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https://www.readbyqxmd.com/read/27911252/chapparvoviruses-occur-in-at-least-three-vertebrate-classes-and-have-a-broad-biogeographic-distribution
#1
William Marciel de Souza, Marilia Farignoli Romeiro, Marcílio Jorge Fumagalli, Sejal Modha, Jansen de Araujo, Luzia Helena Queiroz, Edison Luiz Durigon, Luiz Tadeu Moraes Figueiredo, Pablo Ramiro Murcia, Robert Gifford
Chapparvoviruses are a highly divergent group of parvoviruses (family Parvoviridae) that have recently been identified via metagenomic sampling of animal faeces. Here we report the sequences of six novel chapparvoviruses identified through both metagenomic sampling of bat tissues and in silico screening of published vertebrate genome assemblies. The novel chapparvoviruses share several distinctive genomic features, and group together as a robustly supported monophyletic clade in phylogenetic trees. Our data indicate that chapparvoviruses have a broad host range in vertebrates, and a global distribution...
December 2, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27909433/sponge-microbiota-are-a-reservoir-of-functional-antibiotic-resistance-genes
#2
Dennis Versluis, Mari Rodriguez de Evgrafov, Morten O A Sommer, Detmer Sipkema, Hauke Smidt, Mark W J van Passel
Wide application of antibiotics has contributed to the evolution of multi-drug resistant human pathogens, resulting in poorer treatment outcomes for infections. In the marine environment, seawater samples have been investigated as a resistance reservoir; however, no studies have methodically examined sponges as a reservoir of antibiotic resistance. Sponges could be important in this respect because they often contain diverse microbial communities that have the capacity to produce bioactive metabolites. Here, we applied functional metagenomics to study the presence and diversity of functional resistance genes in the sponges Aplysina aerophoba, Petrosia ficiformis, and Corticium candelabrum...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27907181/the-role-of-ocean-currents-in-the-temperature-selection-of-plankton-insights-from-an-individual-based-model
#3
Ferdi L Hellweger, Erik van Sebille, Benjamin C Calfee, Jeremy W Chandler, Erik R Zinser, Brandon K Swan, Neil D Fredrick
Biogeography studies that correlate the observed distribution of organisms to environmental variables are typically based on local conditions. However, in cases with substantial translocation, like planktonic organisms carried by ocean currents, selection may happen upstream and local environmental factors may not be representative of those that shaped the local population. Here we use an individual-based model of microbes in the global surface ocean to explore this effect for temperature. We simulate up to 25 million individual cells belonging to up to 50 species with different temperature optima...
2016: PloS One
https://www.readbyqxmd.com/read/27907121/environmental-and-geographical-factors-structure-soil-microbial-diversity-in-new-caledonian-ultramafic-substrates-a-metagenomic-approach
#4
Véronique Gourmelon, Laurent Maggia, Jeff R Powell, Sarah Gigante, Sara Hortal, Claire Gueunier, Kelly Letellier, Fabian Carriconde
Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity...
2016: PloS One
https://www.readbyqxmd.com/read/27907010/viral-metagenomic-analysis-displays-the-co-infection-situation-in-healthy-and-pmws-affected-pigs
#5
Anne-Lie Blomström, Caroline Fossum, Per Wallgren, Mikael Berg
The development of high-throughput sequencing technologies have allowed the possibility to investigate and characterise the entire microbiome of individuals, providing better insight to the complex interaction between different microorganisms. This will help to understand how the microbiome influence the susceptibility of secondary agents and development of disease. We have applied viral metagenomics to investigate the virome of lymph nodes from Swedish pigs suffering from the multifactorial disease postweaning multisystemic wasting syndrome (PMWS) as well as from healthy pigs...
2016: PloS One
https://www.readbyqxmd.com/read/27906039/peering-below-the-diffraction-limit-robust-and-specific-sorting-of-viruses-with-flow-cytometry
#6
Shea T Lance, David J Sukovich, Kenneth M Stedman, Adam R Abate
BACKGROUND: Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population...
December 1, 2016: Virology Journal
https://www.readbyqxmd.com/read/27902331/the-plasma-virome-of-febrile-adult-kenyans-shows-frequent-parvovirus-b19-infections-and-a-novel-arbovirus-kadipiro-virus
#7
Carolyne Ngoi, Juliana Siqueira, Linlin Li, Xutao Deng, Peter Mugo, Susan Graham, Matt Price, Eduard Sanders, Eric Delwart
Viral nucleic acids present in the plasma of 498 Kenyan adults with unexplained fever were characterized by metagenomics analysis of 51 sample pools. The highest to lowest fraction of plasma pools was positive for parvovirus B19 (75%), pegivirus C (GBV-C) (67%), alpha anellovirus (59%), gamma anellovirus (55%), beta anellovirus (41%), Dengue virus genotype 2 (DENV-2) (16%), HIV-1 (6%), HHV-6 (6%), HBV (4%), rotavirus (4%), norovirus (4%), rhinovirus C (2%), Merkel cell polyomavirus (MCPyV)(2%) and Kadipiro virus (2%)...
