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https://www.readbyqxmd.com/read/28815469/metagenome-analysis-a-powerful-tool-for-enzyme-bioprospecting
#1
Aravind Madhavan, Raveendran Sindhu, Binod Parameswaran, Rajeev K Sukumaran, Ashok Pandey
Microorganisms are found throughout every corner of nature, and vast number of microorganisms is difficult to cultivate by classical microbiological techniques. The advent of metagenomics has revolutionized the field of microbial biotechnology. Metagenomics allow the recovery of genetic material directly from environmental niches without any cultivation techniques. Currently, metagenomic tools are widely employed as powerful tools to isolate and identify enzymes with novel biocatalytic activities from the uncultivable component of microbial communities...
August 16, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28815328/microbial-diversity-in-acidic-thermal-pools-in-the-uzon-caldera-kamchatka
#2
Andrey V Mardanov, Vadim M Gumerov, Alexey V Beletsky, Nikolai V Ravin
Microbial communities of four acidic thermal pools in the Uzon Caldera, Kamchatka, Russia, were studied using amplification and pyrosequencing of 16S rRNA gene fragments. The sites differed in temperature and pH: 1805 (60 °C, pH 3.7), 1810 (90 °C, pH 4.1), 1818 (80 °C, pH 3.5), and 1807 (86 °C, pH 5.6). Archaea of the order Sulfolobales were present among the dominant groups in all four pools. Acidilobales dominated in pool 1818 but were a minor fraction at the higher temperature in pool 1810. Uncultivated Archaea of the Hot Thaumarchaeota-related clade were present in significant quantities in pools 1805 and 1807, but they were not abundant in pools 1810 and 1818, where high temperatures were combined with low pH...
August 16, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28798101/genomic-exploration-of-the-diversity-ecology-and-evolution-of-the-archaeal-domain-of-life
#3
REVIEW
Anja Spang, Eva F Caceres, Thijs J G Ettema
About 40 years ago, Archaea were recognized as a major prokaryotic domain of life besides Bacteria. Recently, cultivation-independent sequencing methods have produced a wealth of genomic data for previously unidentified archaeal lineages, several of which appear to represent newly revealed branches in the tree of life. Analyses of some recently obtained genomes have uncovered previously unknown metabolic traits and provided insights into the evolution of archaea and their relationship to eukaryotes. On the basis of our current understanding, much archaeal diversity still defies genomic exploration...
August 11, 2017: Science
https://www.readbyqxmd.com/read/28777379/metabolic-and-spatio-taxonomic-response-of-uncultivated-seafloor-bacteria-following-the-deepwater-horizon-oil-spill
#4
K M Handley, Y M Piceno, P Hu, L M Tom, O U Mason, G L Andersen, J K Jansson, J A Gilbert
The release of 700 million liters of oil into the Gulf of Mexico over a few months in 2010 produced dramatic changes in the microbial ecology of the water and sediment. Here, we reconstructed the genomes of 57 widespread uncultivated bacteria from post-spill deep-sea sediments, and recovered their gene expression pattern across the seafloor. These genomes comprised a common collection of bacteria that were enriched in heavily affected sediments around the wellhead. Although rare in distal sediments, some members were still detectable at sites up to 60 km away...
August 4, 2017: ISME Journal
https://www.readbyqxmd.com/read/28770687/ecological-specialization-in-diaeretiella-rapae-hymenoptera-braconidae-aphidiinae-on-aphid-species-from-wild-and-cultivated-plants
#5
Y Navasse, S A P Derocles, M Plantegenest, A Le Ralec
Diaeretiella rapae is an aphid parasitoid with potential for use in biological control strategies. However, several recent genetic studies have challenged the long held view that it is a generalist parasitoid. We investigated its ecological specialization and ability to use resources in cultivated and uncultivated areas. Ecological specialization would reduce its ability to exploit the diversity of aphid species, particularly in uncultivated areas, and to control pest aphids. Four D. rapae strains were studied, three reared on pest aphids on Brassicaceae and one strain on a non-pest aphid on Chenopodiaceae...
