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https://www.readbyqxmd.com/read/28527384/embracing-the-enemy-the-diversification-of-microbial-gene-repertoires-by-phage-mediated-horizontal-gene-transfer
#1
REVIEW
Marie Touchon, Jorge A Moura de Sousa, Eduardo Pc Rocha
Bacteriophages and archaeal viruses contribute, through lysogenic conversion or transduction, to the horizontal transfer of genetic material between microbial genomes. Recent genomics, metagenomics, and single cell studies have shown that lysogenic conversion is widespread and provides hosts with adaptive traits often associated with biotic interactions. The quantification of the evolutionary impact of transduction has lagged behind and requires further theoretical and experimental work. Nevertheless, recent studies suggested that generalized transduction plays a role in the transfer of antibiotic resistance genes and in the acquisition of novel genes during intra-specific bacterial competition...
May 17, 2017: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/28526844/identification-of-extracellular-glycerophosphodiesterases-in-pseudomonas-and-their-role-in-soil-organic-phosphorus-remineralisation
#2
Ian D E A Lidbury, Andrew R J Murphy, Tandra D Fraser, Gary D Bending, Alexandra M E Jones, Jonathan D Moore, Andrew Goodall, Mark Tibbett, John P Hammond, David J Scanlan, Elizabeth M H Wellington
In soils, phosphorus (P) exists in numerous organic and inorganic forms. However, plants can only acquire inorganic orthophosphate (Pi), meaning global crop production is frequently limited by P availability. To overcome this problem, rock phosphate fertilisers are heavily applied, often with negative environmental and socio-economic consequences. The organic P fraction of soil contains phospholipids that are rapidly degraded resulting in the release of bioavailable Pi. However, the mechanisms behind this process remain unknown...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526549/metagenomic-dna-sequencing-for-the-diagnosis-of-intraocular-infections
#3
Thuy Doan, Nisha R Acharya, Benjamin A Pinsky, Malaya K Sahoo, Eric D Chow, Niaz Banaei, Indre Budvytiene, Vicky Cevallos, Lina Zhong, Zhaoxia Zhou, Thomas M Lietman, Joseph L DeRisi
No abstract text is available yet for this article.
May 16, 2017: Ophthalmology
https://www.readbyqxmd.com/read/28525602/aloin-a-component-of-the-aloe-vera-plant-leaf-induces-pathological-changes-and-modulates-the-composition-of-microbiota-in-the-large-intestine-of-f344-n-male-rats
#4
Mary D Boudreau, Greg R Olson, Volodymyr P Tryndyak, Matthew S Bryant, Robert P Felton, Frederick A Beland
In a previous study, the oral administration of an Aloe vera whole leaf extract induced dose-related mucosal and goblet cell hyperplasia in the rat colon after 13-weeks and colon cancer after two years. The primary goal of this study was to determine whether or not the administration of aloin, a component of the Aloe vera plant leaf, would replicate the pathophysiological effects that were observed in rats in the previous study with an Aloe vera whole leaf extract. Groups of 10 male F344/N rats were administered aloin at 0, 6...
May 19, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28524866/succession-in-the-petroleum-reservoir-microbiome-through-an-oil-field-production-lifecycle
#5
Adrien Vigneron, Eric B Alsop, Bartholomeus P Lomans, Nikos C Kyrpides, Ian M Head, Nicolas Tsesmetzis
Subsurface petroleum reservoirs are an important component of the deep biosphere where indigenous microorganisms live under extreme conditions and in isolation from the Earth's surface for millions of years. However, unlike the bulk of the deep biosphere, the petroleum reservoir deep biosphere is subject to extreme anthropogenic perturbation, with the introduction of new electron acceptors, donors and exogenous microbes during oil exploration and production. Despite the fundamental and practical significance of this perturbation, there has never been a systematic evaluation of the ecological changes that occur over the production lifetime of an active offshore petroleum production system...
