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Shotgun metagenomics

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https://www.readbyqxmd.com/read/28099457/comparing-and-evaluating-metagenome-assembly-tools-from-a-microbiologist-s-perspective-not-only-size-matters
#1
John Vollmers, Sandra Wiegand, Anne-Kristin Kaster
With the constant improvement in cost-efficiency and quality of Next Generation Sequencing technologies, shotgun-sequencing approaches -such as metagenomics- have nowadays become the methods of choice for studying and classifying microorganisms from various habitats. The production of data has dramatically increased over the past years and processing and analysis steps are becoming more and more of a bottleneck. Limiting factors are partly the availability of computational resources, but mainly the bioinformatics expertise in establishing and applying appropriate processing and analysis pipelines...
2017: PloS One
https://www.readbyqxmd.com/read/28093073/application-of-meta-omics-techniques-to-understand-greenhouse-gas-emissions-originating-from-ruminal-metabolism
#2
REVIEW
Robert J Wallace, Timothy J Snelling, Christine A McCartney, Ilma Tapio, Francesco Strozzi
Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the rumen microbial community structure, metabolic potential and metabolic activity. Here we explore these developments in relation to GHG emissions. Microbial rumen community analyses based on small subunit ribosomal RNA sequence analysis are not yet predictive of methane emissions from individual animals or treatments...
January 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28079128/parallel-meta-3-comprehensive-taxonomical-and-functional-analysis-platform-for-efficient-comparison-of-microbial-communities
#3
Gongchao Jing, Zheng Sun, Honglei Wang, Yanhai Gong, Shi Huang, Kang Ning, Jian Xu, Xiaoquan Su
The number of metagenomes is increasing rapidly. However, current methods for metagenomic analysis are limited by their capability for in-depth data mining among a large number of microbiome each of which carries a complex community structure. Moreover, the complexity of configuring and operating computational pipeline also hinders efficient data processing for the end users. In this work we introduce Parallel-META 3, a comprehensive and fully automatic computational toolkit for rapid data mining among metagenomic datasets, with advanced features including 16S rRNA extraction for shotgun sequences, 16S rRNA copy number calibration, 16S rRNA based functional prediction, diversity statistics, bio-marker selection, interaction network construction, vector-graph-based visualization and parallel computing...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28074247/trends-in-taxonomic-and-functional-composition-of-soil-microbiome-along-a-precipitation-gradient-in-israel
#4
Binu M Tripathi, Itumeleng Moroenyane, Chen Sherman, Yoo Kyung Lee, Jonathan M Adams, Yosef Steinberger
The soil microbiome is important for the functioning of terrestrial ecosystems. However, the impacts of climate on taxonomic and functional diversity of soil microbiome are not well understood. A precipitation gradient along regional scale transects may offer a model setting for understanding the effect of climate on the composition and function of the soil microbiome. Here, we compared taxonomic and functional attributes of soil microorganisms in arid, semiarid, Mediterranean, and humid Mediterranean climatic conditions of Israel using shotgun metagenomic sequencing...
January 10, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28074246/draft-genome-of-scalindua-rubra-obtained-from-the-interface-above-the-discovery-deep-brine-in-the-red-sea-sheds-light-on-potential-salt-adaptation-strategies-in-anammox-bacteria
#5
Daan R Speth, Ilias Lagkouvardos, Yong Wang, Pei-Yuan Qian, Bas E Dutilh, Mike S M Jetten
Several recent studies have indicated that members of the phylum Planctomycetes are abundantly present at the brine-seawater interface (BSI) above multiple brine pools in the Red Sea. Planctomycetes include bacteria capable of anaerobic ammonium oxidation (anammox). Here, we investigated the possibility of anammox at BSI sites using metagenomic shotgun sequencing of DNA obtained from the BSI above the Discovery Deep brine pool. Analysis of sequencing reads matching the 16S rRNA and hzsA genes confirmed presence of anammox bacteria of the genus Scalindua...
