shotgun metagenomics
Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics
... ABSTRACT Shotgun metagenomics provides a powerful assumption-free approach to the recovery of pathogen genomes from contemporary and historical ...that metagenomics stands ready to document past and ...
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Evaluating the Information Content of Shallow Shotgun Metagenomics
... shallow shotgun sequencing depth across five body subsites representing skin, oral, and gut habitat ...shallow shotgun sequencing data using an accelerated version of fully exhaus- tive gapped ...
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Estimation of the relative abundance of species in artificial mixtures of insects using low-coverage shotgun metagenomics
... the metagenomics approach using insect species whose genome is already sequenced and assembled to an advanced ...We shotgun-sequenced, at low-coverage, 18 species of insects in 22 single-species and 6 ...
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Culture independent detection and characterisation of Mycobacterium tuberculosis and M africanum in sputum samples using shotgun metagenomics on a benchtop sequencer
... Shotgun metagenomics—that is the unbiased sequencing en masse of DNA extracted from a sample without target-specific amplification or capture—has provided a powerful assumption-free approach to the recovery ...
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Recovery of a medieval Brucella melitensis genome using shotgun metagenomics
... ABSTRACT Shotgun metagenomics provides a powerful assumption-free approach to the recovery of pathogen genomes from contemporary and historical ...that metagenomics stands ready to document past and ...
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Improving saliva shotgun metagenomics by chemical host DNA depletion
... To compare lyPMA to other methods of host DNA de- pletion, saliva samples were collected from eight healthy participants (4 mL each). Each sample was homogenized and divided into 18 separate 200-μl aliquots. Triplicate ...
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Effects of inorganic and organic treatments on the microbial community of maize rhizosphere by a shotgun metagenomics approach
... The shotgun raw sequences generated from the microbial community DNA were uploaded to the MG-RAST online server (Meyer et al. 2008). This online annotation system pipeline performed many quality controls following ...
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Human Papillomavirus Community in Healthy Persons, Defined by Metagenomics Analysis of Human Microbiome Project Shotgun Sequencing Data Sets
... the shotgun metagenomics sequencing method provides a broader coverage of HPV types than the am- plicon-based PCR ...theory, shotgun sequencing is capable of detecting all 155 HPV types ...the ...
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Metagenomics in ophthalmology: current findings and future prospectives
... is usually more expensive. It may miss low-abundant species and when host-associated metagenomes are studied, most of the reads derive from the host genome, especially when studying sites with low bacterial biomass. It ...
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Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River
... used shotgun metagenomics to examine the taxonomic compo- sition, functional potential, and resistance profiles of the microbial communities occu- pying a leachate pond at the Riverton City dump and the ...
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Multi-omics Analysis of Periodontal Pocket Microbial Communities Pre- and Posttreatment
... The etiology of periodontal disease has proven to be especially difficult to disen- tangle because of both the complexity of the periodontal biofilm community and the high level of individual variability among patients in ...
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Metagenomics for pathogen detection in public health
... viruses, shotgun metagenomics can potentially catalogue all of the microbes present in a sample, irre- spective of their kingdom of origin, by sequencing all the nucleic acid extracted from a ...a ...
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Diagnosis of a malayan filariasis case using a shotgun diagnostic metagenomics assay
... Shotgun metagenomics, which is applied to the direct sequencing of DNA extracted from a sample without culture or target-specific amplification or capture, has been widely used in virus discovery [7] and ...
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Diagnostic metagenomics : potential applications to bacterial, viral and parasitic infections
... Diagnostic metagenomics has so far seen little use in the detection of parasitic infection, although there is no reason to expect that parasitology will not soon catch up with other branches of micro- biology in ...
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The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data
... Shotgun metagenomics sequencing datasets are among the most challenging types of biological information to successfully handle from the perspectives of both size and complexity ...
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Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease
... used shotgun metagenomics to compare the microbiomes of the infants that developed diarrhea and a subset of those that remained asymptomatic both at the 1-month time point (prior to the onset of dis- ease, ...
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Profiling microbial strains in urban environments using metagenomic sequencing data
... with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a ...urban metagenomics; b) characterizing the organisms in urban environment at the resolution ...
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Metagenomics of Bio Slurry Obtained From A Biogas Plant Using Next-Generation Dna Sequencing
... the metagenomics of biogas fermenter sample showed that Methanoculleus bacteria plays a dominant role in methanogenesis while Clostridia are important for hydrolysis of cellulosic plant biomass in a biogas ...
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Metagenomics: aid to combat antimicrobial resistance in diarrhea
... [47]. Metagenomics has helped in gen- erating enormous information on microbial metabolism leading to new antimicrobial discovery ...using shotgun metagenomic sequenc- ing and came across a plethora of ...
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Soil metagenomics: a prospective approach for novel enzyme discovery
... Sequence-based screening involves direct sequencing of metagenomic DNA, either with or without cloning prior to sequencing and then subjecting the sequences to bioinformatics analyses (Kunin et al., 2008, Sleator et al., ...
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