Metagenomic Sequencing
Reconstruction of the Genomes of Drug-Resistant Pathogens for Outbreak Investigation through Metagenomic Sequencing
... modern metagenomic approaches to derive detailed information from analyses of fecal and rectal swab samples of patients colonized with multidrug-resistant health care-associated organisms—representing crucial ...
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Metagenomic Sequencing of HIV-1 in the Blood and Female Genital Tract Reveals Little Quasispecies Diversity during Acute Infection
... Deep sequencing allowed us to identify intrahost single- nucleotide variants (iSNVs) and to characterize within-sample HIV-1 ...of metagenomic sequencing allowed us to characterize other organisms in ...
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Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
... for sequencing using two li- brary preparation kits: the Nextera XT kit and the Nextera DNA Flex ...shotgun metagenomic sequencing and re- covered approximately 500,000 reads per sample, after host ...
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Towards precision quantification of contamination in metagenomic sequencing experiments
... In summary, Davis et al. present an intuitive and straightforward approach to identifying contamination in metagenomic sequencing experiments. When microbe se- quencing quantity is inversely proportional to ...
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Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak
... Portable metagenomic sequencing of genetically diverse RNA viruses on the MinION, direct from patient sample, with no pathogen specific enrichment, is shown here for the first time to be a feasible ...
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Mycoplasma penetrans bacteremia in an immunocompromised patient detected by metagenomic sequencing: a case report
... years, metagenomic sequencing has proven useful in investigating the pathogenic potential of fas- tidious microorganisms that can just be laboriously cultivated directly from clinical specimens [20, ...or ...
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Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples
... optimize metagenomic sequencing for application in virus diagnostics, we tested different enrichment and amplification procedures on plasma samples spiked with RNA and DNA ...of sequencing reads with ...
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Dissecting microbial community structure and methane-producing pathways of a full-scale anaerobic reactor digesting activated sludge from wastewater treatment by metagenomic sequencing
... the metagenomic sequencing was used to characterize microbial community structure of the anaerobic digestion sludge from a full-scale municipal wastewater treatment ...of metagenomic sequence data ...
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Optimal clustering techniques for metagenomic sequencing data
... Metagenomic sequencing techniques have made it possible to determine the composition of bacterial microbiota of the human body. Clustering algorithms have been used to search for core microbiota types in ...
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First identification of porcine parvovirus 6 in North America by viral metagenomic sequencing of serum from pigs infected with porcine reproductive and respiratory syndrome virus
... Based on the consensus sequences obtained through viral metagenomic sequencing and the PPV6 sequences in GenBank two pairs of primers were designed, using CLC Main Workbench 7.0 (Qiagen, Valencia, CA). One ...
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Profiling microbial strains in urban environments using metagenomic sequencing data
... StrainPhlAn [34] is a tool for identifying the specific strain of a given species within a metagenome. The tool is designed to track strains across large collections of samples and takes as input the raw ...
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Unbiased Metagenomic Sequencing for Pediatric Meningitis in Bangladesh Reveals Neuroinvasive Chikungunya Virus Outbreak and Other Unrealized Pathogens
... for metagenomic analysis; this study used samples stored according to no stringent or consistent guidelines over a period of 6 years, which may have affected the quality of the RNA in the ...and sequencing ...
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A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients
... used metagenomic sequencing of a longitudinal cohort to analyze functionally binned microbial species by their ability to tolerate oxidative stress, and we found increased abundance of facultative anaerobe ...
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Direct from blood RNA sequencing identifies the cause of post bronchoscopy fever
... Metagenomic sequencing was performed on RNA iso- lated from peripheral blood collected at the time of this visit, which was five months after lung ...different sequencing depths for the in- dependent ...
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Search Engine for Antimicrobial Resistance: A Cloud Compatible Pipeline and Web Interface for Rapidly Detecting Antimicrobial Resistance Genes Directly from Sequence Data
... genome sequencing of bacterial isolates as well as uncultured bacteria (metagenomic sequencing), have the potential to identify antimicrobial resistance more quickly and effectively than conventional ...
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The impact of sequence database choice on metaproteomic results in gut microbiota studies
... both sequencing- based and sequencing-independent ...a metagenomic and a metaproteo- mic approach, and therefore to generate a wide gamut of sequence ...experimental metagenomic DBs (i.e., ob- ...
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Evaluation of the CosmosID Bioinformatics Platform for Prosthetic Joint Associated Sonicate Fluid Shotgun Metagenomic Data Analysis
... deep sequencing technologies are revolutionizing the diag- nosis of infectious ...Whole-genome sequencing is being used on cultured isolates to identify them and determine their genetic characteristics, ...
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Lignolytic consortium omics analyses reveal novel genomes and pathways involved in lignin modification and valorization
... a metagenomic discovery platform, based on targeted community enrichment protocols, to depict bacterial biocatalysts and pathways involved in lignin degradation and aromatic compound conversion ...consortium, ...
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Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture
... Metagenomic sequencing is the process of sampling DNA sequences from multiple genomes in a community of organisms, and has been applied to many environ- mental samples to assess both functional diversity ...
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Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling
... Using metagenomic sequencing, we further delineated strain level contributions to the gut LPS pool and found that numerous other members of the order Bacteroidales, which are the dominant Gram-negative ...
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