October 24, 2016: Journal of General Virology
https://www.readbyqxmd.com/read/27901108/survey-of-the-green-picoalga-bathycoccus-genomes-in-the-global-ocean
#8
Thomas Vannier, Jade Leconte, Yoann Seeleuthner, Samuel Mondy, Eric Pelletier, Jean-Marc Aury, Colomban de Vargas, Michael Sieracki, Daniele Iudicone, Daniel Vaulot, Patrick Wincker, Olivier Jaillon
Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27900698/mining-microbial-signals-for-enhanced-biodiscovery-of-secondary-metabolites
#9
F Jerry Reen, Jose A Gutiérrez-Barranquero, Fergal O'Gara
The advent of metagenomics based biodiscovery has provided researchers with previously unforeseen access to the rich tapestry of natural bioactivity that exists in the biosphere. Unhindered by the "culturable bottleneck" that has severely limited the translation of the genetic potential that undoubtedly exists in nature, metagenomics nonetheless requires ongoing technological developments to maximize its efficacy and applicability to the discovery of new chemical entities.Here we describe methodologies for the detection and isolation of quorum sensing (QS) signal molecules from metagenomics libraries...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900697/screening-for-n-ahsl-based-signaling-interfering-enzymes
#10
Stéphane Uroz, Phil M Oger
Quorum sensing (QS)-based signaling is a widespread pathway used by bacteria for the regulation of functions involved in their relation to the environment or their host. QS relies upon the production, accumulation and perception of small diffusable molecules by the bacterial population, hence linking high gene expression with high cell population densities. Among the different QS signal molecules, an important class of signal molecules is the N-acyl homoserine lactone (N-AHSL). In pathogens such as Erwinia or Pseudomonas, N-AHSL based QS is crucial to overcome the host defenses and ensure a successful infection...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900696/activity-based-screening-of-metagenomic-libraries-for-hydrogenase-enzymes
#11
Nicole Adam, Mirjam Perner
Here we outline how to identify hydrogenase enzymes from metagenomic libraries through an activity-based screening approach. A metagenomic fosmid library is constructed in E. coli and the fosmids are transferred into a hydrogenase deletion mutant of Shewanella oneidensis (ΔhyaB) via triparental mating. If a fosmid exhibits hydrogen uptake activity, S. oneidensis' phenotype is restored and hydrogenase activity is indicated by a color change of the medium from yellow to colorless. This new method enables screening of 48 metagenomic fosmid clones in parallel...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900695/function-based-metagenomic-library-screening-and-heterologous-expression-strategy-for-genes-encoding-phosphatase-activity
#12
Genis A Castillo Villamizar, Heiko Nacke, Rolf Daniel
The release of phosphate from inorganic and organic phosphorus compounds can be mediated enzymatically. Phosphate-releasing enzymes, comprising acid and alkaline phosphatases, are recognized as useful biocatalysts in applications such as plant and animal nutrition, bioremediation and diagnostic analysis. Metagenomic approaches provide access to novel phosphatase-encoding genes. Here, we describe a function-based screening approach for rapid identification of genes conferring phosphatase activity from small-insert and large-insert metagenomic libraries derived from various environments...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900694/methods-for-the-isolation-of-genes-encoding-novel-pha-metabolism-enzymes-from-complex-microbial-communities
#13
Jiujun Cheng, Ricardo Nordeste, Maria A Trainer, Trevor C Charles
Development of different PHAs as alternatives to petrochemically derived plastics can be facilitated by mining metagenomic libraries for diverse PHA cycle genes that might be useful for synthesis of bio-plastics. The specific phenotypes associated with mutations of the PHA synthesis pathway genes in Sinorhizobium meliloti and Pseudomonas putida, allows the use of powerful selection and screening tools to identify complementing novel PHA synthesis genes. Identification of novel genes through their function rather than sequence facilitates the functional proteins that may otherwise have been excluded through sequence-only screening methodology...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900693/screening-glycosyltransferases-for-polyphenol-modifications
#14
Nele Ilmberger, Ulrich Rabausch
Glycosyltransferases offer the opportunity to glycosylate a variety of substrates including health beneficial molecules like flavonoids in a regiospecific manner. Flavonoids are plant secondary metabolites that have antimicrobial, antioxidative, and health beneficial effects. Glycosylation often has impact on these properties and furthermore enhances the water solubility, the stability, and the bioavailability of the molecules. To detect flavonoid glycosylating enzymes we established a metagenome screen for the discovery of modifying clones...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900692/liquid-phase-multiplex-high-throughput-screening-of-metagenomic-libraries-using-p-nitrophenyl-linked-substrates-for-accessory-lignocellulosic-enzymes
