keyword
MENU ▼
Read by QxMD icon Read
search

Metagenomics

keyword
https://www.readbyqxmd.com/read/27932654/draft-genome-sequence-of-antarctic-methanogen-enriched-from-dry-valley-permafrost
#1
Joy Buongiorno, Jordan T Bird, Kirill Krivushin, Victoria Oshurkova, Victoria Shcherbakova, Elizaveta M Rivkina, Karen G Lloyd, Tatiana A Vishnivetskaya
A genomic reconstruction belonging to the genus Methanosarcina was assembled from metagenomic data from a methane-producing enrichment of Antarctic permafrost. This is the first methanogen genome reported from permafrost of the Dry Valleys and can help shed light on future climate-affected methane dynamics.
December 8, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27932640/complete-genome-sequence-of-a-genotype-iii-japanese-encephalitis-virus-isolated-from-pigs-in-sichuan-china
#2
Yuancheng Zhou, Xiuping Zhuo, Jianqiang Ye, Yuhan Cai
A complete genomic sequence of Japanese encephalitis virus (JEV) was detected by viral metagenome analysis on aborted piglets. A phylogenetic analysis of this genome reveals that it is highly similar to previously reported India JEV genomes. The complete JEV sequence is 10,718 nucleotides long.
December 8, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27932285/candidate-new-rotavirus-species-in-schreiber-s-bats-serbia
#3
Krisztián Bányai, Gábor Kemenesi, Ivana Budinski, Fanni Földes, Brigitta Zana, Szilvia Marton, Renáta Varga-Kugler, Miklós Oldal, Kornélia Kurucz, Ferenc Jakab
The genus Rotavirus comprises eight species designated A to H and one tentative species, Rotavirus I. In a virus metagenomic analysis of Schreiber's bats sampled in Serbia in 2014 we obtained sequences likely representing novel rotavirus species. Whole genome sequencing and phylogenetic analysis classified the representative strain into a tentative tenth rotavirus species, we provisionally called Rotavirus J. The novel virus shared a maximum of 50% amino acid sequence identity within the VP6 gene to currently known members of the genus...
December 5, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27931678/diagnosing-tuberculosis-in-the-21st-century-dawn-of-a-genomics-revolution
#4
REVIEW
Christopher Jeanes, Justin O'Grady
Tuberculosis (TB) ranks alongside HIV as the leading cause of death worldwide, killing 1.5million people in 2014. Traditional laboratory techniques do not provide sufficiently rapid results to inform clinicians on appropriate treatment, especially in the face of increasingly prevalent drug-resistant TB. Rapid molecular methods such as PCR and LAMP are vital tools in the fight against TB, however, rapid advances in next generation sequencing (NGS) technology are allowing increasingly rapid and accurate sequencing of entire bacterial genomes at ever decreasing cost, providing unprecedented depth of information...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/27930729/strain-level-discrimination-of-shiga-toxin-producing-escherichia-coli-in-spinach-using-metagenomic-sequencing
#5
Susan R Leonard, Mark K Mammel, David W Lacher, Christopher A Elkins
Consumption of fresh bagged spinach contaminated with Shiga toxin-producing Escherichia coli (STEC) has led to severe illness and death; however current culture-based methods to detect foodborne STEC are time consuming. Since not all STEC strains are considered pathogenic to humans, it is crucial to incorporate virulence characterization of STEC in the detection method. In this study, we assess the comprehensiveness of utilizing a shotgun metagenomics approach for detection and strain-level identification by spiking spinach with a variety of genomically disparate STEC strains at a low contamination level of 0...
