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Shotgun sequence metagenome

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https://www.readbyqxmd.com/read/28424662/untangling-genomes-of-novel-planctomycetal-and-verrucomicrobial-species-from-monterey-bay-kelp-forest-metagenomes-by-refined-binning
#1
John Vollmers, Martinique Frentrup, Patrick Rast, Christian Jogler, Anne-Kristin Kaster
The kelp forest of the Pacific temperate rocky marine coastline of Monterey Bay in California is a dominant habitat for large brown macro-algae in the order of Laminariales. It is probably one of the most species-rich, structurally complex and productive ecosystems in temperate waters and well-studied in terms of trophic ecology. However, still little is known about the microorganisms thriving in this habitat. A growing body of evidence suggests that bacteria associated with macro-algae represent a huge and largely untapped resource of natural products with chemical structures that have been optimized by evolution for biological and ecological purposes...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28421041/metagenome-wide-association-study-and-machine-learning-prediction-of-bulk-soil-microbiome-and-crop-productivity
#2
Hao-Xun Chang, James S Haudenshield, Charles R Bowen, Glen L Hartman
Areas within an agricultural field in the same season often differ in crop productivity despite having the same cropping history, crop genotype, and management practices. One hypothesis is that abiotic or biotic factors in the soils differ between areas resulting in these productivity differences. In this study, bulk soil samples collected from a high and a low productivity area from within six agronomic fields in Illinois were quantified for abiotic and biotic characteristics. Extracted DNA from these bulk soil samples were shotgun sequenced...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28394451/ancient-dna-analysis-identifies-marine-mollusc-shells-as-new-metagenomic-archives-of-the-past
#3
Clio Der Sarkissian, Vianney Pichereau, Catherine Dupont, Peter C Ilsøe, Mickael Perrigault, Paul Butler, Laurent Chauvaud, Jón Eiríksson, James Scourse, Christine Paillard, Ludovic Orlando
Marine mollusc shells enclose a wealth of information on coastal organisms and their environment. Their life history traits as well as (palaeo-) environmental conditions, including temperature, food availability, salinity, and pollution, can be traced through the analysis of their shell (micro-) structure and biogeochemical composition. Adding to this list the DNA entrapped in shell carbonate biominerals potentially offers a novel and complementary proxy both for reconstructing palaeoenvironments and tracking mollusc evolutionary trajectories...
April 10, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28389755/soda-pans-of-the-pannonian-steppe-harbor-unique-bacterial-communities-adapted-to-multiple-extreme-conditions
#4
Attila Szabó, Kristóf Korponai, Csaba Kerepesi, Boglárka Somogyi, Lajos Vörös, Dániel Bartha, Károly Márialigeti, Tamás Felföldi
Soda pans of the Pannonian steppe are unique environments regarding their physical and chemical characteristics: shallowness, high turbidity, intermittent character, alkaline pH, polyhumic organic carbon concentration, hypertrophic condition, moderately high salinity, sodium and carbonate ion dominance. The pans are highly productive environments with picophytoplankton predominance. Little is known about the planktonic bacterial communities inhabiting these aquatic habitats; therefore, amplicon sequencing and shotgun metagenomics were applied to reveal their composition and functional properties...
April 7, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28384336/filthy-lucre-a-metagenomic-pilot-study-of-microbes-found-on-circulating-currency-in-new-york-city
#5
Julia M Maritz, Steven A Sullivan, Robert J Prill, Emre Aksoy, Paul Scheid, Jane M Carlton
BACKGROUND: Paper currency by its very nature is frequently transferred from one person to another and represents an important medium for human contact with-and potential exchange of-microbes. In this pilot study, we swabbed circulating $1 bills obtained from a New York City bank in February (Winter) and June (Summer) 2013 and used shotgun metagenomic sequencing to profile the communities found on their surface. Using basic culture conditions, we also tested whether viable microbes could be recovered from bills...
