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Metagenomics

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https://www.readbyqxmd.com/read/29346586/plasflow-predicting-plasmid-sequences-in-metagenomic-data-using-genome-signatures
#1
Pawel S Krawczyk, Leszek Lipinski, Andrzej Dziembowski
Plasmids are mobile genetics elements that play an important role in the environmental adaptation of microorganisms. Although plasmids are usually analyzed in cultured microorganisms, there is a need for methods that allow for the analysis of pools of plasmids (plasmidomes) in environmental samples. To that end, several molecular biology and bioinformatics methods have been developed; however, they are limited to environments with low diversity and cannot recover large plasmids. Here, we present PlasFlow, a novel tool based on genomic signatures that employs a neural network approach for identification of bacterial plasmid sequences in environmental samples...
January 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29345635/genetic-risk-dysbiosis-and-treatment-stratification-using-host-genome-and-gut-microbiome-in-inflammatory-bowel-disease
#2
Ahmed Moustafa, Weizhong Li, Ericka L Anderson, Emily H M Wong, Parambir S Dulai, William J Sandborn, William Biggs, Shibu Yooseph, Marcus B Jones, J Craig Venter, Karen E Nelson, John T Chang, Amalio Telenti, Brigid S Boland
OBJECTIVES: Inflammatory bowel diseases (IBD), comprised of Crohn's disease (CD) and ulcerative colitis (UC), are characterized by a complex pathophysiology that is thought to result from an aberrant immune response to a dysbiotic luminal microbiota in genetically susceptible individuals. New technologies support the joint assessment of host-microbiome interaction. METHODS: Using whole genome sequencing and shotgun metagenomics, we studied the clinical features, host genome, and stool microbial metagenome of 85 IBD patients, and compared the results to 146 control individuals...
January 18, 2018: Clinical and Translational Gastroenterology
https://www.readbyqxmd.com/read/29345009/choosing-non-redundant-representative-subsets-of-protein-sequence-data-sets-using-submodular-optimization
#3
Maxwell W Libbrecht, Jeffrey A Bilmes, William Stafford Noble
Selecting a non-redundant representative subset of sequences is a common step in many bioinformatics workflows, such as the creation of non-redundant training sets for sequence and structural models or selection of "operational taxonomic units" from metagenomics data. Previous methods for this task, such as CD-HIT, PISCES and UCLUST, apply a heuristic threshold-based algorithm that has no theoretical guarantees. We propose a new approach based on submodular optimization. Submodular optimization, a discrete analogue to continuous convex optimization, has been used with great success for other representative set selection problems...
January 18, 2018: Proteins
https://www.readbyqxmd.com/read/29343831/novel-hydrogenases-from-deep-sea-hydrothermal-vent-metagenomes-identified-by-a-recently-developed-activity-based-screen
#4
Nicole Adam, Mirjam Perner
Hydrogen is one of the most common elements on Earth. The enzymes converting molecular hydrogen into protons and electrons are the hydrogenases. Hydrogenases are ubiquitously distributed in all three domains of life where they play a central role in cell metabolism. So far, the recovery of hydrogenases has been restricted to culture-dependent and sequence-based approaches. We have recently developed the only activity-based screen for seeking H2-uptake enzymes from metagenomes without having to rely on enrichment and isolation of hydrogen-oxidizing microorganisms or prior metagenomic sequencing...
January 17, 2018: ISME Journal
https://www.readbyqxmd.com/read/29342236/magnamwar-an-r-package-for-genome-wide-association-studies-of-bacterial-orthologs
#5
Corinne E Sexton, Hayden Z Smith, Peter D Newell, Angela E Douglas, John M Chaston
Summary: Here we report on an R package for genome-wide association studies of orthologous genes in bacteria. Before using the software, orthologs from bacterial genomes or metagenomes are defined using local or online implementations of OrthoMCL. These presence-absence patterns are statistically associated with variation in user-collected phenotypes using the Mono-Associated GNotobiotic Animals Metagenome-Wide Association R package (MAGNAMWAR). Genotype-phenotype associations can be performed with several different statistical tests based on the type and distribution of the data...
