Results 41 to 50 of about 2,805,364 (358)

Genome-wide insights into population structure and host specificity of Campylobacter jejuni

Scientific Reports, 2021
The zoonotic pathogen Campylobacter jejuni is among the leading causes of foodborne diseases worldwide. While C. jejuni colonises many wild animals and livestock, persistence mechanisms enabling the bacterium to adapt to host species' guts are not fully ...
Lennard Epping, Birgit Walther, Rosario M. Piro, Marie-Theres Knüver, Charlotte Huber, Andrea Thürmer, Antje Flieger, Angelika Fruth, Nicol Janecko, Lothar H. Wieler, Kerstin Stingl, Torsten Semmler   +11 more
doaj   +1 more source

One bacterial cell, one complete genome. [PDF]

PLoS ONE, 2010
While the bulk of the finished microbial genomes sequenced to date are derived from cultured bacterial and archaeal representatives, the vast majority of microorganisms elude current culturing attempts, severely limiting the ability to recover complete ...
Tanja Woyke, Damon Tighe, Konstantinos Mavromatis, Alicia Clum, Alex Copeland, Wendy Schackwitz, Alla Lapidus, Dongying Wu, John P McCutcheon, Bradon R McDonald, Nancy A Moran, James Bristow, Jan-Fang Cheng   +12 more
doaj   +1 more source

Cronobacter, the emergent bacterial pathogen Enterobacter sakazakii comes of age; MLST and whole genome sequence analysis [PDF]

, 2014
Background: Following the association of Cronobacter spp. to several publicized fatal outbreaks in neonatal intensive care units of meningitis and necrotising enterocolitis, the World Health Organization (WHO) in 2004 requested the establishment of a ...
Keith A Jolley, Forsythe, SJ, Stephen J Forsythe, Jolley, KA, Benjamin Dickins, Dickins, B   +5 more
core   +1 more source

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

Bioinform., 2019
Summary The Genome Taxonomy Database Toolkit (GTDB-Tk) provides objective taxonomic assignments for bacterial and archaeal genomes based on the GTDB. GTDB-Tk is computationally efficient and able to classify thousands of draft genomes in parallel.
Pierre-Alain Chaumeil, A. Mussig, P. Hugenholtz, Donovan H. Parks   +3 more
semanticscholar   +1 more source

B-assembler: a circular bacterial genome assembler

BMC Genomics, 2022
Background Accurate bacteria genome de novo assembly is fundamental to understand the evolution and pathogenesis of new bacteria species. The advent and popularity of Third-Generation Sequencing (TGS) enables assembly of bacteria genomes at an ...
Fengyuan Huang, Li Xiao, Min Gao, Ethan J. Vallely, Kevin Dybvig, T. Prescott Atkinson, Ken B. Waites, Zechen Chong   +7 more
doaj   +1 more source

CRISPR/FnCas12a-mediated efficient multiplex and iterative genome editing in bacterial plant pathogens without donor DNA templates.

PLoS Pathogens, 2023
CRISPR-based genome editing technology is revolutionizing prokaryotic research, but it has been rarely studied in bacterial plant pathogens. Here, we have developed a targeted genome editing method with no requirement of donor templates for convenient ...
Fang Yan, Jingwen Wang, Sujie Zhang, Zhenwan Lu, Shaofang Li, Zhiyuan Ji, Congfeng Song, Gongyou Chen, Jin Xu, Jie Feng, Xueping Zhou, Huanbin Zhou   +11 more
doaj   +1 more source

KvarQ: targeted and direct variant calling from fastq reads of bacterial genomes [PDF]

, 2014
High-throughput DNA sequencing produces vast amounts of data, with millions of short reads that usually have to be mapped to a reference genome or newly assembled.
Steiner, Andreas, Sebastien Gagneux, David Stucki, Andreas Steiner, Borrell, Sonia, Stucki, David, Sonia Borrell, Gagneux, Sebastien, Mireia Coscolla, Coscolla, Mireia   +9 more
core   +1 more source

Optical mapping as a routine tool for bacterial genome sequence finishing [PDF]

, 2007
Background: In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts.
Norton, S., Miller, N., Zijin Du, Goldman, Barry S., Latreille Phil, Bode, Helge Björn, Henkhaus John, Forst, Steve, John Henkhaus, Goodrich-Blair, H., Miller, Nancy, Slater Steven, Stacie Norton, Bode, H., Goldman Barry S, Henkhaus, J., Gaudriault, S., Steve Forst, Creg Darby, Gaudriault Sophie, Darby Creg, Goldman, B., Gaudriault, Sophie, Darby, C., Du, Z., Goodner, B., Norton, Stacie, Sophie Gaudriault, Miller Nancy, Goodrich-Blair, Heidi, Henkhaus, John, Heidi Goodrich-Blair, Gaudriault, Sophie, S., Latreille, Phil, Slater, S., Goodrich-Blair Heidi, Goodner, Brad, Goodner Brad, Latreille, P., Bode, Helge B., Nancy Miller, Norton Stacie, Brad Barbazuk, Phil Latreille, Steven Slater, Slater, Steven, Forst Steve, Helge B Bode, Forst, S., Barbazuk, Brad, Barbazuk Brad, Du, Zijin, Bode Helge B, Barry S Goldman, Du Zijin, Brad Goodner, Barbazuk, B., Darby, Creg   +57 more
core   +1 more source

CRISPR RNA-guided integrases for high-efficiency, multiplexed bacterial genome engineering

Nature Biotechnology, 2020
Existing technologies for site-specific integration of kilobase-sized DNA sequences in bacteria are limited by low efficiency, a reliance on recombination, the need for multiple vectors, and challenges in multiplexing.
P. Vo, Carlotta Ronda, Sanne E. Klompe, Ethan E. Chen, Christopher Acree, Harris H. Wang, S. H. Sternberg   +6 more
semanticscholar   +1 more source

Extra-Chromosomal DNA Sequencing Reveals Episomal Prophages Capable of Impacting Virulence Factor Expression in Staphylococcus aureus

Frontiers in Microbiology, 2018
Staphylococcus aureus is a major human pathogen with well-characterized bacteriophage contributions to its virulence potential. Recently, we identified plasmidial and episomal prophages in S.
Douglas R. Deutsch, Bryan Utter, Kathleen J. Verratti, Heike Sichtig, Luke J. Tallon, Vincent A. Fischetti   +5 more
doaj   +1 more source