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Research: Colibactin leads to a bacteria-specific mutation pattern and self-inflicted DNA damage
- Emily Lowry,
- Yiqing Wang,
- Tal Dagan,
- and Amir Mitchell
Genome Res. August 2024 34: 1154-1164; Published in Advance August 16, 2024, doi:10.1101/gr.279517.124
...are a common mechanism underlying such competitive interactions. Colibactin is a bacteria-secreted genotoxin that can bind DNA in neighboring cells (Nougayrède et al. 2006; Vizcaino and Crawford 2015; Pleguezuelos-Manzano et al. 2020). Colibactin damage is toxic for some bacteria species (Chen et al. 2022...
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Research: Transporter genes in biosynthetic gene clusters predict metabolite characteristics and siderophore activity
- Alexander Crits-Christoph,
- Nicholas Bhattacharya,
- Matthew R. Olm,
- Yun S. Song,
- and Jillian F. Banfield
Genome Res. February 2021 31: 239-250; Published in Advance December 23, 2020, doi:10.1101/gr.268169.120
...therefore often underlie both cooperative and competitive interactions between microbes and microbial interactions with the physiochemical environment (Davies 2013; Sharon et al. 2014; Tyc et al. 2017). The vast majority of specialized metabolites in bacteria are produced by biosynthetic gene clusters (BGCs...
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Research: Genome-wide detection of novel regulatory RNAs in E. coli
- Rahul Raghavan,
- Eduardo A. Groisman,
- and Howard Ochman
Genome Res. September 2011 21: 1487-1497; Published in Advance June 10, 2011, doi:10.1101/gr.119370.110
...; 2Microbial Diversity Institute, Yale University, New Haven, Connecticut 06516, USA; 3Howard Hughes Medical Institute, Section of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut 06516, USA Abstract The intergenic regions in bacterial genomes can contain...
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Research: The altered landscape of the human skin microbiome in patients with primary immunodeficiencies
- Julia Oh,
- Alexandra F. Freeman,
- NISC Comparative Sequencing Program,
- Morgan Park,
- Robert Sokolic,
- Fabio Candotti,
- Steven M. Holland,
- Julia A. Segre,
- and Heidi H. Kong
Genome Res. December 2013 23: 2103-2114; Published in Advance October 29, 2013, doi:10.1101/gr.159467.113
...distinction between apparent colonization and infection. Potentially pathogenic bacteria that colonize humans are influenced not only by host factors, but also by their native microbial community. This paradigm requires that diseases of microbial origin must be investigated within the context...
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ARTICLE: A systems view of haloarchaeal strategies to withstand stress from transition metals
- Amardeep Kaur,
- Min Pan,
- Megan Meislin,
- Marc T. Facciotti,
- Raafat El-Gewely,
- and Nitin S. Baliga
Genome Res. July 2006 16: 841-854; Published in Advance June 2, 2006, doi:10.1101/gr.5189606
...transition metal induced growth arrest, attempts to minimize oxidative stress, toxic ion scavenging, increased protein turnover and DNA repair, and modulation of active ion transport. While several of these constitute generalized stress responses, up-regulation of active efflux of Co(II), Ni(II), Cu...
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LETTER: Patterns of large-scale genomic variation in virulent and avirulent Burkholderia species
- Catherine Ong,
- Chia Huey Ooi,
- Dongling Wang,
- Hweeling Chong,
- Kim Chong Ng,
- Fiona Rodrigues,
- May Ann Lee,
- and Patrick Tan
Genome Res. November 2004 14: 2295-2307; doi:10.1101/gr.1608904
...and glanders are caused by the bacteria Burkholderia pseudomallei and B. mallei respectively, and both species are regarded as potential biowarfare agents. We used B. pseudomallei DNA microarrays to compare the genomes of several clinical and environmental isolates of B. pseudomallei, B. mallei , and B...
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LETTER: Large-Scale Analysis of the Meningococcus Genome by Gene Disruption: Resistance to Complement-Mediated Lysis
- Marie-Claude Geoffroy,
- Stéphanie Floquet,
- Arnaud Métais,
- Xavier Nassif,
- and Vladimir Pelicic
Genome Res. March 1, 2003 13: 391-398; Published in Advance February 12, 2003, doi:10.1101/gr.664303
...to understanding gene function, we used high-density signature-tagged transposon mutagenesis, followed by a large-scale sequencing of the transposon insertion sites, to construct a genome-wide collection of mutants. The sequencing results for the first half of the 4548 mutants composing the library suggested...
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Resource: Precision environmental health monitoring by longitudinal exposome and multi-omics profiling
- Peng Gao,
- Xiaotao Shen,
- Xinyue Zhang,
- Chao Jiang,
- Sai Zhang,
- Xin Zhou,
- Sophia Miryam Schüssler-Fiorenza Rose,
- and Michael Snyder
Genome Res. June 2022 32: 1199-1214; Published in Advance June 6, 2022, doi:10.1101/gr.276521.121
...at the individual level. Exposomics research aims to characterize all physical, chemical, and biological components collectively in the human external and internal environment and investigate the internal molecular, physiological, and health-related effects of these exposures (Gao and Snyder 2021). The external...
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Research: Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131
- Teemu Kallonen,
- Hayley J. Brodrick,
- Simon R. Harris,
- Jukka Corander,
- Nicholas M. Brown,
- Veronique Martin,
- Sharon J. Peacock,
- and Julian Parkhill
Genome Res. August 2017 27: 1437-1449; Published in Advance July 18, 2017, doi:10.1101/gr.216606.116
...to analyze a systematic 11-yr hospital-based survey of E. coli associated with bacteremia using isolates collected from across England by the British Society for Antimicrobial Chemotherapy and from the Cambridge University Hospitals NHS Foundation Trust. Population dynamics analysis of the most successful...
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ARTICLE: Coping with cold: The genome of the versatile marine Antarctica bacterium Pseudoalteromonas haloplanktis TAC125
- Claudine Médigue,
- Evelyne Krin,
- Géraldine Pascal,
- Valérie Barbe,
- Andreas Bernsel,
- Philippe N. Bertin,
- Frankie Cheung,
- Stéphane Cruveiller,
- Salvino D'Amico,
- Angela Duilio,
- Gang Fang,
- Georges Feller,
- Christine Ho,
- Sophie Mangenot,
- Gennaro Marino,
- Johan Nilsson,
- Ermenegilda Parrilli,
- Eduardo P.C. Rocha,
- Zoé Rouy,
- Agnieszka Sekowska,
- Maria Luisa Tutino,
- David Vallenet,
- Gunnar von Heijne,
- and Antoine Danchin
Genome Res. October 2005 15: 1325-1335; Published in Advance September 16, 2005, doi:10.1101/gr.4126905
...% of its surface experiences yearly temperatures &lt;15°C, asking for a remarkable adaptation of life to cold conditions. Several marine bacteria have been studied, but so far we possess only limited information about life in the sea at medium and low temperatures ( Bartlett 1999 ; Raven et al. 2002...

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