Searching journal content for articles similar to van Opijnen and Camilli 22 (12): 2541.

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  1. Method: An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
    • Stephen Nayfach,
    • Beltran Rodriguez-Mueller,
    • Nandita Garud,
    • and Katherine S. Pollard
    Genome Res. November 2016 26: 1612-1625; Published in Advance October 18, 2016, doi:10.1101/gr.201863.115
    ...into a pathogen (Snitkin et al. 2011), or lead to outbreaks of highly virulent strains (Rasko et al. 2011). Metagenomic shotgun sequencing has the potential to shed light onto strain-level heterogeneity among bacterial s within and between microbial communities, yielding a genomic resolution not achievable...
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  2. Method: Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs
    • Juri Kuronen,
    • Samuel T. Horsfield,
    • Anna K. Pöntinen,
    • Sudaraka Mallawaarachchi,
    • Sergio Arredondo-Alonso,
    • Harry Thorpe,
    • Rebecca A. Gladstone,
    • Rob J.L. Willems,
    • Stephen D. Bentley,
    • Nicholas J. Croucher,
    • Johan Pensar,
    • John A. Lees,
    • Gerry Tonkin-Hill,
    • and Jukka Corander
    Genome Res. July 2024 34: 1081-1088; Published in Advance August 12, 2024, doi:10.1101/gr.278485.123
    ...approaches to -scale analysis of covariation at single-nucleotide resolution, termed as the -wide epistasis and coselection study (GWES), have demonstrated ample potential to uncover drivers of adaptation, virulence, survival, and antimicrobial resistance from densely sampled populations of major pathogens...
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  3. Letter: Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes
    • Tadasuke Ooka,
    • Yoshitoshi Ogura,
    • Md Asadulghani,
    • Makoto Ohnishi,
    • Keisuke Nakayama,
    • Jun Terajima,
    • Haruo Watanabe,
    • and Tetsuya Hayashi
    Genome Res. October 2009 19: 1809-1816; Published in Advance June 29, 2009, doi:10.1101/gr.089615.108
    ...are the smallest autonomously mobile genetic elements (generally 700–2500 base pairs [bp] in size) and are widely distributed in both eukaryotic and bacterial s.Most bacterial IS elements are of theDNA type (Chandler and Mahillon 2002). They only encode transposases (TPases) and thus are phenotypically cryptic...
  4. Review: De novo gene birth and the conundrum of ORFan genes in bacteria
    • Md. Hassan uz-Zaman and
    • Howard Ochman
    Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
    ...the functional potential of proteins encoded by nongenic sequences. Such evidence is usually achieved by expressing large pools of protein libraries in bacterial cells and testing for a functional phenotype. Using this approach, Knopp et al. (2019, 2021) have demonstrated the ability of random proteins...
  5. Method: Genealogical inference and more flexible sequence clustering using iterative PopPUNK
    • Bin Zhao,
    • John A. Lees,
    • Hongjin Wu,
    • Chao Yang,
    • and Daniel Falush
    Genome Res. May 30, 2023 gr.277395.122; Published in Advance May 30, 2023, doi:10.1101/gr.277395.122
    ...transmission chains, 45 it is necessary to establish which of the sequenced strains share very recent common 46 ancestors, indicating a shared source (Croucher and Didelot 2015; Sintchenko and Holmes 47 2015). To map genotype-phenotype relationships, it is often helpful to delineate lineages. 48 Organisms from...
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  6. Resource: Phenotypic diversity and genotypic flexibility of Burkholderia cenocepacia during long-term chronic infection of cystic fibrosis lungs
    • Amy Huei-Yi Lee,
    • Stephane Flibotte,
    • Sunita Sinha,
    • Adrianna Paiero,
    • Rachel L. Ehrlich,
    • Sergey Balashov,
    • Garth D. Ehrlich,
    • James E.A. Zlosnik,
    • Joshua Chang Mell,
    • and Corey Nislow
    Genome Res. April 2017 27: 650-662; Published in Advance March 21, 2017, doi:10.1101/gr.213363.116
    ...patients, spanning a periodof 2–20yr and a broad range of epidemic lineages. Systematic phenotypic tests identified longitudinal bacterial series that manifested progressive changes in liquid media growth, motility, biofilm formation, and acute insect virulence, but not in mucoidy. The results suggest...
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  7. LETTER: Probing genomic diversity and evolution of Escherichia coli O157 by single nucleotide polymorphisms
    • Wei Zhang,
    • Weihong Qi,
    • Thomas J. Albert,
    • Alifiya S. Motiwala,
    • David Alland,
    • Eija K. Hyytia-Trees,
    • Efrain M. Ribot,
    • Patricia I. Fields,
    • Thomas S. Whittam,
    • and Bala Swaminathan
    Genome Res. June 2006 16: 757-767; Published in Advance April 10, 2006, doi:10.1101/gr.4759706
    ...of this bacterial pathogen. To systematically examine single nucleotide polymorphisms (SNPs) at a scale, we designed comparative sequencing microarrays and analyzed 1199 chromosomal genes (a total of 1,167,948 bp) and 92,721 bp of the large virulence plasmid (pO157) of eleven outbreak-associated STEC O157 strains...
  8. Research: The effect of recombination on the evolution of a population of Neisseria meningitidis
    • Neil MacAlasdair,
    • Maiju Pesonen,
    • Ola Brynildsrud,
    • Vegard Eldholm,
    • Paul A. Kristiansen,
    • Jukka Corander,
    • Dominique A. Caugant,
    • and Stephen D. Bentley
    Genome Res. July 2021 31: 1258-1268; Published in Advance June 9, 2021, doi:10.1101/gr.264465.120
    ...) is a major human pathogen with a history of high invasive disease burden, particularly in sub-Saharan Africa. Our current understanding of the evolution of meningococcal s is limited by the rarity of large-scale genomic population studies and lack of in-depth investigation of the genomic events associated...
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  9. Resource: The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
    • Zhemin Zhou,
    • Nabil-Fareed Alikhan,
    • Khaled Mohamed,
    • Yulei Fan,
    • the Agama Study Group,
    • and Mark Achtman
    Genome Res. January 2020 30: 138-152; Published in Advance December 6, 2019, doi:10.1101/gr.251678.119
    ..., Vibrio, and Moraxella and genotyped those assemblies by core multilocus sequence typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads...
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  10. Research: Unique genetic basis of the distinct antibiotic potency of high acetic acid production in the probiotic yeast Saccharomyces cerevisiae var. boulardii
    • Benjamin Offei,
    • Paul Vandecruys,
    • Stijn De Graeve,
    • María R. Foulquié-Moreno,
    • and Johan M. Thevelein
    Genome Res. September 2019 29: 1478-1494; Published in Advance August 29, 2019, doi:10.1101/gr.243147.118
    ...by bacterial enteropathogens (Czerucka et al. 2007). Certain strains of S. cerevisiae also appear to have probiotic capacity (Martins et al. 2007; Zanello et al. 2011a,b), but protection against enteric bacterial pathogens has not been reported. Their phylogenetic relationship with S. boulardii is not known...
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