From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool.
Sign Up to like & getrecommendations! Published in 2018 at "Methods in molecular biology"
DOI: 10.1007/978-1-4939-7683-6_14
Abstract: ViromeScan is an innovative metagenomic analysis tool that allows the viral community characterization in terms of taxonomy from raw data of metagenomics sequencing. It efficiently denoises samples from reads of other microorganisms. Users can adopt… read more here.
Keywords: whole genome; genome shotgun; tool; shotgun sequencing ... See more keywords
Whole genome shotgun sequencing of POPs degrading bacterial community dwelling tannery effluents and petrol contaminated soil.
Sign Up to like & getrecommendations! Published in 2020 at "Microbiological research"
DOI: 10.1016/j.micres.2020.126504
Abstract: The present study involved identification of genes which are present in the genome of native bacteria to make them effective tools for bioremediation of persistent organic pollutants (POPs). During this study, forty-one POPs (naphthalene, toluene… read more here.
Keywords: petrol; genome shotgun; whole genome; shotgun sequencing ... See more keywords
16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis
Sign Up to like & getrecommendations! Published in 2022 at "Scientific Reports"
DOI: 10.1038/s41598-022-07995-7
Abstract: Dysbiosis of human gut microbiota has been reported in association with ulcerative colitis (UC) in both children and adults using either 16S rRNA gene or shotgun sequencing data. However, these studies used either 16S rRNA… read more here.
Keywords: rrna metagenomic; 16s rrna; sequencing data; metagenomic shotgun ... See more keywords
Shotgun sequencing of clinical biofilm following scanning electron microscopy identifies bacterial community composition
Sign Up to like & getrecommendations! Published in 2019 at "Pathogens and Disease"
DOI: 10.1093/femspd/ftz013
Abstract: &NA; Bacterial biofilm infections often involve aggregates of bacteria heterogeneously distributed throughout a tissue or on a surface (such as an implanted medical device). Identification of a biofilm infection requires direct visualization via microscopy, followed… read more here.
Keywords: microscopy; community; shotgun sequencing; electron microscopy ... See more keywords
Performance of amplicon and shotgun sequencing for accurate biomass estimation in invertebrate community samples
Sign Up to like & getrecommendations! Published in 2018 at "Molecular Ecology Resources"
DOI: 10.1111/1755-0998.12888
Abstract: New applications of DNA and RNA sequencing are expanding the field of biodiversity discovery and ecological monitoring, yet questions remain regarding precision and efficiency. Due to primer bias, the ability of metabarcoding to accurately depict… read more here.
Keywords: amplicon shotgun; performance amplicon; biomass; shotgun sequencing ... See more keywords
Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Clinical Microbiology"
DOI: 10.1128/jcm.02402-16
Abstract: ABSTRACT Whole-genome amplification (WGA) is a useful tool for amplification of very small quantities of DNA for many uses, including metagenomic shotgun sequencing for infection diagnosis. Depending on the application, background DNA from WGA kits… read more here.
Keywords: whole genome; sequencing infection; shotgun sequencing; metagenomic shotgun ... See more keywords
Using Shotgun Sequencing to Describe the Changes Induced by In-Feed Zinc Oxide and Apramycin in the Microbiomes of Pigs One Week Postweaning
Sign Up to like & getrecommendations! Published in 2022 at "Microbiology Spectrum"
DOI: 10.1128/spectrum.01597-22
Abstract: Weaning is a critical period for piglets, during which potentially harmful bacteria such as Escherichia coli can increase in abundance in the intestine, creating digestive problems and diarrhea. In-feed antibiotics, the most frequent administration route… read more here.
Keywords: shotgun sequencing; feed; abundance; using shotgun ... See more keywords
Metagenomic shotgun sequencing to identify specific human gut microbes associated with immune checkpoint therapy efficacy in melanoma patients.
Sign Up to like & getrecommendations! Published in 2017 at "Journal of Clinical Oncology"
DOI: 10.1200/jco.2017.35.15_suppl.9516
Abstract: 9516Background: Immune checkpoint inhibitor therapy, ICT, achieves durable remissions in 30-50% of patients (pts) with metastatic melanoma (Larkin et al. NEJM 2015). It is still unclear what host f... read more here.
Keywords: melanoma; immune checkpoint; shotgun sequencing; metagenomic shotgun ... See more keywords
Metagenomic shotgun sequencing and metabolomic profiling identify specific human gut microbiota associated with diabetic retinopathy in patients with type 2 diabetes
Sign Up to like & getrecommendations! Published in 2022 at "Frontiers in Immunology"
DOI: 10.3389/fimmu.2022.943325
Abstract: Background Diabetic retinopathy (DR) is a common microvascular complication of diabetes mellitus (DM) and is one of the leading causes of blindness among DM patients. However, the molecular mechanism involving DR remains unclear. Methods A… read more here.
Keywords: gut microbiota; shotgun sequencing; metabolomic profiling; group ... See more keywords
Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data
Sign Up to like & getrecommendations! Published in 2019 at "Frontiers in Microbiology"
DOI: 10.3389/fmicb.2019.01683
Abstract: Identifying the microbes present in probiotic products is an important issue in product quality control and public health. The most common methods used to identify genera containing species that produce lactic acid are matrix-assisted laser… read more here.
Keywords: based pipeline; shotgun sequencing; coverage; coverage based ... See more keywords
Exploring the Microbial Community and Functional Characteristics of the Livestock Feces Using the Whole Metagenome Shotgun Sequencing
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Microbiology and Biotechnology"
DOI: 10.4014/jmb.2209.09013
Abstract: The foodborne illness is the important public health concerns, and the livestock feces are known to be one of the major reservoirs of foodborne pathogens. Also, it was reported that 45.5% of foodborne illness outbreaks… read more here.
Keywords: foodborne pathogens; shotgun sequencing; livestock feces; whole metagenome ... See more keywords