2016: PloS One
https://www.readbyqxmd.com/read/27925857/analysis-of-the-intestinal-microbial-community-and-inferred-functional-capacities-during-the-host-response-to-pneumocystis-pneumonia
#6
Derrick R Samuelson, Tysheena P Charles, Nicholas M de la Rua, Christopher M Taylor, Eugene E Blanchard, Meng Luo, Judd E Shellito, David A Welsh
BACKGROUND: Pneumocystis pneumonia is a major cause of morbidity and mortality in patients infected with HIV/AIDS. In this study, we evaluated the intestinal microbial communities associated with the development of experimental Pneumocystis pneumonia, as there is growing evidence that the intestinal microbiota is critical for host defense against fungal pathogens. METHODS: C57BL/6 mice were infected with live Pneumocystis murina (P. murina) via intratracheal inoculation and sacrificed 7 and 14 days postinfection for microbiota analysis...
December 7, 2016: Experimental Lung Research
https://www.readbyqxmd.com/read/27921234/simultaneous-virus-identification-and-characterization-of-severe-unexplained-pneumonia-cases-using-a-metagenomics-sequencing-technique
#7
Xiaohui Zou, Guangpeng Tang, Xiang Zhao, Yan Huang, Tao Chen, Mingyu Lei, Wenbing Chen, Lei Yang, Wenfei Zhu, Li Zhuang, Jing Yang, Zhaomin Feng, Dayan Wang, Dingming Wang, Yuelong Shu
Many viruses can cause respiratory diseases in humans. Although great advances have been achieved in methods of diagnosis, it remains challenging to identify pathogens in unexplained pneumonia (UP) cases. In this study, we applied next-generation sequencing (NGS) technology and a metagenomic approach to detect and characterize respiratory viruses in UP cases from Guizhou Province, China. A total of 33 oropharyngeal swabs were obtained from hospitalized UP patients and subjected to NGS. An unbiased metagenomic analysis pipeline identified 13 virus species in 16 samples...
December 2, 2016: Science China. Life Sciences
https://www.readbyqxmd.com/read/27918579/a-graph-centric-approach-for-metagenome-guided-peptide-and-protein-identification-in-metaproteomics
#8
Haixu Tang, Sujun Li, Yuzhen Ye
Metaproteomic studies adopt the common bottom-up proteomics approach to investigate the protein composition and the dynamics of protein expression in microbial communities. When matched metagenomic and/or metatranscriptomic data of the microbial communities are available, metaproteomic data analyses often employ a metagenome-guided approach, in which complete or fragmental protein-coding genes are first directly predicted from metagenomic (and/or metatranscriptomic) sequences or from their assemblies, and the resulting protein sequences are then used as the reference database for peptide/protein identification from MS/MS spectra...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27918230/mechanisms-of-cross-talk-between-the-diet-the-intestinal-microbiome-and-the-undernourished-host
#9
Helene Velly, Robert A Britton, Geoffrey A Preidis
Undernutrition remains one of the most pressing global health challenges today, contributing to nearly half of all deaths in children under five years of age. Although insufficient dietary intake and environmental enteric dysfunction are often inciting factors, evidence now suggests that unhealthy gut microbial populations perpetuate the vicious cycle of pathophysiology that results in persistent growth impairment in children. The metagenomics era has facilitated new research identifying an altered microbiome in undernourished hosts and has provided insight into a number of mechanisms by which these alterations may affect growth...