January 10, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28070487/unraveling-the-microbial-and-functional-diversity-of-coamo-thermal-spring-in-puerto-rico-using-metagenomic-library-generation-and-shotgun-sequencing
#6
Ricky Padilla-Del Valle, Luis R Morales-Vale, Carlos Ríos-Velázquez
In Puerto Rico, the microbial diversity of the thermal spring (ThS) in Coamo has never been studied using metagenomics. The focus of our research was to generate a metagenomic library from the ThS of Coamo, Puerto Rico and explore the microbial and functional diversity. The metagenomic library from the ThS waters was generated using direct DNA isolation. High molecular weight (40 kbp) DNA was end-repaired, electro eluted and ligated into a fosmid vector (pCCFOS1); then transduced into Escherichia coli EPI300-T1R using T1 bacteriophages...
March 2017: Genomics Data
https://www.readbyqxmd.com/read/28057678/afs-identification-and-quantification-of-species-composition-by-metagenomic-sequencing
#7
Yongchao Liu, Fabian Ripp, Rene Koeppel, Hanno Schmidt, Sören Lukas Hellmann, Mathias Weber, Christopher Felix Krombholz, Bertil Schmidt, Thomas Hankeln
: DNA-based methods to detect and quantify taxon composition in biological materials are often based on species-specific polymerase chain reaction, limited to detecting species targeted by the assay. Next-generation sequencing overcomes this drawback by untargeted shotgun sequencing of whole metagenomes at affordable cost. Here we present AFS, a software pipeline for quantification of species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions...
January 5, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28006002/unbiased-rna-shotgun-metagenomics-in-social-and-solitary-wild-bees-detects-associations-with-eukaryote-parasites-and-new-viruses
#8
Karel Schoonvaere, Lina De Smet, Guy Smagghe, Andy Vierstraete, Bart P Braeckman, Dirk C de Graaf
The diversity of eukaryote organisms and viruses associated with wild bees remains poorly characterized in contrast to the well-documented pathosphere of the western honey bee, Apis mellifera. Using a deliberate RNA shotgun metagenomic sequencing strategy in combination with a dedicated bioinformatics workflow, we identified the (micro-)organisms and viruses associated with two bumble bee hosts, Bombus terrestris and Bombus pascuorum, and two solitary bee hosts, Osmia cornuta and Andrena vaga. Ion Torrent semiconductor sequencing generated approximately 3...
2016: PloS One
https://www.readbyqxmd.com/read/28004480/a-metagenomic-study-of-the-preventive-effect-of-lactobacillus-rhamnosus-gg-on-intestinal-polyp-formation-in-apc-min-mice
#9
Yueqiong Ni, Victoria Ho Yee Wong, William Chi Shing Tai, Jun Li, Wing Yan Wong, Magnolia Muk Lan Lee, Fiona Long Yan Fong, Hani El-Nezami, Gianni Panagiotou
AIMS: To investigate the in vivo effects of Lactobacillus rhamnosus GG (LGG) on intestinal polyp development and the interaction between this single-organism probiotic and the gut microbiota therein. METHODS AND RESULTS: The Apc(Min/+) mouse model was used to study the potential preventive effect of LGG on intestinal polyposis, while shotgun metagenomic sequencing was employed to characterize both taxonomic and functional changes within gut microbial community. We found that the progression of intestinal polyps in the control group altered the community functional profile remarkably despite small variation in the taxonomic diversity...
December 22, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28000755/the-balance-of-metagenomic-elements-shapes-the-skin-microbiome-in-acne-and-health
#10
Emma Barnard, Baochen Shi, Dezhi Kang, Noah Craft, Huiying Li
Studies have emphasized the importance of disease-associated microorganisms in perturbed communities, however, the protective roles of commensals are largely under recognized and poorly understood. Using acne as a model disease, we investigated the determinants of the overall virulence property of the skin microbiota when disease- and health-associated organisms coexist in the community. By ultra-deep metagenomic shotgun sequencing, we revealed higher relative abundances of propionibacteria and Propionibacterium acnes phage in healthy skin...
