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https://www.readbyqxmd.com/read/28340372/shotgun-metagenomic-sequencing-reveals-freshwater-beach-sands-as-reservoir-of-bacterial-pathogens
#1
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/28340310/viruses-in-cystic-fibrosis-patients-airways
#2
Lisa Billard, Rozenn Le Berre, Léa Pilorgé, Christopher Payan, Geneviève Héry-Arnaud, Sophie Vallet
Although bacteria have historically been considered to play a major role in cystic fibrosis (CF) airway damage, a strong impact of respiratory viral infections (RVI) is also now recognized. Emerging evidence confirms that respiratory viruses are associated with deterioration of pulmonary function and exacerbation and facilitation of bacterial colonization in CF patients. The aim of this review is to provide an overview of the current knowledge on respiratory viruses in CF airways, to discuss the resulting inflammation and RVI response, to determine how to detect the viruses, and to assess their clinical consequences, prevalence, and interactions with bacteria...
March 24, 2017: Critical Reviews in Microbiology
https://www.readbyqxmd.com/read/28338745/circadian-oscillations-of-microbial-and-functional-composition-in-the-human-salivary-microbiome
#3
Lena Takayasu, Wataru Suda, Kageyasu Takanashi, Erica Iioka, Rina Kurokawa, Chie Shindo, Yasue Hattori, Naoko Yamashita, Suguru Nishijima, Kenshiro Oshima, Masahira Hattori
The human microbiomes across the body evidently interact with various signals in response to biogeographical physiological conditions. To understand such interactions in detail, we investigated how the salivary microbiome in the oral cavity would be regulated by host-related signals. Here, we show that the microbial abundance and gene participating in keeping the human salivary microbiome exhibit global circadian rhythm. Analysis of the 16S rRNA sequences of salivary microbial samples of six healthy adults collected at 4-h intervals for three days revealed that the microbial genera accounting for 68...
February 23, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28338677/integrated-metabolism-in-sponge-microbe-symbiosis-revealed-by-genome-centered-metatranscriptomics
#4
Lucas Moitinho-Silva, Cristina Díez-Vives, Giampiero Batani, Ana Is Esteves, Martin T Jahn, Torsten Thomas
Despite an increased understanding of functions in sponge microbiomes, the interactions among the symbionts and between symbionts and host are not well characterized. Here we reconstructed the metabolic interactions within the sponge Cymbastela concentrica microbiome in the context of functional features of symbiotic diatoms and the host. Three genome bins (CcPhy, CcNi and CcThau) were recovered from metagenomic data of C. concentrica, belonging to the proteobacterial family Phyllobacteriaceae, the Nitrospira genus and the thaumarchaeal order Nitrosopumilales...
March 24, 2017: ISME Journal
https://www.readbyqxmd.com/read/28337072/precision-metagenomics-rapid-metagenomic-analyses-for-infectious-disease-diagnostics-and-public-health-surveillance
#5
Ebrahim Afshinnekoo, Chou Chou, Noah Alexander, Sofia Ahsanuddin, Audrey N Schuetz, Christopher E Mason
Next-generation sequencing (NGS) technologies have ushered in the era of precision medicine, transforming the way we treat cancer patients and diagnose disease. Concomitantly, the advent of these technologies has created a surge of microbiome and metagenomic studies over the last decade, many of which are focused on investigating the host-gene-microbial interactions responsible for the development and spread of infectious diseases, as well as delineating their key role in maintaining health. As we continue to discover more information about the etiology of infectious diseases, the translational potential of metagenomic NGS methods for treatment and rapid diagnosis is becoming abundantly clear...
March 21, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28337071/international-standards-for-genomes-transcriptomes-and-metagenomes
#6
Christopher E Mason, Ebrahim Afshinnekoo, Scott Tighe, Shixiu Wu, Shawn Levy
Challenges and biases in preparing, characterizing, and sequencing DNA and RNA can have significant impacts on research in genomics across all kingdoms of life, including experiments in single-cells, RNA profiling, and metagenomics (across multiple genomes). Technical artifacts and contamination can arise at each point of sample manipulation, extraction, sequencing, and analysis. Thus, the measurement and benchmarking of these potential sources of error are of paramount importance as next-generation sequencing (NGS) projects become more global and ubiquitous...
