emerging diseases in both human and animal populations and have been recently identified in bats. In this study, we blended metagenomics, phylogenetics, homology modeling, and in vitro assays to characterize two novel bat calicivirus (BtCalV) capsid sequences, corresponding to strain BtCalV/A10/USA/2009, identified in Perimyotis subflavus near Little Orleans, MD, and bat norovirus...
May 22, 2018: MBio
https://www.readbyqxmd.com/read/29789027/ethanolamine-enhances-intestinal-functions-by-altering-gut-microbiome-and-mucosal-anti-stress-capacity-in-weaned-rats
#13
Jian Zhou, Xia Xiong, Ke-Xing Wang, Li-Jun Zou, Peng Ji, Yu-Long Yin
Ethanolamine (Etn) contained in milk is the base constituent of phosphatidylethanolamine and is required for the proliferation of intestinal epithelial cells and bacteria, which is important for maintenance of the gut microbiome and intestinal development. The present study investigated the effect of Etn on intestinal function and microbiome using 21-d-old Sprague-Dawley rats treated with 0, 250, 500 and 1000 μm Etn in drinking water for 2 weeks immediately after weaning. Growth performance, intestinal morphology, antioxidant capacity and mucosal immunity, as well as gut microbiota community composition, were evaluated...
May 23, 2018: British Journal of Nutrition
https://www.readbyqxmd.com/read/29788417/poor-feed-efficiency-in-sheep-is-associated-with-several-structural-abnormalities-in-the-community-metabolic-network-of-their-ruminal-microbes
#14
Rocky D Patil, Melinda J Ellison, Sara M Wolff, Courtney Shearer, Anna M Wright, Rebecca R Cockrum, Kathy J Austin, William R Lamberson, Kristi M Cammack, Gavin C Conant
Ruminant animals have a symbiotic relationship with the microorganisms in their rumens. In this relationship, rumen microbes efficiently degrade complex plant-derived compounds into smaller digestible compounds, a process that is very likely associated with host animal feed efficiency. The resulting simpler metabolites can then be absorbed by the host and converted into other compounds by host enzymes. We used a microbial community metabolic network inferred from shotgun metagenomics data to assess how this metabolic system differs between animals that are able to turn ingested feedstuffs into body mass with high efficiency and those that are not...
May 18, 2018: Journal of Animal Science
https://www.readbyqxmd.com/read/29788084/microbial-activity-during-a-coastal-phytoplankton-bloom-on-the-western-antarctic-peninsula-in-late-summer
#15
María E Alcamán-Arias, Laura Farías, Josefa Verdugo, Tomás Alarcón-Schumacher, Beatriz Díez
Phytoplankton biomass during the austral summer is influenced by freezing and melting cycles as well as oceanographic processes that enable nutrient redistribution in the West Antarctic Peninsula (WAP). Microbial functional capabilities, metagenomic and metatranscriptomic activities as well as inorganic 13C- and 15N-assimilation rates were studied in the surface waters of Chile Bay during two contrasting summer periods in 2014. Concentrations of Chlorophyll a (Chla) varied from 0.3 mg m-3 in February to a maximum of 2...
May 1, 2018: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/29787889/diagnosis-of-bloodstream-infections-from-positive-blood-cultures-and-directly-from-blood-samples-recent-developments-in-molecular-approaches
#16
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/29786880/metagenomic-study-of-bacterial-microbiota-in-persistent-endodontic-infections-using-next-generation-sequencing
#17
G Sánchez-Sanhueza, H Bello-Toledo, G González-Rocha, A T Gonçalves, V Valenzuela, C Gallardo-Escárate
AIM: To determine the bacterial microbiota in root canals associated with persistent apical periodontitis and their relationship with the clinical characteristics of patients using next-generation sequencing (NGS). METHODOLOGY: Bacterial samples from root canals associated with teeth having persistent apical periodontitis were taken from 24 patients undergoing root canal retreatment. Bacterial DNA was extracted, and V3-V4 variable regions of the 16S rRNA gene were amplified...
May 22, 2018: International Endodontic Journal
https://www.readbyqxmd.com/read/29786634/virophages-and-their-interactions-with-giant-viruses-and-host-cells
#18
REVIEW
Haitham Sobhy
Virophages are small dsDNA viruses that were first isolated in association with some giant viruses (GVs), and then found in metagenomics samples. They encode about 20⁻34 proteins. Some virophages share protein similarity with Maverick/Polinton transposons or are considered as a provirophage, whereas about half of the protein's repertoire remain of unknown function. In this review, we aim to highlight the current understanding of the biology of virophages, as well as their interactions with giant viruses and host cells...
May 22, 2018: Proteomes
https://www.readbyqxmd.com/read/29786119/full-length-and-defective-enterovirus-g-genomes-with-distinct-torovirus-protease-insertions-are-highly-prevalent-on-a-chinese-pig-farm
#19
Yan Wang, Wen Zhang, Zhijian Liu, Xingli Fu, Jiaqi Yuan, Jieji Zhao, Yuan Lin, Quan Shen, Xiaochun Wang, Xutao Deng, Eric Delwart, Tongling Shan, Shixing Yang
Recombination occurs frequently between enteroviruses (EVs) which are classified within the same species of the Picornaviridae family. Here, using viral metagenomics, the genomes of two recombinant EV-Gs (strains EVG 01/NC_CHI/2014 and EVG 02/NC_CHI/2014) found in the feces of pigs from a swine farm in China are described. The two strains are characterized by distinct insertion of a papain-like protease gene from toroviruses classified within the Coronaviridae family. According to recent reports the site of the torovirus protease insertion was located at the 2C/3A junction region in EVG 02/NC_CHI/2014...
May 21, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29785845/bromate-and-nitrate-bio-reduction-coupled-with-poly-%C3%AE-hydroxybutyrate-production-in-a-methane-based-membrane-biofilm-reactor
#20
Chun-Yu Lai, Pan-Long Lv, Qiu-Yi Dong, Shi Lei Yeo, Bruce E Rittmann, He-Ping Zhao
This work demonstrates bromate (BrO3-) reduction in a methane (CH4)-based membrane biofilm reactor (MBfR), and it documents contrasting impacts of nitrate (NO3-) on BrO3- reduction, as well as formation of poly--hydroxybutyrate (PHB), an internal C- and electron-storage material. When the electron donor, CH4, was in ample supply, NO3- enhanced BrO3- reduction by stimulating the growth of denitrifying bacteria (Meiothermus, Comamonadaceae, and Anaerolineaceae) able to reduce BrO3- and NO3- simultaneously...
May 22, 2018: Environmental Science & Technology
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