December 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27991530/comparative-metagenomics-reveals-taxonomically-idiosyncratic-yet-functionally-congruent-communities-in-periodontitis
#11
Shareef M Dabdoub, Sukirth M Ganesan, Purnima S Kumar
The phylogenetic characteristics of microbial communities associated with periodontitis have been well studied, however, little is known about the functional endowments of this ecosystem. The present study examined 73 microbial assemblages from 25 individuals with generalized chronic periodontitis and 25 periodontally healthy individuals using whole genome shotgun sequencing. Core metabolic networks were computed from taxa and genes identified in at least 80% of individuals in each group. 50% of genes and species identified in health formed part of the core microbiome, while the disease-associated core microbiome contained 33% of genes and only 1% of taxa...
December 19, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27988122/deciphering-upper-respiratory-tract-microbiota-complexity-in-healthy-calves-and-calves-that-develop-respiratory-disease-using-shotgun-metagenomics
#12
Natália C Gaeta, Svetlana F Lima, Andre G Teixeira, Erika K Ganda, Georgios Oikonomou, Lilian Gregory, Rodrigo C Bicalho
Bovine respiratory disease (BRD) is a multifactorial disorder responsible for severe economic losses in dairy and feedlot herds. Advances in next-generation sequencing mean that microbial communities in clinical samples, including non-culturable bacteria, can be characterized. Our aim was to evaluate the microbiota of the upper respiratory tract of healthy calves and calves with BRD using whole-genome sequencing (shotgun metagenomics). We performed deep nasopharyngeal swabs on 16 Holstein heifer calves (10 healthy and 6 diagnosed with BRD during the study) at 14 and 28 d of life in 1 dairy herd near Ithaca, New York...
December 14, 2016: Journal of Dairy Science
https://www.readbyqxmd.com/read/27984592/inferring-aggregated-functional-traits-from-metagenomic-data-using-constrained-non-negative-matrix-factorization-application-to-fiber-degradation-in-the-human-gut-microbiota
#13
Sébastien Raguideau, Sandra Plancade, Nicolas Pons, Marion Leclerc, Béatrice Laroche
Whole Genome Shotgun (WGS) metagenomics is increasingly used to study the structure and functions of complex microbial ecosystems, both from the taxonomic and functional point of view. Gene inventories of otherwise uncultured microbial communities make the direct functional profiling of microbial communities possible. The concept of community aggregated trait has been adapted from environmental and plant functional ecology to the framework of microbial ecology. Community aggregated traits are quantified from WGS data by computing the abundance of relevant marker genes...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27980708/bioinformatics-strategies-for-taxonomy-independent-binning-and-visualization-of-sequences-in-shotgun-metagenomics
#14
REVIEW
Karel Sedlar, Kristyna Kupkova, Ivo Provaznik
One of main steps in a study of microbial communities is resolving their composition, diversity and function. In the past, these issues were mostly addressed by the use of amplicon sequencing of a target gene because of reasonable price and easier computational postprocessing of the bioinformatic data. With the advancement of sequencing techniques, the main focus shifted to the whole metagenome shotgun sequencing, which allows much more detailed analysis of the metagenomic data, including reconstruction of novel microbial genomes and to gain knowledge about genetic potential and metabolic capacities of whole environments...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27976331/deconvolution-of-complete-microbial-genomes-from-shotgun-metagenomes
#15
I J Miller, J G Lopera, K Montgomery, M Puglisi, W Rose, J C Kwan
No abstract text is available yet for this article.
December 2016: Planta Medica
https://www.readbyqxmd.com/read/27975225/bioinformatics-tools-for-proteomics-data-interpretation
#16
Karla Grisel Calderón-González, Jesús Hernández-Monge, María Esther Herrera-Aguirre, Juan Pedro Luna-Arias
Biological systems function via intricate cellular processes and networks in which RNAs, metabolites, proteins and other cellular compounds have a precise role and are exquisitely regulated (Kumar and Mann, FEBS Lett 583(11):1703-1712, 2009). The development of high-throughput technologies, such as the Next Generation DNA Sequencing (NGS) and DNA microarrays for sequencing genomes or metagenomes, have triggered a dramatic increase in the last few years in the amount of information stored in the GenBank and UniProt Knowledgebase (UniProtKB)...