2017: PloS One
https://www.readbyqxmd.com/read/28384184/assessing-biosynthetic-potential-of-agricultural-groundwater-through-metagenomic-sequencing-a-diverse-anammox-community-dominates-nitrate-rich-groundwater
#6
William B Ludington, Thaddeus D Seher, Olin Applegate, Xunde Li, Joseph I Kliegman, Charles Langelier, Edward R Atwill, Thomas Harter, Joseph L DeRisi
BACKGROUND: Climate change produces extremes in both temperature and precipitation causing increased drought severity and increased reliance on groundwater resources. Agricultural practices, which rely on groundwater, are sensitive to but also sources of contaminants, including nitrate. How agricultural contamination drives groundwater geochemistry through microbial metabolism is poorly understood. METHODS: On an active cow dairy in the Central Valley of California, we sampled groundwater from three wells at depths of 4...
2017: PloS One
https://www.readbyqxmd.com/read/28383679/ezmap-a-simple-pipeline-for-reproducible-analysis-of-the-human-virome
#7
Patrick Czeczko, Steven C Greenway, A P Jason de Koning
Summary: In solid-organ transplant recipients, a delicate balance between immunosuppression and immunocompetence must be achieved, which can be difficult to monitor in real-time. Shotgun sequencing of cell-free DNA (cfDNA) has been recently proposed as a new way to indirectly assess immune function in transplant recipients through analysis of the status of the human virome. To facilitate exploration of the utility of the human virome as an indicator of immune status, and to enable rapid, straightforward analyses by clinicians, we developed a fully-automated computational pipeline, EzMap, for performing metagenomic analysis of the human virome...
April 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28382231/metagenomic-analysis-exploring-taxonomic-and-functional-diversity-of-soil-microbial-communities-in-chilean-vineyards-and-surrounding-native-forests
#8
Luis E Castañeda, Olga Barbosa
Mediterranean biomes are biodiversity hotspots, and vineyards are important components of the Mediterranean landscape. Over the last few decades, the amount of land occupied by vineyards has augmented rapidly, thereby increasing threats to Mediterranean ecosystems. Land use change and agricultural management have important effects on soil biodiversity, because they change the physical and chemical properties of soil. These changes may also have consequences on wine production considering that soil is a key component of terroir...
2017: PeerJ
https://www.readbyqxmd.com/read/28379472/a-possible-novel-prosthetic-joint-infection-pathogen-mycoplasma-salivarium-identified-by-metagenomic-shotgun-sequencing
#9
Matthew Thoendel, Patricio Jeraldo, Kerryl E Greenwood-Quaintance, Nicholas Chia, Matthew P Abdel, James M Steckelberg, Douglas R Osmon, Robin Patel
Defining the microbial etiology of culture-negative prosthetic joint infection (PJI) can be challenging. Metagenomic shotgun sequencing is a new tool to identify organisms undetected by conventional methods. We present a case where metagenomics was used to identify Mycoplasma salivarium as a novel PJI pathogen in a hypogammaglobulinemic individual.
April 1, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28373716/microbial-functional-capacity-is-preserved-within-engineered-soil-formulations-used-in-mine-site-restoration
#10
Deepak Kumaresan, Adam T Cross, Benjamin Moreira-Grez, Khalil Kariman, Paul Nevill, Jason Stevens, Richard J N Allcock, Anthony G O'Donnell, Kingsley W Dixon, Andrew S Whiteley
Mining of mineral resources produces substantial volumes of crushed rock based wastes that are characterised by poor physical structure and hydrology, unstable geochemistry and potentially toxic chemical conditions. Recycling of these substrates is desirable and can be achieved by blending waste with native soil to form a 'novel substrate' which may be used in future landscape restoration. However, these post-mining substrate based 'soils' are likely to contain significant abiotic constraints for both plant and microbial growth...