May 19, 2017: ISME Journal
https://www.readbyqxmd.com/read/28523623/microbial-population-shift-caused-by-sulfamethoxazole-in-engineered-soil-aquifer-treatment-e-sat-system
#6
Ashwinkumar P Rudrashetti, Niti B Jadeja, Deepa Gandhi, Asha A Juwarkar, Abhinav Sharma, Atya Kapley, R A Pandey
The engineered-Soil Aquifer Treatment (e-SAT) system was exploited for the biological degradation of Sulfamethoxazole (SMX) which is known to bio-accumulate in the environment. The fate of SMX in soil column was studied through laboratory simulation for a period of 90 days. About 20 ppm SMX concentration could be removed in four consecutive cycles in e-SAT. To understand the microbial community change and biological degradation of SMX in e-SAT system, metagenomic analysis was performed for the soil samples before (A-EBD) and after SMX exposure (B-EBD) in the e-SAT...
June 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28523519/erratum-to-a-metagenomics-study-for-the-identification-of-respiratory-viruses-in-mixed-clinical-specimens-an-application-of-the-iterative-mapping-approach
#7
Yu-Nong Gong, Shu-Li Yang, Guang-Wu Chen, Yu-Wen Chen, Yhu-Chering Huang, Hsiao-Chen Ning, Kuo-Chien Tsao
No abstract text is available yet for this article.
May 18, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28523377/mining-lipolytic-enzymes-in-community-dna-from-high-andean-soils-using-a-targeted-approach
#8
Daniel Borda-Molina, José Salvador Montaña, María Mercedes Zambrano, Sandra Baena
Microbial enrichments cultures are a useful strategy to speed up the search for enzymes that can be employed in industrial processes. Lipases have gained special attention because they show unique properties such as: broad substrate specificity, enantio- and regio-selectivity and stability in organic solvents. A major goal is to identify novel lipolytic enzymes from microorganisms living in cold extreme environments such as high Andean soils, of relevance to our study being their capability be used in industrial processes...
May 18, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28520993/effects-of-short-and-long-course-antibiotics-on-the-lower-intestinal-microbiome-as-they-relate-to-traveller-s-diarrhea
#9
Lawrence Clifford McDonald
BACKGROUND: Antibiotics have profound and lasting effects on the lower intestinal (gut) microbiome that can both promote resistance and increase susceptibility to colonization and infection; knowledge of these changes is important to the prevention and treatment of traveler's diarrhea. METHODS: Recent data from epidemiologic and modern metagenomics studies were reviewed in regard to how such findings could inform the prevention and treatment of traveler's diarrhea...
April 1, 2017: Journal of Travel Medicine
https://www.readbyqxmd.com/read/28520472/a-study-of-the-microbial-spatial-heterogeneity-of-bahamian-thrombolites-using-molecular-biochemical-and-stable-isotope-analyses
#10
Artemis S Louyakis, Jennifer M Mobberley, Brooke E Vitek, Pieter T Visscher, Paul D Hagan, R Pamela Reid, Reinhard Kozdon, Ian J Orland, John W Valley, Noah J Planavsky, Giorgio Casaburi, Jamie S Foster
Thrombolites are buildups of carbonate that exhibit a clotted internal structure formed through the interactions of microbial mats and their environment. Despite recent advances, we are only beginning to understand the microbial and molecular processes associated with their formation. In this study, a spatial profile of the microbial and metabolic diversity of thrombolite-forming mats of Highborne Cay, The Bahamas, was generated by using 16S rRNA gene sequencing and predictive metagenomic analyses. These molecular-based approaches were complemented with microelectrode profiling and in situ stable isotope analysis to examine the dominant taxa and metabolic activities within the thrombolite-forming communities...
May 2017: Astrobiology
https://www.readbyqxmd.com/read/28517029/carbon-driven-enrichment-of-the-crucial-nitrate-reducing-bacteria-in-limed-peat-soil-microcosms
#11
Ying Zhu, Xiaoyuan Zhang, Xiaogang Wu, Guanzhou Chen, Lars R Bakken, Liping Zhao, Åsa Frostegård, Xiaojun Zhang
Bacteria of Dechloromonas were recognized as potential functional important denitrifiers in a long term shell sand amended peat soil. Different microcosms in a solid matrix and slurry systems with the addition of carbon and nitrogen sources, e.g., clover leaves, glutamate, and nitrate, were established. The bacterial community structures were analyzed by pyrosequencing of the 16S rRNA gene to select the conditions for enriching bacteria of Dechloromonas. The results showed that a relatively even bacterial community in the initial soil shifted to communities dominated by a few types of nitrate reducing bacteria after the incubation, which strongly responded to the carbon substrates addition and consumption...