January 12, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29340947/the-impact-of-depuration-on-mussel-hepatopancreas-bacteriome-composition-and-predicted-metagenome
#6
J A Rubiolo, A Lozano-Leon, R Rodriguez-Souto, N Fol Rodríguez, M R Vieytes, L M Botana
Due to the rapid elimination of bacteria through normal behaviour of filter feeding and excretion, the decontamination of hazardous contaminating bacteria from shellfish is performed by depuration. This process, under conditions that maximize shellfish filtering activity, is a useful method to eliminate microorganisms from bivalves. The microbiota composition in bivalves reflects that of the environment of harvesting waters, so quite different bacteriomes would be expected in shellfish collected in different locations...
January 17, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29340642/identifying-corneal-infections-in-formalin-fixed-specimens-using-next-generation-sequencing
#7
Zhigang Li, Florian P Breitwieser, Jennifer Lu, Albert S Jun, Laura Asnaghi, Steven L Salzberg, Charles G Eberhart
Purpose: We test the ability of next-generation sequencing, combined with computational analysis, to identify a range of organisms causing infectious keratitis. Methods: This retrospective study evaluated 16 cases of infectious keratitis and four control corneas in formalin-fixed tissues from the pathology laboratory. Infectious cases also were analyzed in the microbiology laboratory using culture, polymerase chain reaction, and direct staining. Classified sequence reads were analyzed with two different metagenomics classification engines, Kraken and Centrifuge, and visualized using the Pavian software tool...
January 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29340239/fastviromeexplorer-a-pipeline-for-virus-and-phage-identification-and-abundance-profiling-in-metagenomics-data
#8
Saima Sultana Tithi, Frank O Aylward, Roderick V Jensen, Liqing Zhang
With the increase in the availability of metagenomic data generated by next generation sequencing, there is an urgent need for fast and accurate tools for identifying viruses in host-associated and environmental samples. In this paper, we developed a stand-alone pipeline called FastViromeExplorer for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets...
2018: PeerJ
https://www.readbyqxmd.com/read/29339831/detection-of-antimicrobial-resistance-genes-associated-with-the-international-space-station-environmental-surfaces
#9
C Urbaniak, A Checinska Sielaff, K G Frey, J E Allen, N Singh, C Jaing, K Wheeler, K Venkateswaran
Antimicrobial resistance (AMR) is a global health issue. In an effort to minimize this threat to astronauts, who may be immunocompromised and thus at a greater risk of infection from antimicrobial resistant pathogens, a comprehensive study of the ISS "resistome' was conducted. Using whole genome sequencing (WGS) and disc diffusion antibiotic resistance assays, 9 biosafety level 2 organisms isolated from the ISS were assessed for their antibiotic resistance. Molecular analysis of AMR genes from 24 surface samples collected from the ISS during 3 different sampling events over a span of a year were analyzed with Ion AmpliSeq™ and metagenomics...
January 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29339259/perturbations-of-the-gut-microbiome-genes-in-infants-with-atopic-dermatitis-according-to-feeding-type
#10
Min-Jung Lee, Mi-Jin Kang, So-Yeon Lee, Eun Lee, Kangjin Kim, Sungho Won, Dong In Suh, Kyung Won Kim, Youn Ho Sheen, Kangmo Ahn, Bong-Soo Kim, Soo-Jong Hong
BACKGROUND: Perturbations of the infant gut microbiota can shape the development of the immune system and link to the risk of allergic diseases. OBJECTIVE: To understand the role of the gut microbiome in atopic dermatitis, the metagenome of the infant gut microbiome was analyzed according to feeding types. METHODS: The composition of gut microbiota was analyzed in fecal samples from 129 infants (6-month-old) by pyrosequencing, including 66 healthy infants and 63 infants with atopic dermatitis...