#15
Mariette Smart, Robert J Huddy, Don A Cowan, Marla Trindade
To access the genetic potential contained in large metagenomic libraries, suitable high-throughput functional screening methods are required. Here we describe a high-throughput screening approach which enables the rapid identification of metagenomic library clones expressing functional accessory lignocellulosic enzymes. The high-throughput nature of this method hinges on the multiplexing of both the E. coli metagenomic library clones and the colorimetric p-nitrophenyl linked substrates which allows for the simultaneous screening for β-glucosidases, β-xylosidases, and α-L-arabinofuranosidases...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900691/screening-for-cellulase-encoding-clones-in-metagenomic-libraries
#16
Nele Ilmberger, Wolfgang R Streit
For modern biotechnology there is a steady need to identify novel enzymes. In biotechnological applications, however, enzymes often must function under extreme and nonnatural conditions (i.e., in the presence of solvents, high temperature and/or at extreme pH values). Cellulases have many industrial applications from the generation of bioethanol, a realistic long-term energy source, to the finishing of textiles. These industrial processes require cellulolytic activity under a wide range of pH, temperature, and ionic conditions, and they are usually carried out by mixtures of cellulases...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900689/novel-tools-for-the-functional-expression-of-metagenomic-dna
#17
Nadine Katzke, Andreas Knapp, Anita Loeschcke, Thomas Drepper, Karl-Erich Jaeger
Functional expression of genes from metagenomic libraries is limited by various factors including inefficient transcription and/or translation of target genes as well as improper folding and assembly of the corresponding proteins caused by the lack of appropriate chaperones and cofactors. It is now well accepted that the use of different expression hosts of distinct phylogeny and physiology can dramatically increase the rate of success. In the following chapter, we therefore describe tools and protocols allowing for the comparative heterologous expression of genes in five bacterial expression hosts, namely Escherichia coli, Pseudomonas putida, Bacillus subtilis, Burkholderia glumae, and Rhodobacter capsulatus...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900688/degradation-network-reconstruction-guided-by-metagenomic-data
#18
Rafael Bargiela, Manuel Ferrer
Network reconstruction procedures based on meta-"omics" data are an invaluable tool for inferring total and active set of reactions mediated by different members in a microbial community. Within them, network-based methods for automatic analysis of catabolic capacities in metagenomes are currently limited. Here, we describe the complete workflow, scripts, and commands allowing the automatic reconstruction of biodegradation networks using as an input meta-sequences generated by direct DNA sequencing.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900687/cloning-and-expression-of-metagenomic-dna-in-streptomyces-lividans-and-subsequent-fermentation-for-optimized-production
#19
Yuriy Rebets, Jan Kormanec, Andriy Lutzhetskyy, Kristel Bernaerts, Jozef Anné
The choice of an expression system for the metagenomic DNA of interest is of vital importance for the detection of any particular gene or gene cluster. Most of the screens to date have used the gram-negative bacterium Escherichia coli as a host for metagenomic gene libraries. However, the use of E. coli introduces a potential host bias since only 40 % of the enzymatic activities may be readily recovered by random cloning in E. coli. To recover some of the remaining 60 %, alternative cloning hosts such as Streptomyces spp...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27900686/shotgun-metagenomic-sequencing-analysis-of-soft-rot-enterobacteriaceae-in-polymicrobial-communities
#20
James Doonan, Sandra Denman, James E McDonald, Peter N Golyshin
Shotgun metagenomic sequencing of bacterial communities in necrotic plant lesions allows insights of host-pathogen molecular interactions. Soft-rot Enterobacteriaceae are significant crop pathogens with a wide host range. Reconstructed polymicrobial community DNA from soft-rot affected crops provides details of species relative abundance and functional potential, enabling significant insights into their lifestyle. Here, we describe a workflow for DNA recovery, metagenomic shotgun sequencing and in particular, an in silico analysis of bacterial isolates from affected plant tissue...
2017: Methods in Molecular Biology
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