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Akademický článek

Multi-factorial examination of amplicon sequencing workflows from sample preparation to bioinformatic analysis

Autor: Travis J. De Wolfe, Erik S. Wright

Publikováno v: BMC Microbiology, Vol 23, Iss 1, Pp 1-17 (2023)

Abstract Background The development of sequencing technologies to evaluate bacterial microbiota composition has allowed new insights into the importance of microbial ecology. However, the variety of methodologies used among amplicon sequencing workfl

Externí odkaz: https://doaj.org/article/f640f2cf732f4966833dbc56de325333

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Akademický článek

The eDNA-Container App: A Simple-to-Use Cross-Platform Package for the Reproducible Analysis of eDNA Sequencing Data

Autor: David Wheeler, Lillian Brancalion, Akitomo Kawasaki, Meaghan L. Rourke

Publikováno v: Applied Sciences, Vol 14, Iss 6, p 2641 (2024)

The analysis of environmental DNA (eDNA) is a powerful and non-invasive method for monitoring the presence of species in ecosystems. However, ecologists and laboratory staff can find it challenging to use eDNA analysis software effectively due to the

Externí odkaz: https://doaj.org/article/314cd4b45bb344b5ade8689aef39da65

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Akademický článek

Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats

Autor: Huasong Bai, Tong Liu, Songjun Wang, Wenhui Gong, Liya Shen, Song Zhang, Zhanzhong Wang

Publikováno v: Microbiology Spectrum, Vol 11, Iss 4 (2023)

ABSTRACT Changes in diet and environment can lead to acute diarrhea in companion animals, but the composition and interactions of the gut microbiome during acute diarrhea remain unclear. In this multicenter case-control study, we investigated the rel

Externí odkaz: https://doaj.org/article/4f6cdb1995f542dea197d7344d215144

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Interspecies and spatial differences in the shell microbiome of Atlantic rock crab Cancer irrotatus and European green crab Carcinus maenas from Atlantic Canada

Autor: Svenja Koepper, Shannon Kelley, Krishna Kumar Thakur, K. Fraser Clark

Publikováno v: Frontiers in Marine Science, Vol 10 (2023)

IntroductionThe native Atlantic rock crab (Cancer irrotatus) and the invasive European green crab (Carcinus maenas) are commercially and ecologically important crustacean species in Atlantic Canada. The importance of microbiomes for host health and e

Externí odkaz: https://doaj.org/article/f4d3564988aa4c078299a378b04a79a2

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Akademický článek

A detailed workflow to develop QIIME2-formatted reference databases for taxonomic analysis of DNA metabarcoding data

Autor: Benjamin Dubois, Frédéric Debode, Louis Hautier, Julie Hulin, Gilles San Martin, Alain Delvaux, Eric Janssen, Dominique Mingeot

Publikováno v: BMC Genomic Data, Vol 23, Iss 1, Pp 1-14 (2022)

Abstract Background The DNA metabarcoding approach has become one of the most used techniques to study the taxa composition of various sample types. To deal with the high amount of data generated by the high-throughput sequencing process, a bioinform

Externí odkaz: https://doaj.org/article/08efc7daac61456f94cb13010b3b87bd

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Akademický článek

Influence of Agaricus bisporus establishment and fungicidal treatments on casing soil metataxonomy during mushroom cultivation

Autor: Maria Luisa Tello Martín, Rebeca Lavega, Jaime Carrasco Carrasco, Margarita Pérez, Antonio J. Pérez-Pulido, Michael Thon, Ernesto Pérez Benito

Publikováno v: BMC Genomics, Vol 23, Iss 1, Pp 1-12 (2022)

Abstract The cultivation of edible mushroom is an emerging sector with a potential yet to be discovered. Unlike plants, it is a less developed agriculture where many studies are lacking to optimize the cultivation. In this work we have employed high-

Externí odkaz: https://doaj.org/article/1f96f456b1a84380b50c98370bf1e225

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Akademický článek

High-throughput amplicon sequencing datasets of coastal sediments from three locations of the Gulf of Mexico, USA

Autor: George B.H. Green, Angelo DePaola, Jason G. Linville, Casey D. Morrow, Asim K. Bej

Publikováno v: Data in Brief, Vol 47, Iss , Pp 108895- (2023)

We present high-throughput amplicon sequence (HTS) datasets of the purified microbial metacommunity DNA of coastal surface sediments from Portersville Bay (PVB) (n = 3), Bayou La Batre (BLB) (n = 3), and Mobile Bay (MOB) (n = 3) of the U.S. Gulf of M

Externí odkaz: https://doaj.org/article/ddb0db4e15124420bea4cab914d4ed9f

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Akademický článek

ASVmaker: A New Tool to Improve Taxonomic Identifications for Amplicon Sequencing Data

Autor: Clément Plessis, Thomas Jeanne, Antoine Dionne, Julien Vivancos, Arnaud Droit, Richard Hogue

Publikováno v: Plants, Vol 12, Iss 21, p 3678 (2023)

The taxonomic assignment of sequences obtained by high throughput amplicon sequencing poses a limitation for various applications in the biomedical, environmental, and agricultural fields. Identifications are constrained by the length of the obtained

Externí odkaz: https://doaj.org/article/fafaebe445fa4b5c84c6c36b60ad4cb1

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Cross-comparison of microbiota in the oropharynx, hypopharyngeal squamous cell carcinoma and their adjacent tissues through quantitative microbiome profiling

Autor: Hui-Ching Lau, Yujie Shen, Huiying Huang, Xiaohui Yuan, Mengyou Ji, Hongli Gong, Chi-Yao Hsueh, Liang Zhou

Publikováno v: Journal of Oral Microbiology, Vol 14, Iss 1 (2022)

Aims To clarify the absolute abundance of microbial communities on hypopharyngeal squamous cell carcinoma and their correlation to those in the oropharynx.Methods Clinical data, swabs, and tissue samples from 27 HPSCC patients were collected in this

Externí odkaz: https://doaj.org/article/14f30f772b964e7785df7c782eb9ca8f

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