May 18, 2017: Letters in Applied Microbiology
https://www.readbyqxmd.com/read/28511148/computational-studies-of-membrane-proteins-from-sequence-to-structure-to-simulation
#12
REVIEW
Phillip J Stansfeld
In this review, I discuss the recent advances in computational approaches to studying membrane protein structures, covering the latest methods for predicting a protein structure from its amino acid sequence, through to methods for assessing the structural dynamics and lipid interactions within molecular simulations of complex biological membranes. These approaches have not only benefited from advances in the computational software and architectures, but have also been assisted by a prodigious rise in the number of both the molecular sequences and experimentally determined membrane protein structures...
May 13, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28509857/microbial-diversity-in-extreme-marine-habitats-and-their-biomolecules
#13
REVIEW
Annarita Poli, Ilaria Finore, Ida Romano, Alessia Gioiello, Licia Lama, Barbara Nicolaus
Extreme marine environments have been the subject of many studies and scientific publications. For many years, these environmental niches, which are characterized by high or low temperatures, high-pressure, low pH, high salt concentrations and also two or more extreme parameters in combination, have been thought to be incompatible to any life forms. Thanks to new technologies such as metagenomics, it is now possible to detect life in most extreme environments. Starting from the discovery of deep sea hydrothermal vents up to the study of marine biodiversity, new microorganisms have been identified, and their potential uses in several applied fields have been outlined...
May 16, 2017: Microorganisms
https://www.readbyqxmd.com/read/28506730/-the-human-gut-microbiota-interactions-with-the-host-and-dysfunctions
#14
P Lepage
The human intestinal microbiota is composed of approximately 100,000 billion microorganisms with the average total number of different commensal bacterial species estimated at over 500 per individual. The human intestinal microbiota can be considered as an organ within another, which co-evolved with its host to achieve a symbiotic relationship leading to physiological homeostasis. The host provides an environment enriched in nutrients and the microbiota provides essential functions. Dysbiosis of the intestinal microbiota (changes in bacterial composition) has been associated with local dysfunctions of the gastrointestinal tract, such as inflammatory bowel disease or irritable bowel syndrome but also with obesity and metabolic diseases...
May 12, 2017: Revue des Maladies Respiratoires
https://www.readbyqxmd.com/read/28506638/ionic-liquid-based-reagents-improve-the-stability-of-midterm-fecal-sample-storage
#15
Lilan Hao, Zhongkui Xia, Huanming Yang, Jian Wang, Mo Han
Fecal samples are widely used in metagenomic research, which aims to elucidate the relationship between human health and the intestinal microbiota. However, the best conditions for stable and reliable storage and transport of these samples at room temperature are still unknown, and whether samples stored at room temperature for several days will maintain their microbiota composition is still unknown. Here, we established and tested a preservation method using reagents containing imidazolium- or pyridinium-based ionic liquids...
May 13, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28506279/uncovering-the-trimethylamine-producing-bacteria-of-the-human-gut-microbiota
#16
Silke Rath, Benjamin Heidrich, Dietmar H Pieper, Marius Vital
BACKGROUND: Trimethylamine (TMA), produced by the gut microbiota from dietary quaternary amines (mainly choline and carnitine), is associated with atherosclerosis and severe cardiovascular disease. Currently, little information on the composition of TMA producers in the gut is available due to their low abundance and the requirement of specific functional-based detection methods as many taxa show disparate abilities to produce that compound. RESULTS: In order to examine the TMA-forming potential of microbial communities, we established databases for the key genes of the main TMA-synthesis pathways, encoding choline TMA-lyase (cutC) and carnitine oxygenase (cntA), using a multi-level screening approach on 67,134 genomes revealing 1107 and 6738 candidates to exhibit cutC and cntA, respectively...