2016: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/27959345/new-roles-in-hemicellulosic-sugar-fermentation-for-the-uncultivated-bacteroidetes-family-bs11
#17
Lindsey M Solden, David W Hoyt, William B Collins, Johanna E Plank, Rebecca A Daly, Erik Hildebrand, Timothy J Beavers, Richard Wolfe, Carrie D Nicora, Sam O Purvine, Michelle Carstensen, Mary S Lipton, Donald E Spalinger, Jeffrey L Firkins, Barbara A Wolfe, Kelly C Wrighton
Ruminants have co-evolved with their gastrointestinal microbial communities that digest plant materials to provide energy for the host. Some arctic and boreal ruminants have already shown to be vulnerable to dietary shifts caused by changing climate, yet we know little about the metabolic capacity of the ruminant microbiome in these animals. Here, we use meta-omics approaches to sample rumen fluid microbial communities from Alaskan moose foraging along a seasonal lignocellulose gradient. Winter diets with increased hemicellulose and lignin strongly enriched for BS11, a Bacteroidetes family lacking cultivated or genomically sampled representatives...
December 13, 2016: ISME Journal
https://www.readbyqxmd.com/read/27943589/paleomicrobiology-to-investigate-copper-resistance-in-bacteria-isolation-and-description-of-cupriavidus-necator-b9-in-the-soil-of-a-medieval-foundry
#18
David C Gillan, Van Camp Camille, Max Mergeay, Ann Provoost, Nicolas Thomas, Laurent Vermard, Gabriel Billon, Ruddy Wattiez
Remains of a medieval foundry were excavated by archaeologists in 2013 in Verdun (France). Ancient workshops specialized in brass and copper alloys were found with an activity between 13th to 16th c. Levels of Cu, Zn and Pb reached 20000, 7000 and 6000 mg kg(-1) (dw), respectively, in several soil horizons. The objective of the present work was to examine the microbial community in this contaminated site. A total of 8-22 10(6) reads were obtained by shotgun metagenomics in 4 soil horizons. Bioinformatic analyses suggest the presence of complex bacterial communities dominated by Proteobacteria...
December 10, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27943515/agricultural-soil-denitrifiers-possess-extensive-nitrite-reductase-gene-diversity
#19
Sara Coyotzi, Andrew C Doxey, Ian D Clark, David R Lapen, Philippe Van Cappellen, Josh D Neufeld
Denitrification transforms nitrogen applied as fertilizer and emits N2 O, which is a potent greenhouse gas. Very little is known about the identities of abundant and active denitrifiers in agricultural soils. We coupled DNA stable-isotope probing (DNA-SIP) with flow-through reactors (FTRs) to detect active agricultural soil denitrifiers. The FTRs were incubated with nitrate and (13) C6 -glucose under anoxic conditions and sampled at multiple time points. Labelled DNA from active microorganisms was analyzed by 16S rRNA gene fingerprinting, amplicon and shotgun metagenomic sequencing...
December 10, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27941956/microbial-community-structure-and-dynamics-in-thermophilic-composting-viewed-through-metagenomics-and-metatranscriptomics
#20
Luciana Principal Antunes, Layla Farage Martins, Roberta Verciano Pereira, Andrew Maltez Thomas, Deibs Barbosa, Leandro Nascimento Lemos, Gianluca Major Machado Silva, Livia Maria Silva Moura, George Willian Condomitti Epamino, Luciano Antonio Digiampietri, Karen Cristina Lombardi, Patricia Locosque Ramos, Ronaldo Bento Quaggio, Julio Cezar Franco de Oliveira, Renata Castiglioni Pascon, João Batista da Cruz, Aline Maria da Silva, João Carlos Setubal
Composting is a promising source of new organisms and thermostable enzymes that may be helpful in environmental management and industrial processes. Here we present results of metagenomic- and metatranscriptomic-based analyses of a large composting operation in the São Paulo Zoo Park. This composting exhibits a sustained thermophilic profile (50 °C to 75 °C), which seems to preclude fungal activity. The main novelty of our study is the combination of time-series sampling with shotgun DNA, 16S rRNA gene amplicon, and metatranscriptome high-throughput sequencing, enabling an unprecedented detailed view of microbial community structure, dynamics, and function in this ecosystem...
December 12, 2016: Scientific Reports
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