December 5, 2016: Gut Microbes
https://www.readbyqxmd.com/read/27917931/metagenomic-profiling-of-historic-colorado-front-range-flood-impact-on-distribution-of-riverine-antibiotic-resistance-genes
#10
Emily Garner, Joshua S Wallace, Gustavo Arango Argoty, Caitlin Wilkinson, Nicole Fahrenfeld, Lenwood S Heath, Liqing Zhang, Mazdak Arabi, Diana S Aga, Amy Pruden
Record-breaking floods in September 2013 caused massive damage to homes and infrastructure across the Colorado Front Range and heavily impacted the Cache La Poudre River watershed. Given the unique nature of this watershed as a test-bed for tracking environmental pathways of antibiotic resistance gene (ARG) dissemination, we sought to determine the impact of extreme flooding on ARG reservoirs in river water and sediment. We utilized high-throughput DNA sequencing to obtain metagenomic profiles of ARGs before and after flooding, and investigated 23 antibiotics and 14 metals as putative selective agents during post-flood recovery...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917166/temporal-metagenomic-and-metabolomic-characterization-of-fresh-perennial-ryegrass-degradation-by-rumen-bacteria
#11
Olga L Mayorga, Alison H Kingston-Smith, Eun J Kim, Gordon G Allison, Toby J Wilkinson, Matthew J Hegarty, Michael K Theodorou, Charles J Newbold, Sharon A Huws
Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached bacteria. In this study, we investigated temporal niche specialization of primary and secondary populations of attached rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27916124/alkaline-phosphatase-fused-repebody-as-a-new-format-of-immuno-reagent-for-an-immunoassay
#12
Hyo-Deok Seo, Joong-Jae Lee, Yu Jung Kim, Oliver Hantschel, Seung-Goo Lee, Hak-Sung Kim
Enzyme-linked immunoassays based on an antibody-antigen interaction are widely used in biological and medical sciences. However, the conjugation of an enzyme to antibodies needs an additional chemical process, usually resulting in randomly cross-linked molecules and a loss of the binding affinity and enzyme activity. Herein, we present the development of an alkaline phosphatase-fused repebody as a new format of immuno-reagent for immunoassays. A repebody specifically binding to human TNF-α (hTNF-α) was selected through a phage display, and its binding affinity was increased up to 49 nM using a modular engineering approach...
January 15, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/27915377/crystal-structure-and-characterization-of-esterase-est25-mutants-reveal-improved-enantioselectivity-toward-s-ketoprofen-ethyl-ester
#13
Jinyeong Kim, Seung-Hyeon Seok, Eunsoo Hong, Tae Hyeon Yoo, Min-Duk Seo, Yeonwoo Ryu
Esterases comprise a group of enzymes that catalyze the cleavage and synthesis of ester bonds. They are important in biotechnological applications owing to their enantioselectivity, regioselectivity, broad substrate specificity, and the fact that they do not require cofactors. In a previous study, we isolated the esterase Est25 from a metagenomic library. Est25 showed catalytic activity toward the (R,S)-ketoprofen ethyl ester but had low enantioselectivity toward the (S)-ketoprofen ethyl ester. Because (S)-ketoprofen has stronger anti-inflammatory effects and fewer side effects than (R)-ketoprofen, enantioselectivity of this esterase is important...
December 3, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27915291/the-landscape-of-microbial-phenotypic-traits-and-associated-genes
#14
Maria Brbić, Matija Piškorec, Vedrana Vidulin, Anita Kriško, Tomislav Šmuc, Fran Supek
Bacteria and Archaea display a variety of phenotypic traits and can adapt to diverse ecological niches. However, systematic annotation of prokaryotic phenotypes is lacking. We have therefore developed ProTraits, a resource containing ∼545 000 novel phenotype inferences, spanning 424 traits assigned to 3046 bacterial and archaeal species. These annotations were assigned by a computational pipeline that associates microbes with phenotypes by text-mining the scientific literature and the broader World Wide Web, while also being able to define novel concepts from unstructured text...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27912769/three-novel-bacteriophages-isolated-from-the-east-african-rift-valley-soda-lakes
#15
Leonardo Joaquim van Zyl, Shonisani Nemavhulani, James Cass, Donald Arthur Cowan, Marla Trindade
BACKGROUND: Soda lakes are unique environments in terms of their physical characteristics and the biology they harbour. Although well studied with respect to their microbial composition, their viral compositions have not, and consequently few bacteriophages that infect bacteria from haloalkaline environments have been described. METHODS: Bacteria were isolated from sediment samples of lakes Magadi and Shala. Three phages were isolated on two different Bacillus species and one Paracoccus species using agar overlays...
December 3, 2016: Virology Journal
https://www.readbyqxmd.com/read/27911252/chapparvoviruses-occur-in-at-least-three-vertebrate-classes-and-have-a-broad-biogeographic-distribution
#16
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
#17
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
#18
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
#19
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
#20
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
keyword
keyword
10898
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"