January 12, 2018: Journal of Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/29337704/the-what-when-and-how-in-performing-and-interpreting-microbiological-diagnostic-tests-in-skin-and-soft-tissue-infections
#11
Carolina Navarro-San Francisco, Patricia Ruiz-Garbajosa, Rafael Cantón
PURPOSE OF REVIEW: To summarize and classify the most recent and relevant microbiological studies for each type of skin and soft tissue infection (SSTI). RECENT FINDINGS: Following Infectious Diseases Society of America and Food and Drug Administration classifications of SSTIs, we differentiate between two large groups, the superficial or uncomplicated infections and the complicated infections with deep involvement. It is not usually necessary to obtain microbiological samples in uncomplicated infections, except in cases of recurrences or for epidemiological control purposes...
January 11, 2018: Current Opinion in Infectious Diseases
https://www.readbyqxmd.com/read/29337314/the-reconstruction-of-2-631-draft-metagenome-assembled-genomes-from-the-global-oceans
#12
Benjamin J Tully, Elaina D Graham, John F Heidelberg
Microorganisms play a crucial role in mediating global biogeochemical cycles in the marine environment. By reconstructing the genomes of environmental organisms through metagenomics, researchers are able to study the metabolic potential of Bacteria and Archaea that are resistant to isolation in the laboratory. Utilizing the large metagenomic dataset generated from 234 samples collected during the Tara Oceans circumnavigation expedition, we were able to assemble 102 billion paired-end reads into 562 million contigs, which in turn were co-assembled and consolidated in to 7...
January 16, 2018: Scientific Data
https://www.readbyqxmd.com/read/29336480/species-co-occurrence-networks-can-they-reveal-trophic-and-non-trophic-interactions-in-ecological-communities
#13
Mara A Freilich, Evie Wieters, Bernardo R Broitman, Pablo A Marquet, Sergio A Navarrete
Co-occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is difficult to obtain. Their use is particularly common, but not restricted to, microbial networks constructed from metagenomic analyses. In this study, we test the efficacy of this procedure by comparing an inferred network constructed using spatially intensive co-occurrence data from the rocky intertidal zone in central Chile to a well-resolved, empirically-based, species interaction network from the same region...
January 16, 2018: Ecology
https://www.readbyqxmd.com/read/29335577/salmonella-enterica-genomes-from-victims-of-a-major-sixteenth-century-epidemic-in-mexico
#14
Åshild J Vågene, Alexander Herbig, Michael G Campana, Nelly M Robles García, Christina Warinner, Susanna Sabin, Maria A Spyrou, Aida Andrades Valtueña, Daniel Huson, Noreen Tuross, Kirsten I Bos, Johannes Krause
Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Through the introduction of a new metagenomic analysis tool called MALT, applied here to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico...
January 15, 2018: Nature Ecology & Evolution
https://www.readbyqxmd.com/read/29335567/metagenomic-analysis-of-microbial-communities-yields-insight-into-impacts-of-nanoparticle-design
#15
Jacob W Metch, Nathan D Burrows, Catherine J Murphy, Amy Pruden, Peter J Vikesland
Next-generation DNA sequencing and metagenomic analysis provide powerful tools for the environmentally friendly design of nanoparticles. Herein we demonstrate this approach using a model community of environmental microbes (that is, wastewater-activated sludge) dosed with gold nanoparticles of varying surface coatings and morphologies. Metagenomic analysis was highly sensitive in detecting the microbial community response to gold nanospheres and nanorods with either cetyltrimethylammonium bromide or polyacrylic acid surface coatings...
January 15, 2018: Nature Nanotechnology
https://www.readbyqxmd.com/read/29335555/metatranscriptome-of-human-faecal-microbial-communities-in-a-cohort-of-adult-men
#16
Galeb S Abu-Ali, Raaj S Mehta, Jason Lloyd-Price, Himel Mallick, Tobyn Branck, Kerry L Ivey, David A Drew, Casey DuLong, Eric Rimm, Jacques Izard, Andrew T Chan, Curtis Huttenhower
The gut microbiome is intimately related to human health, but it is not yet known which functional activities are driven by specific microorganisms' ecological configurations or transcription. We report a large-scale investigation of 372 human faecal metatranscriptomes and 929 metagenomes from a subset of 308 men in the Health Professionals Follow-Up Study. We identified a metatranscriptomic 'core' universally transcribed over time and across participants, often by different microorganisms. In contrast to the housekeeping functions enriched in this core, a 'variable' metatranscriptome included specialized pathways that were differentially expressed both across participants and among microorganisms...
