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Shotgun sequencing

Comparison of qPCR and metagenomic sequencing methods for quantifying antibiotic resistance genes in wastewater

Gihan Daw Elbait, Mariane Daou, Miral Abuoudah, Ahmed Elmekawy, Shadi W. Hasan, Dean B. Everett, Habiba Alsafar, Andreas Henschel, Ahmed F. Yousef

published 05 Apr 2024

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High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing

Thomas Bygh Nymann Jensen, Sebastian Mølvang Dall, Simon Knutsson, Søren Michael Karst, Mads Albertsen

published 04 Apr 2024

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Shotgun metagenomics to investigate unknown viral etiologies of pediatric meningoencephalitis

Andrea Castellot, Juan Camacho, María Dolores Fernández-García, David Tarragó

published 21 Dec 2023

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Are the predicted known bacterial strains in a sample really present? A case study

Minerva Ventolero, Saidi Wang, Haiyan Hu, Xiaoman Li

published 13 Oct 2023

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Tracking gut microbiome and bloodstream infection in critically ill adults

Christopher H. Gu, Layla A. Khatib, Ayannah S. Fitzgerald, Jevon Graham-Wooten, Caroline A. Ittner, Scott Sherrill-Mix, YuChung Chuang, Laurel J. Glaser, Nuala J. Meyer, Frederic D. Bushman, Ronald G. Collman

published 10 Oct 2023

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Shotgun metagenomics captures more microbial diversity than targeted 16S rRNA gene sequencing for field specimens and preserved museum specimens

Joseph D. Madison, Brandon C. LaBumbard, Douglas C. Woodhams

published 19 Sep 2023

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Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori

Dita Gudra, Ivars Silamikelis, Janis Pjalkovskis, Ilva Danenberga, Darta Pupola, Girts Skenders, Maija Ustinova, Kaspars Megnis, Marcis Leja, Reinis Vangravs, Davids Fridmanis

published 10 Aug 2023

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Validation of the shotgun metabarcoding approach for comprehensively identifying herbal products containing plant, fungal, and animal ingredients

Zhaolei Zhang, Weishan Mu, Weijun Kong, Jiali Liu, Jingyi Zhao, Qing Zhao, Mengmeng Shi, Hongye Zhao, Jinxin Liu, Linchun Shi

published 03 Jul 2023

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AirDNA sampler: An efficient and simple device enabling high-yield, high-quality airborne environment DNA for metagenomic applications

Piyanun Harnpicharnchai, Panyapon Pumkaeo, Paopit Siriarchawatana, Somsak Likhitrattanapisal, Sermsiri Mayteeworakoon, Lily Ingsrisawang, Worawongsin Boonsin, Lily Eurwilaichitr, Supawadee Ingsriswang

published 29 Jun 2023

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Distinctive microbial community and genome structure in coastal seawater from a human-made port and nearby offshore island in northern Taiwan facing the Northwestern Pacific Ocean

Chi-Yu Shih, Shiow-Yi Chen, Chun-Ru Hsu, Ching-Hsiang Chin, Wei-Chih Chiu, Mei-Hung Chang, Lee-Kuo Kang, Cing-Han Yang, Tun-Wen Pai, Chin-Hwa Hu, Pang-Hung Hsu, Wen-Shyong Tzou

published 09 Jun 2023

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The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection

Ruijie Xu, Sreekumari Rajeev, Liliana C. M. Salvador

published 07 Apr 2023

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Combining vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing to investigate the diet of the leopard cat (Prionailurus bengalensis) in Korea

Cheolwoon Woo, Priyanka Kumari, Kyung Yeon Eo, Woo-Shin Lee, Junpei Kimura, Naomichi Yamamoto

published 31 Jan 2023

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Drastic reduction of false positive species in samples of insects by intersecting the default output of two popular metagenomic classifiers

Lidia Garrido-Sanz, Miquel Àngel Senar, Josep Piñol

published 25 Oct 2022

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