March 17, 2017: Journal of Biomolecular Techniques: JBT
https://www.readbyqxmd.com/read/28337070/genomic-methods-and-microbiological-technologies-for-profiling-novel-and-extreme-environments-for-the-extreme-microbiome-project-xmp
#7
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/28336917/acclimation-of-a-low-iron-adapted-ostreococcus-strain-to-iron-limitation-through-cell-biomass-lowering
#8
Hugo Botebol, Gaelle Lelandais, Christophe Six, Emmanuel Lesuisse, Arnaud Meng, Lucie Bittner, Stéphane Lecrom, Robert Sutak, Jean-Claude Lozano, Philippe Schatt, Valérie Vergé, Stéphane Blain, François-Yves Bouget
Iron is an essential micronutrient involved in many biological processes and is often limiting for primary production in large regions of the World Ocean. Metagenomic and physiological studies have identified clades or ecotypes of marine phytoplankton that are specialized in iron depleted ecological niches. Although less studied, eukaryotic picophytoplankton does contribute significantly to primary production and carbon transfer to higher trophic levels. In particular, metagenomic studies of the green picoalga Ostreococcus have revealed the occurrence of two main clades distributed along coast-offshore gradients, suggesting niche partitioning in different nutrient regimes...
March 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28335808/potential-for-hydrogen-oxidizing-chemolithoautotrophic-and-diazotrophic-populations-to-initiate-biofilm-formation-in-oligotrophic-deep-terrestrial-subsurface-waters
#9
Xiaofen Wu, Karsten Pedersen, Johanna Edlund, Lena Eriksson, Mats Åström, Anders F Andersson, Stefan Bertilsson, Mark Dopson
BACKGROUND: Deep terrestrial biosphere waters are separated from the light-driven surface by the time required to percolate to the subsurface. Despite biofilms being the dominant form of microbial life in many natural environments, they have received little attention in the oligotrophic and anaerobic waters found in deep bedrock fractures. This study is the first to use community DNA sequencing to describe biofilm formation under in situ conditions in the deep terrestrial biosphere. RESULTS: In this study, flow cells were attached to boreholes containing either "modern marine" or "old saline" waters of different origin and degree of isolation from the light-driven surface of the earth...
March 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28335731/highly-diverse-population-of-picornaviridae-and-other-members-of-the-picornavirales-in-cameroonian-fruit-bats
#10
Claude Kwe Yinda, Roland Zell, Ward Deboutte, Mark Zeller, Nádia Conceição-Neto, Elisabeth Heylen, Piet Maes, Nick J Knowles, Stephen Mbigha Ghogomu, Marc Van Ranst, Jelle Matthijnssens
BACKGROUND: The order Picornavirales represents a diverse group of positive-stranded RNA viruses with small non-enveloped icosahedral virions. Recently, bats have been identified as an important reservoir of several highly pathogenic human viruses. Since many members of the Picornaviridae family cause a wide range of diseases in humans and animals, this study aimed to characterize members of the order Picornavirales in fruit bat populations located in the Southwest region of Cameroon...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335448/a-community-multi-omics-approach-towards-the-assessment-of-surface-water-quality-in-an-urban-river-system
#11
David J Beale, Avinash V Karpe, Warish Ahmed, Stephen Cook, Paul D Morrison, Christopher Staley, Michael J Sadowsky, Enzo A Palombo
A multi-omics approach was applied to an urban river system (the Brisbane River (BR), Queensland, Australia) in order to investigate surface water quality and characterize the bacterial population with respect to water contaminants. To do this, bacterial metagenomic amplicon-sequencing using Illumina next-generation sequencing (NGS) of the V5-V6 hypervariable regions of the 16S rRNA gene and untargeted community metabolomics using gas chromatography coupled with mass spectrometry (GC-MS) were utilized. The multi-omics data, in combination with fecal indicator bacteria (FIB) counts, trace metal concentrations (by inductively coupled plasma mass spectrometry (ICP-MS)) and in-situ water quality measurements collected from various locations along the BR were then used to assess the health of the river ecosystem...
March 14, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28334407/organismal-and-spatial-partitioning-of-energy-and-macronutrient-transformations-within-a-hypersaline-mat
#12
Jennifer M Mobberley, Stephen R Lindemann, Hans C Bernstein, James J Moran, Ryan S Renslow, Jerome Babauta, Dehong Hu, Haluk Beyenal, William C Nelson
Phototrophic mat communities are model ecosystems for studying energy cycling and elemental transformations because complete biogeochemical cycles occur over millimeter-to-centimeter scales. Characterization of energy and nutrient capture within hypersaline phototrophic mats has focused on specific processes and organisms, however little is known about community-wide distribution of and linkages between these processes. To investigate energy and macronutrient capture and flow through a structured community, the spatial and organismal distribution of metabolic functions within a compact hypersaline mat community from Hot Lake have been broadly elucidated through species-resolved metagenomics and geochemical, microbial diversity, and metabolic gradient measurements...