August 3, 2017: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/28742284/aquatic-animals-promote-antibiotic-resistance-gene-dissemination-in-water-via-conjugation-role-of-different-regions-within-the-zebra-fish-intestinal-tract-and-impact-on-fish-intestinal-microbiota
#6
Jialun Fu, Dong Yang, Min Jin, Weili Liu, Xin Zhao, Chenyu Li, Tianyu Zhao, Jingfeng Wang, Zhixian Gao, Zhiqiang Shen, Zhigang Qiu, Jun-Wen Li
The aqueous environment is one of many reservoirs of antibiotic resistance genes (ARGs). Fish, as important aquatic animals which possess ideal intestinal niches for bacteria to grow and multiply, may ingest antibiotic resistance bacteria from aqueous environment. The fish gut would be a suitable environment for conjugal gene transfer including those encoding antibiotic resistance. However, little is known in relation to the impact of ingested ARGs or ARB on gut microbiota. Here, we applied the cultivation method, qPCR, nuclear molecular genetic marker and 16S rDNA amplicon sequencing technologies to develop a plasmid-mediated ARG transfer model of zebrafish...
July 25, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28737159/health-and-environmental-risk-assessment-project-for-bottlenose-dolphins-tursiops-truncatus-from-the-southeastern-usa-i-infectious-diseases
#7
REVIEW
Gregory D Bossart, Patricia Fair, Adam M Schaefer, John S Reif
From 2003 to 2015, 360 free-ranging Atlantic bottlenose dolphins Tursiops truncatus inhabiting the Indian River Lagoon (IRL, n = 246), Florida, and coastal waters of Charleston (CHS, n = 114), South Carolina, USA, were captured, given comprehensive health examinations, and released as part of a multidisciplinary and multi-institutional study of individual and population health. The aim of this review is to summarize the substantial health data generated by this study and to examine morbidity between capture sites and over time...
July 24, 2017: Diseases of Aquatic Organisms
https://www.readbyqxmd.com/read/28731467/uncultivated-microbes-in-need-of-their-own-taxonomy
#8
Konstantinos T Konstantinidis, Ramon Rosselló-Móra, Rudolf Amann
The great majority of microbial species remains uncultured, severely limiting their taxonomic characterization and thus communication among scientists. Although Candidatus was devised as a provisional category to classify uncultured taxa, it has not been widely accepted owing to technical limitations and lack of priority of Candidatus names in the official nomenclature. High-throughput sequencing provides the potential for data-rich taxonomic descriptions of uncultivated microbes, comparable in quality to those of cultured organisms...
July 21, 2017: ISME Journal
https://www.readbyqxmd.com/read/28729688/improved-genome-recovery-and-integrated-cell-size-analyses-of-individual-uncultured-microbial-cells-and-viral-particles
#9
Ramunas Stepanauskas, Elizabeth A Fergusson, Joseph Brown, Nicole J Poulton, Ben Tupper, Jessica M Labonté, Eric D Becraft, Julia M Brown, Maria G Pachiadaki, Tadas Povilaitis, Brian P Thompson, Corianna J Mascena, Wendy K Bellows, Arvydas Lubys
Microbial single-cell genomics can be used to provide insights into the metabolic potential, interactions, and evolution of uncultured microorganisms. Here we present WGA-X, a method based on multiple displacement amplification of DNA that utilizes a thermostable mutant of the phi29 polymerase. WGA-X enhances genome recovery from individual microbial cells and viral particles while maintaining ease of use and scalability. The greatest improvements are observed when amplifying high G+C content templates, such as those belonging to the predominant bacteria in agricultural soils...
July 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28726611/added-value-of-next-generation-sequencing-for-multilocus-sequence-typing-analysis-of-a-pneumocystis-jirovecii-pneumonia-outbreak1
#10
Elena Charpentier, Cécile Garnaud, Claire Wintenberger, Sébastien Bailly, Jean-Benjamin Murat, John Rendu, Patricia Pavese, Thibault Drouet, Caroline Augier, Paolo Malvezzi, Anne Thiébaut-Bertrand, Marie-Reine Mallaret, Olivier Epaulard, Muriel Cornet, Sylvie Larrat, Danièle Maubon
Pneumocystis jirovecii is a major threat for immunocompromised patients, and clusters of pneumocystis pneumonia (PCP) have been increasingly described in transplant units during the past decade. Exploring an outbreak transmission network requires complementary spatiotemporal and strain-typing approaches. We analyzed a PCP outbreak and demonstrated the added value of next-generation sequencing (NGS) for the multilocus sequence typing (MLST) study of P. jirovecii strains. Thirty-two PCP patients were included...