April 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28367376/slimm-species-level-identification-of-microorganisms-from-metagenomes
#11
Temesgen Hailemariam Dadi, Bernhard Y Renard, Lothar H Wieler, Torsten Semmler, Knut Reinert
Identification and quantification of microorganisms is a significant step in studying the alpha and beta diversities within and between microbial communities respectively. Both identification and quantification of a given microbial community can be carried out using whole genome shotgun sequences with less bias than when using 16S-rDNA sequences. However, shared regions of DNA among reference genomes and taxonomic units pose a significant challenge in assigning reads correctly to their true origins. The existing microbial community profiling tools commonly deal with this problem by either preparing signature-based unique references or assigning an ambiguous read to its least common ancestor in a taxonomic tree...
2017: PeerJ
https://www.readbyqxmd.com/read/28356418/impact-of-contaminating-dna-in-whole-genome-amplification-kits-used-for-metagenomic-shotgun-sequencing-for-infection-diagnosis
#12
Matthew Thoendel, Patricio Jeraldo, Kerryl E Greenwood-Quaintance, Janet Yao, Nicholas Chia, Arlen D Hanssen, Matthew P Abdel, Robin Patel
Whole genome amplification (WGA) is a useful tool for amplification of very small quantities of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis. Depending on the application, background DNA from WGA kits can be problematic. Three WGA kits were tested for their utility in a metagenomics approach to identify pathogens in sonicate fluid comprised of biofilms and other materials dislodged from the surfaces of explanted prosthetic joints using sonication. The Illustra Genomiphi V2, Illustra Single Cell Genomiphi, and Qiagen REPLI-g Single Cell kits were tested on identical sonicate fluid samples...
March 29, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28352255/metaproteogenomics-reveals-taxonomic-and-functional-changes-between-cecal-and-fecal-microbiota-in-mouse
#13
Alessandro Tanca, Valeria Manghina, Cristina Fraumene, Antonio Palomba, Marcello Abbondio, Massimo Deligios, Michael Silverman, Sergio Uzzau
Previous studies on mouse models report that cecal and fecal microbial communities may differ in the taxonomic structure, but little is known about their respective functional activities. Here, we employed a metaproteogenomic approach, including 16S rRNA gene sequencing, shotgun metagenomics and shotgun metaproteomics, to analyze the microbiota of paired mouse cecal contents (CCs) and feces, with the aim of identifying changes in taxon-specific functions. As a result, Gram-positive anaerobes were observed as considerably higher in CCs, while several key enzymes, involved in oxalate degradation, glutamate/glutamine metabolism, and redox homeostasis, and most actively expressed by Bacteroidetes, were clearly more represented in feces...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28350876/mipe-a-metagenome-based-community-structure-explorer-and-ssu-primer-evaluation-tool
#14
Bin Zou, JieFu Li, Quan Zhou, Zhe-Xue Quan
An understanding of microbial community structure is an important issue in the field of molecular ecology. The traditional molecular method involves amplification of small subunit ribosomal RNA (SSU rRNA) genes by polymerase chain reaction (PCR). However, PCR-based amplicon approaches are affected by primer bias and chimeras. With the development of high-throughput sequencing technology, unbiased SSU rRNA gene sequences can be mined from shotgun sequencing-based metagenomic or metatranscriptomic datasets to obtain a reflection of the microbial community structure in specific types of environment and to evaluate SSU primers...
2017: PloS One
https://www.readbyqxmd.com/read/28345059/health-and-disease-imprinted-in-the-time-variability-of-the-human-microbiome
#15
Jose Manuel Martí, Daniel Martínez-Martínez, Teresa Rubio, César Gracia, Manuel Peña, Amparo Latorre, Andrés Moya, Carlos P Garay
The animal microbiota (including the human microbiota) plays an important role in keeping the physiological status of the host healthy. Research seeks greater insight into whether changes in the composition and function of the microbiota are associated with disease. We analyzed published 16S rRNA and shotgun metagenomic sequencing (SMS) data pertaining to the gut microbiotas of 99 subjects monitored over time. Temporal fluctuations in the microbial composition revealed significant differences due to factors such as dietary changes, antibiotic intake, age, and disease...