May 15, 2017: Microbiome
https://www.readbyqxmd.com/read/28506246/vipie-web-pipeline-for-parallel-characterization-of-viral-populations-from-multiple-ngs-samples
#17
Jake Lin, Lenka Kramna, Reija Autio, Heikki Hyöty, Matti Nykter, Ondrej Cinek
BACKGROUND: Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. RESULTS: We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters...
May 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28505128/a-proposal-for-a-study-on-treatment-selection-and-lifestyle-recommendations-in-chronic-inflammatory-diseases-a-danish-multidisciplinary-collaboration-on-prognostic-factors-and-personalised-medicine
#18
Vibeke Andersen, Uffe Holmskov, Signe Bek Sørensen, Mohamad Jawhara, Karina W Andersen, Anette Bygum, Lone Hvid, Jakob Grauslund, Jimmi Wied, Henning Glerup, Ulrich Fredberg, Jan Alexander Villadsen, Søren Geill Kjær, Jan Fallingborg, Seyed A G R Moghadd, Torben Knudsen, Jacob Brodersen, Jesper Frøjk, Jens F Dahlerup, Ole Haagen Nielsen, Robin Christensen, Anders Bo Bojesen, Grith Lykke Sorensen, Steffen Thiel, Nils J Færgeman, Ivan Brandslund, Allan Stensballe, Erik Berg Schmidt, Andre Franke, David Ellinghaus, Philip Rosenstiel, Jeroen Raes, Berit Heitmann, Mette Boye, Charlotte Lindgaard Nielsen, Lars Werner, Jens Kjeldsen, Torkell Ellingsen
Chronic inflammatory diseases (CIDs), including Crohn's disease and ulcerative colitis (inflammatory bowel diseases, IBD), rheumatoid arthritis, psoriasis, psoriatic arthritis, spondyloarthritides, hidradenitis suppurativa, and immune-mediated uveitis, are treated with biologics targeting the pro-inflammatory molecule tumour necrosis factor-α (TNF) (i.e., TNF inhibitors). Approximately one-third of the patients do not respond to the treatment. Genetics and lifestyle may affect the treatment results. The aims of this multidisciplinary collaboration are to identify (1) molecular signatures of prognostic value to help tailor treatment decisions to an individual likely to initiate TNF inhibitor therapy, followed by (2) lifestyle factors that support achievement of optimised treatment outcome...
May 15, 2017: Nutrients
https://www.readbyqxmd.com/read/28500719/novel-thermostable-flavin-binding-fluorescent-proteins-from-thermophilic-organisms
#19
Marcus Wingen, Karl-Erich Jaeger, Thomas Gensch, Thomas Drepper
Flavin-binding fluorescent proteins (FbFPs) are small, oxygen-independent in vivo reporters, derived from Light Oxygen Voltage (LOV) domains of photoreceptors. Here, we investigated the thermostability of existing, as well as novel FbFPs, whose genes were identified in genome sequences of various thermophilic bacteria as well as metagenomic libraries from hot springs in the Yellowstone National Park. Detailed in vitro analyses revealed that two of those fluorescent reporter proteins were highly thermostable, exhibiting melting temperatures above 75°C...
May 2017: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/28499958/unexpected-persistence-of-extended-spectrum-%C3%AE-lactamase-producing-enterobacteriaceae-in-the-faecal-microbiota-of-hospitalised-patients-treated-with-imipenem
#20
N Grall, V Lazarevic, N Gaïa, C Couffignal, C Laouénan, E Ilic-Habensus, I Wieder, P Plesiat, C Angebault, M E Bougnoux, L Armand-Lefevre, A Andremont, X Duval, J Schrenzel
Imipenem is active against extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-E) but favours the intestinal emergence of resistance. The effects of imipenem on intestinal microbiota have been studied using culture-based techniques. In this study, the effects were investigated in patients using culture and metagenomic techniques. Seventeen hospitalised adults receiving imipenem were included in a multicentre study (NCT01703299, http://www.clinicaltrials.gov). Most patients had a history of antibiotic use and/or hospitalisation...
May 9, 2017: International Journal of Antimicrobial Agents
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