August 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28708078/spatial-variation-of-soil-organic-carbon-and-total-nitrogen-in-the-coastal-area-of-mid-eastern-china
#11
Yan Xu, Lijie Pu, Qilin Liao, Ming Zhu, Xue Yu, Tianying Mao, Chenxing Xu
Soils play an important role in sequestrating atmospheric CO₂. Coastal tidal flats have been intensively reclaimed for food security and living spaces worldwide. We aimed to identify the changes of soil organic carbon (SOC) and total nitrogen (TN) following coastal reclamation and their spatial variation in the coastal area of mid-Eastern China to provide information for coastal cropland management. We measured SOC and TN of 463 soil samples in the coastal plain of mid-Eastern China. The results showed that SOC and TN increased highly from the uncultivated coastal tidal flat (2...
July 14, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28696720/bacterial-production-of-a-pederin-analogue-by-a-free-living-marine-alphaproteobacterium
#12
Carmen Schleissner, Librada M Cañedo, Pilar Rodríguez, Cristina Crespo, Paz Zúñiga, Ana Peñalver, Fernando de la Calle, Carmen Cuevas
The polyketide pederin family are cytotoxic compounds isolated from insects, lichen, and marine sponges. During the past decade, different uncultivable bacteria symbionts have been proposed as the real producers of these compounds, such as those found in insects, lichen, and marine sponges, and their trans-AT polyketide synthase gene clusters have been identified. Herein we report the isolation and biological activities of a new analogue of the pederin family, compound 1, from the culture of a marine heterotrophic alphaproteobacterium, Labrenzia sp...
July 11, 2017: Journal of Natural Products
https://www.readbyqxmd.com/read/28687345/molecular-diversity-geographic-distribution-and-host-range-of-monocot-infecting-mastreviruses-in-africa-and-surrounding-islands
#13
Simona Kraberger, Salem Saumtally, Daniel Pande, Michel H R Khoodoo, Sonalall Dhayan, Asha Dookun-Saumtally, Dionne N Shepherd, Penelope Hartnady, Richard Atkinson, Francisco M Lakay, Britt Hanson, Devasha Redhi, Adérito L Monjane, Oliver P Windram, Matthew Walters, Sunday Oluwafemi, Jean Michel-Lett, Pierre Lefeuvre, Darren P Martin, Arvind Varsani
Maize streak virus (MSV), an important pathogen of maize in Africa, is the most extensively studied member of the Mastrevirus genus in the family Geminiviridae. Comparatively little is known about other monocot-infecting African mastreviruses, most of which infect uncultivated grasses. Here we determine the complete sequences of 134 full African mastrevirus genomes from predominantly uncultivated Poaceae species. Based on established taxonomic guidelines for the genus Mastrevirus, these genomes could be classified as belonging to the species Maize streak virus, Eragrostis minor streak virus, Maize streak Reunion virus, Panicum streak virus, Sugarcane streak Reunion virus and Sugarcane streak virus...
July 4, 2017: Virus Research
https://www.readbyqxmd.com/read/28686606/plant-fed-versus-chemicals-fed-rhizobacteria-of-lucerne-plant-only-teabags-culture-media-not-only-increase-culturability-of-rhizobacteria-but-also-recover-a-previously-uncultured-lysobacter-sp-novosphingobium-sp-and-pedobacter-sp
#14
Nabil A Hegazi, Mohamed S Sarhan, Mohamed Fayez, Sascha Patz, Brian R Murphy, Silke Ruppel
In an effort to axenically culture the previously uncultivable populations of the rhizobacteria of Lucerne (Medicago sativa L.), we propose plant-only teabags culture media to mimic the nutritional matrix available in the rhizosphere. Here, we show that culture media prepared from Lucerne powder teabags substantially increased the cultivability of Lucerne rhizobacteria compared with a standard nutrient agar, where we found that the cultivable populations significantly increased by up to 60% of the total bacterial numbers as estimated by Quantitative Real-time Polymerase Chain Reaction (qRT-PCR)...
2017: PloS One
https://www.readbyqxmd.com/read/28684155/novel-mastreviruses-identified-in-australian-wild-rice
#15
Simona Kraberger, Andrew D W Geering, Matthew Walters, Darren P Martin, Arvind Varsani
Most known mastreviruses (family Geminiviridae) infect members of the grass family, Poaceae. Although the greatest number of grass-infecting mastrevirus species have been discovered in Africa, it is apparent that the ten grass-infecting mastrevirus species that have so far only been discovered in south-east Queensland have a degree of diversity that rivals that observed in Africa. In this study, we have used a deep sequencing approach to identify two new mastrevirus species, tentatively named rice latent virus 1 and 2 (RLV 1 and 2), from two, undescribed wild rice species (Oryza AA genome group) in Cape York Peninsula, Queensland...