March 2017: MSystems
https://www.readbyqxmd.com/read/28342734/integration-of-microbiome-and-epigenome-to-decipher-the-pathogenesis-of-autoimmune-diseases
#16
REVIEW
Beidi Chen, Luxi Sun, Xuan Zhang
The interaction between genetic predisposition and environmental factors are of great significance in the pathogenesis and development of autoimmune diseases (AIDs). The human mucosa is the most frequent site that interacts with the exterior environment, and commensal microbiota at the gut and other human mucosal cavities play a crucial role in the regulation of immune system. Growing evidence has shown that the compositional and functional changes of mucosal microbiota are closely related to AIDs. Gut dysbiosis not only influence the expression level of Toll-like receptors (TLRs) of antigen presenting cells, but also contribute to Th17/Treg imbalance...
March 23, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/28340372/shotgun-metagenomic-sequencing-reveals-freshwater-beach-sands-as-reservoir-of-bacterial-pathogens
#17
Mahi M Mohiuddin, Yasser Salama, Herb E Schellhorn, G Brian Golding
Recreational waters and adjacent beach sands harbor complex microbial communities which may contain human pathogens that cannot be detected by conventional methods. Here, we investigate the diversity of bacterial populations inhabiting four freshwater beaches of the Great Lakes region using shotgun metagenomic sequencing approach. Our analysis suggests that average taxonomic richness and alpha diversity are significantly higher (P < 0.001) in beach sands compared to the corresponding water environments...
March 1, 2017: Water Research
https://www.readbyqxmd.com/read/28337070/genomic-methods-and-microbiological-technologies-for-profiling-novel-and-extreme-environments-for-the-extreme-microbiome-project-xmp
#18
Scott Tighe, Ebrahim Afshinnekoo, Tara M Rock, Ken McGrath, Noah Alexander, Alexa McIntyre, Sofia Ahsanuddin, Daniela Bezdan, Stefan J Green, Samantha Joye, Sarah Stewart Johnson, Don A Baldwin, Nathan Bivens, Nadim Ajami, Joseph R Carmical, Ian Charold Herriott, Rita Colwell, Mohamed Donia, Jonathan Foox, Nick Greenfield, Tim Hunter, Jessica Hoffman, Joshua Hyman, Ellen Jorgensen, Diana Krawczyk, Jodie Lee, Shawn Levy, Natàlia Garcia-Reyero, Matthew Settles, Kelley Thomas, Felipe Gómez, Lynn Schriml, Nikos Kyrpides, Elena Zaikova, Jon Penterman, Christopher E Mason
The Extreme Microbiome Project (XMP) is a project launched by the Association of Biomolecular Resource Facilities Metagenomics Research Group (ABRF MGRG) that focuses on whole genome shotgun sequencing of extreme and unique environments using a wide variety of biomolecular techniques. The goals are multifaceted, including development and refinement of new techniques for the following: 1) the detection and characterization of novel microbes, 2) the evaluation of nucleic acid techniques for extremophilic samples, and 3) the identification and implementation of the appropriate bioinformatics pipelines...
March 10, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28330225/metagenomics-analysis-of-microbial-communities-associated-with-a-traditional-rice-wine-starter-culture-xaj-pitha-of-assam-india
#19
Sudipta Sankar Bora, Jyotshna Keot, Saurav Das, Kishore Sarma, Madhumita Barooah
This is the first report on the microbial diversity of xaj-pitha, a rice wine fermentation starter culture through a metagenomics approach involving Illumine-based whole genome shotgun (WGS) sequencing method. Metagenomic DNA was extracted from rice wine starter culture concocted by Ahom community of Assam and analyzed using a MiSeq(®) System. A total of 2,78,231 contigs, with an average read length of 640.13 bp, were obtained. Data obtained from the use of several taxonomic profiling tools were compared with previously reported microbial diversity studies through the culture-dependent and culture-independent method...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28298908/serpentinization-influenced-groundwater-harbors-extremely-low-diversity-microbial-communities-adapted-to-high-ph
#20
Katrina I Twing, William J Brazelton, Michael D Y Kubo, Alex J Hyer, Dawn Cardace, Tori M Hoehler, Tom M McCollom, Matthew O Schrenk
Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U...
2017: Frontiers in Microbiology
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