Jesse J. Kerkvliet

Calibrating for absolute microbiome abundances without spike-ins

Nimrod Theodoor de Wit, Amulya Baral, Alessandro Fuschi, Guusje Jacobs et autres

Abstract Metagenomics is a widely used approach in microbiome research. However, a major limitation of metagenomic datasets is their compositional nature, which prevents direct quantification of absolute abundances and complicates cross-sample comparisons. Existing strategies for absolute quantification typically require additional experiments or …

nl, no, it, hu, dk (code pays fourni par la source)

MGCalibrator - Calibrating for absolute microbiome abundances without spike-ins

Nimrod de Wit, Amulya Baral, Patrick Munk, Alessandro Fuschi et autres

MetaGenome Calibrator (MGCalibrator) is a tool that enables spike-in free, absolute abundance estimation based on routine DNA concentration measurements.

nl, no, dk, it (code pays fourni par la source)

MGCalibrator - Calibrating for absolute microbiome abundances without spike-ins

Nimrod de Wit, Amulya Baral, Patrick Munk, Alessandro Fuschi et autres

MetaGenome Calibrator (MGCalibrator) is a tool that enables spike-in free, absolute abundance estimation based on routine DNA concentration measurements.

nl, no, dk, it (code pays fourni par la source)

Coccidiosis prevention strategies shape the microbiome, resistome and mobilome composition in the broiler gut

Matteo Buffoni, Jesse J. Kerkvliet, H. Enting, Jannigje Gerdien Kers et autres

BACKGROUND: Coccidiosis is a parasitic infection in the gut of livestock that poses a significant health challenge in poultry farming, underscoring the important role of intervention and prevention strategies in the poultry industry. The use of anticoccidial drugs raises concerns about antimicrobial …

nl (code pays fourni par la source)

gplasCC: classification and recovery of plasmids from short-read sequencing data for any bacterial species

Julián Paganini, Jesse J. Kerkvliet, Oscar Jordan, Gijs Teunis et autres

Abstract Plasmids play a pivotal role in the spread of antibiotic resistance genes. Accurately reconstructing plasmids often requires long-read sequencing, but bacterial genomic data in publicly accessible repositories have historically been derived from short-read sequencing technology. We recently presented an approach for …

nl, no, gb (code pays fourni par la source)

gplasCC: classification and reconstruction of plasmids from short-read sequencing data for any bacterial species

Julián Paganini, Jesse J. Kerkvliet, Gijs Teunis, Oscar Jordan et autres

ABSTRACT Plasmids play a pivotal role in the spread of antibiotic resistance genes. Accurately reconstructing plasmids often requires long-read sequencing, but bacterial genomic data in publicly accessible repositories has historically been derived from short-read sequencing technology. We recently presented an approach for …

nl, no, gb (code pays fourni par la source)

Antimicrobial resistance on the move

Jesse J. Kerkvliet

Antimicrobial resistance (AMR) is a growing challenge for public health. In 2019 alone, 1.27 million people have died of causes directly linked to infections caused by resistant bacteria. This problem does not only focus on the clinical health of humans, but also …

PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli

Julián Paganini, Jesse J. Kerkvliet, Lisa Vader, Nienke L. Plantinga et autres

Accurate reconstruction of Escherichia coli antibiotic resistance gene (ARG) plasmids from Illumina sequencing data has proven to be a challenge with current bioinformatic tools. In this work, we present an improved method to reconstruct E. coli plasmids using short reads. We developed …

nl, fi, no, gb (code pays fourni par la source)

Enterococcus faecium - Centrifuge Plasmid Database

Julián Paganini, Jesse J. Kerkvliet

nl (code pays fourni par la source)

Enterococcus faecalis - Centrifuge Plasmid Database

Julián Paganini, Jesse J. Kerkvliet

nl (code pays fourni par la source)

Enterococcus faecalis - Centrifuge Plasmid Database

Julián Paganini, Jesse J. Kerkvliet

nl (code pays fourni par la source)

Enterococcus faecium - Centrifuge Plasmid Database

Julián Paganini, Jesse J. Kerkvliet

nl (code pays fourni par la source)