March 15, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334267/resistomap-online-visualization-of-human-gut-microbiota-antibiotic-resistome
#13
Konstantin S Yarygin, Boris A Kovarsky, Tatyana S Bibikova, Damir S Melnikov, Alexander V Tyakht, Dmitry G Alexeev
Summary: We created ResistoMap - a Web-based interactive visualization of the presence of genetic determinants conferring resistance to antibiotics, biocides and heavy metals in human gut microbiota. ResistoMap displays the data on more than 1500 published gut metagenomes of world populations including both healthy subjects and patients. Multiparameter display filters allow visual assessment of the associations between the meta-data and proportions of resistome. The geographic map navigation layer allows to state hypotheses regarding the global trends of antibiotic resistance and correlate the gut resistome variations with the national clinical guidelines on antibiotics application...
March 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334086/pseudoalignment-for-metagenomic-read-assignment
#14
L Schaeffer, H Pimentel, N Bray, P Melsted, L Pachter
Motivation: Read assignment is an important first step in many metagenomic analysis workflows, providing the basis for identification and quantification of species. However ambiguity among the sequences of many strains makes it difficult to assign reads at the lowest level of taxonomy, and reads are typically assigned to taxonomic levels where they are unambiguous. We explore connections between metagenomic read assignment and the quantification of transcripts from RNA-Seq data in order to develop novel methods for rapid and accurate quantification of metagenomic strains...
February 21, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28331945/from-a-metagenomic-source-to-a-high-resolution-structure-of-a-novel-alkaline-esterase
#15
Mariana Rangel Pereira, Thaís Carvalho Maester, Gustavo Fernando Mercaldi, Eliana Gertrudes de Macedo Lemos, Marko Hyvönen, Andrea Balan
Esterases catalyze the cleavage and formation of ester bonds and are members of the diverse family of α/β hydrolase fold. They are useful in industries from different sectors, such as food, detergent, fine chemicals, and biofuel production. In a previous work, 30 positive clones for lipolytic activity were identified from a metagenomic library of a microbial consortium specialized in diesel oil degradation. In this study, a putative gene encoding an esterase/lipase, denominated est8, has been cloned and the corresponding protein expressed recombinantly, purified to homogeneity and characterized functional and structurally...
March 22, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28330508/proteobacteria-explain-significant-functional-variability-in-the-human-gut-microbiome
#16
Patrick H Bradley, Katherine S Pollard
BACKGROUND: While human gut microbiomes vary significantly in taxonomic composition, biological pathway abundance is surprisingly invariable across hosts. We hypothesized that healthy microbiomes appear functionally redundant due to factors that obscure differences in gene abundance between individuals. RESULTS: To account for these biases, we developed a powerful test of gene variability called CCoDA, which is applicable to shotgun metagenomes from any environment and can integrate data from multiple studies...
March 23, 2017: Microbiome
https://www.readbyqxmd.com/read/28330292/comparative-assessment-of-methods-for-metagenomic-dna-isolation-from-soils-of-different-crop-growing-fields
#17
Aiman Tanveer, Sangeeta Yadav, Dinesh Yadav
The isolation of good quality metagenomic DNA from diverse soil, in appreciable amount, is a prerequisite for metagenomics. The availability of commercial kits for isolation of genomic DNAs from soil has drastically expedited the application of metagenomics approach for identifying novel sources of industrially important enzymes. The quantitative and qualitative assessment of metagenomic DNA isolated using either the manual method or the kit-based method should be performed prior to its use in downstream applications...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330232/high-quality-metagenomic-dna-from-marine-sediment-samples-for-genomic-studies-through-a-preprocessing-approach
#18
Solly Solomon, Bhavya Kachiprath, G Jayanath, T P Sajeevan, I S Bright Singh, Rosamma Philip
Recent advances in culture-independent studies of microbes had proved to be more reliable and efficient than the conventional ones. The isolation of good quality and quantity of total community DNA are one of the major hurdles in this endeavour. Shearing of DNA during the extraction process and the co-extraction of inhibitory compounds reduce the quality of the isolated nucleic acids making it unsuitable for the construction of large insert metagenomic libraries. In the present study, a multi-level filtration step was brought in which efficiently isolated total bacterial DNA from three different environment samples...
December 2016: 3 Biotech
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/28330093/exploration-of-nifh-gene-through-soil-metagenomes-of-the-western-indian-himalayas
#20
Ravindra Soni, Deep Chandra Suyal, Santosh Sai, Reeta Goel
This group has previously highlighted the prevalence of Csp genes from cold Himalayan environments. However, this study has explored the uncultured diazotrophs from metagenomes of western Indian Himalayas. The metagenomic nifH gene clone library was constructed from the Temperate, Subtropical and Tarai soils of Western Himalaya, India followed by polymerase chain reaction (PCR) amplification. After preliminary screening, selected clones were sequenced. In silico analysis of the clones was done, which documented 83...
June 2016: 3 Biotech
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