July 4, 2017: Virus Research
https://www.readbyqxmd.com/read/28677304/integrated-structural-biology-and-molecular-ecology-of-n-cycling-enzymes-from-ammonia-oxidizing-archaea
#16
Bradley B Tolar, Jonathan Herrmann, John R Bargar, Henry van den Bedem, Soichi Wakatsuki, Christopher A Francis
Knowledge of the molecular ecology and environmental determinants of ammonia-oxidizing organisms is critical to understanding and predicting the global nitrogen (N) and carbon cycles, but an incomplete biochemical picture hinders in vitro studies of N-cycling enzymes. Although an integrative structural and dynamic characterization at the atomic scale would advance our understanding of function tremendously, structural knowledge of key N-cycling enzymes from ecologically-relevant ammonia oxidizers is unfortunately extremely limited...
July 5, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28674200/the-deep-hot-biosphere-twenty-five-years-of-retrospection
#17
Daniel R Colman, Saroj Poudel, Blake W Stamps, Eric S Boyd, John R Spear
Twenty-five years ago this month, Thomas Gold published a seminal manuscript suggesting the presence of a "deep, hot biosphere" in the Earth's crust. Since this publication, a considerable amount of attention has been given to the study of deep biospheres, their role in geochemical cycles, and their potential to inform on the origin of life and its potential outside of Earth. Overwhelming evidence now supports the presence of a deep biosphere ubiquitously distributed on Earth in both terrestrial and marine settings...
July 3, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28658759/revisiting-the-utility-of-histopathological-examination-of-biopsy-a-necessity-in-microbiology
#18
Priyamvada Roy, Shukla Das, Sonal Sharma, Vaibhav Girotra, Neelima Gupta, Rumpa Saha, Iqbal Rajinder Kaur
INTRODUCTION: Culture is the gold standard, while potassium hydroxide mount is simplest technique used for diagnosis of fungal pathogens. Histopathological examination is the only definitive means to identify certain uncultivable fungi. AIM: To analyse role of histopathological examination and potassium hydroxide (KOH) mount for diagnosing fungal infections by correlating them with culture. MATERIALS AND METHODS: In this nine year retrospective study, all biopsy specimens submitted for microbiological examination were included...
May 2017: Journal of Clinical and Diagnostic Research: JCDR
https://www.readbyqxmd.com/read/28648396/25-years-of-serving-the-community-with-ribosomal-rna-gene-reference-databases-and-tools
#19
Frank Oliver Glöckner, Pelin Yilmaz, Christian Quast, Jan Gerken, Alan Beccati, Andreea Ciuprina, Gerrit Bruns, Pablo Yarza, Jörg Peplies, Ralf Westram, Wolfgang Ludwig
SILVA (lat. forest) is a comprehensive web resource, providing services around up to date, high-quality datasets of aligned ribosomal RNA gene (rDNA) sequences from the Bacteria, Archaea, and Eukaryota domains. SILVA dates back to the year 1991 when Dr. Wolfgang Ludwig from the Technical University Munich started the integrated software workbench ARB (lat. tree) to support high-quality phylogenetic inference and taxonomy based on the SSU and LSU rDNA marker genes. At that time, the ARB project maintained both, the sequence reference datasets and the software package for data analysis...
June 22, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28630471/candidatus-mycoplasma-girerdii-replicates-diversifies-and-co-occurs-with-trichomonas-vaginalis-in-the-oral-cavity-of-a-premature-infant
#20
Elizabeth K Costello, Christine L Sun, Erica M Carlisle, Michael J Morowitz, Jillian F Banfield, David A Relman
Genital mycoplasmas, which can be vertically transmitted, have been implicated in preterm birth, neonatal infections, and chronic lung disease of prematurity. Our prior work uncovered 16S rRNA genes belonging to a novel, as-yet-uncultivated mycoplasma (lineage 'Mnola') in the oral cavity of a premature neonate. Here, we characterize the organism's associated community, growth status, metabolic potential, and population diversity. Sequencing of genomic DNA from the infant's saliva yielded 1.44 Gbp of high-quality, non-human read data, from which we recovered three essentially complete (including 'Mnola') and three partial draft genomes (including Trichomonas vaginalis)...
June 19, 2017: Scientific Reports
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