January 15, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29335554/stability-of-the-human-faecal-microbiome-in-a-cohort-of-adult-men
#17
Raaj S Mehta, Galeb S Abu-Ali, David A Drew, Jason Lloyd-Price, Ayshwarya Subramanian, Paul Lochhead, Amit D Joshi, Kerry L Ivey, Hamed Khalili, Gordon T Brown, Casey DuLong, Mingyang Song, Long H Nguyen, Himel Mallick, Eric B Rimm, Jacques Izard, Curtis Huttenhower, Andrew T Chan
Characterizing the stability of the gut microbiome is important to exploit it as a therapeutic target and diagnostic biomarker. We metagenomically and metatranscriptomically sequenced the faecal microbiomes of 308 participants in the Health Professionals Follow-Up Study. Participants provided four stool samples-one pair collected 24-72 h apart and a second pair ~6 months later. Within-person taxonomic and functional variation was consistently lower than between-person variation over time. In contrast, metatranscriptomic profiles were comparably variable within and between subjects due to higher within-subject longitudinal variation...
January 15, 2018: Nature Microbiology
https://www.readbyqxmd.com/read/29335466/deeply-sourced-formate-fuels-sulfate-reducers-but-not-methanogens-at-lost-city-hydrothermal-field
#18
Susan Q Lang, Gretchen L Früh-Green, Stefano M Bernasconi, William J Brazelton, Matthew O Schrenk, Julia M McGonigle
Hydrogen produced during water-rock serpentinization reactions can drive the synthesis of organic compounds both biotically and abiotically. We investigated abiotic carbon production and microbial metabolic pathways at the high energy but low diversity serpentinite-hosted Lost City hydrothermal field. Compound-specific 14C data demonstrates that formate is mantle-derived and abiotic in some locations and has an additional, seawater-derived component in others. Lipids produced by the dominant member of the archaeal community, the Lost City Methanosarcinales, largely lack 14C, but metagenomic evidence suggests they cannot use formate for methanogenesis...
January 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29335008/multi-omics-differentially-classify-disease-state-and-treatment-outcome-in-pediatric-crohn-s-disease
#19
Gavin M Douglas, Richard Hansen, Casey M A Jones, Katherine A Dunn, André M Comeau, Joseph P Bielawski, Rachel Tayler, Emad M El-Omar, Richard K Russell, Georgina L Hold, Morgan G I Langille, Johan Van Limbergen
BACKGROUND: Crohn's disease (CD) has an unclear etiology, but there is growing evidence of a direct link with a dysbiotic microbiome. Many gut microbes have previously been associated with CD, but these have mainly been confounded with patients' ongoing treatments. Additionally, most analyses of CD patients' microbiomes have focused on microbes in stool samples, which yield different insights than profiling biopsy samples. RESULTS: We sequenced the 16S rRNA gene (16S) and carried out shotgun metagenomics (MGS) from the intestinal biopsies of 20 treatment-naïve CD and 20 control pediatric patients...
January 15, 2018: Microbiome
https://www.readbyqxmd.com/read/29335005/in-depth-resistome-analysis-by-targeted-metagenomics
#20
Val F Lanza, Fernando Baquero, José Luís Martínez, Ricardo Ramos-Ruíz, Bruno González-Zorn, Antoine Andremont, Antonio Sánchez-Valenzuela, Stanislav Dusko Ehrlich, Sean Kennedy, Etienne Ruppé, Willem van Schaik, Rob J Willems, Fernando de la Cruz, Teresa M Coque
BACKGROUND: Antimicrobial resistance is a major global health challenge. Metagenomics allows analyzing the presence and dynamics of "resistomes" (the ensemble of genes encoding antimicrobial resistance in a given microbiome) in disparate microbial ecosystems. However, the low sensitivity and specificity of available metagenomic methods preclude the detection of minority populations (often present below their detection threshold) and/or the identification of allelic variants that differ in the resulting phenotype...
January 15, 2018: Microbiome
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