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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
...://github.com/zheminzhou/EToKi) of useful modules (Supplemental Fig. S2B–E) that facilitate genomic assemblies (EToKi modules prepare and assemble), MLST (MLSType), calling nonrepetitive SNPs against a reference (EToKi modules align and phylo), or predicting serotypes of Escherichia coli from assemblies (EBEis).EnteroBase performs daily...
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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
..., but characterization of their roles in phage lifecycles is limited, and their impact on phage replication is controversial. To address these issues, we have searched for phages whose growth is impacted by the major recombination-promoting helicase-nuclease of Escherichia coli, the RecBCD enzyme. Although no phages...
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Research: Genomic characterization of the Bacillus cereus sensu lato species: Backdrop to the evolution of Bacillus anthracis
- Michael E. Zwick,
- Sandeep J. Joseph,
- Xavier Didelot,
- Peter E. Chen,
- Kimberly A. Bishop-Lilly,
- Andrew C. Stewart,
- Kristin Willner,
- Nichole Nolan,
- Shannon Lentz,
- Maureen K. Thomason,
- Shanmuga Sozhamannan,
- Alfred J. Mateczun,
- Lei Du,
- and Timothy D. Read
Genome Res. August 2012 22: 1512-1524; Published in Advance May 29, 2012, doi:10.1101/gr.134437.111
...and Escherichia coli (F > 0.3), and the more restricted species, such as S. aureus (0.15) (Kislyuk et al. 2011). Values of F calculated for the clade 1 and clade 2 s only were both 0.17, significantly lower than the 0.25 for clade 3 (P < 0.05), reflecting the greater phylogenetic diversity of clade 3. Thus...
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Method: Microbial strain-level population structure and genetic diversity from metagenomes
- Duy Tin Truong,
- Adrian Tett,
- Edoardo Pasolli,
- Curtis Huttenhower,
- and Nicola Segata
Genome Res. April 2017 27: 626-638; Published in Advance February 6, 2017, doi:10.1101/gr.216242.116
...with host tissues (Bron et al. 2012), modulation of immune homeostasis (Needham et al. 2013), and xenobiotic metabolism (Spanogiannopoulos et al. 2016). Pathogenic potential is also strain-specific in many species, including Escherichia coli, which is prevalent in the healthy human gut despite some strains...
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Research: Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth
- Christina A. Cuomo,
- Christopher A. Desjardins,
- Malina A. Bakowski,
- Jonathan Goldberg,
- Amy T. Ma,
- James J. Becnel,
- Elizabeth S. Didier,
- Lin Fan,
- David I. Heiman,
- Joshua Z. Levin,
- Sarah Young,
- Qiandong Zeng,
- and Emily R. Troemel
Genome Res. December 2012 22: 2478-2488; Published in Advance July 18, 2012, doi:10.1101/gr.142802.112
...Pfam analysis also identified a putative nucleoside H+ symporter, which is specific to Microsporidia (Table 2). Expression of this nucleoside transporter in N. parisii (ERTm1) (NEPG_00699) can be detected throughout infection (Supplemental Table S5). This symporter is homologous to the Escherichia coli...
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Resource: A fine scale phenotype–genotype virulence map of a bacterial pathogen
- Tim van Opijnen and
- Andrew Camilli
Genome Res. December 2012 22: 2541-2551; Published in Advance July 23, 2012, doi:10.1101/gr.137430.112
...remains elusive and their overall contribution unclear. Moreover, a large fraction (>30%) within the unknown category contains responsive genes (279) and core genes (19), indicating that the data set is rich in novel genotype–phenotype relationships. Recently, it was shown for Escherichia coli that both...
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PERSPECTIVE: Genomics in C. elegans: So many genes, such a little worm
- LaDeana W. Hillier,
- Alan Coulson,
- John I. Murray,
- Zhirong Bao,
- John E. Sulston,
- and Robert H. Waterston
Genome Res. December 2005 15: 1651-1660; doi:10.1101/gr.3729105
...al. 2000 ; Maeda et al. 2001 ; Kamath and Ahringer 2003 ; Sonnichsen et al. 2005 ), and currently &gt;18,000 Escherichia coli strains have been constructed and have been widely distributed. Initial screens were for easily scored phenotypes such as viability, slow growth, or altered movement and body...
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Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
- Marcus W. Fedarko,
- Mikhail Kolmogorov,
- and Pavel A. Pevzner
Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
...) is important because strains with small genomic differences may have vastly different phenotypes: for example, although some Escherichia coli strains are harmless, others may cause disease outbreaks (Frank et al. 2011; Vicedomini et al. 2021). The detection and phasing of rare mutations are prerequisites...
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Research: Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts
- Catherine Lozupone,
- Karoline Faust,
- Jeroen Raes,
- Jeremiah J. Faith,
- Daniel N. Frank,
- Jesse Zaneveld,
- Jeffrey I. Gordon,
- and Rob Knight
Genome Res. October 2012 22: 1974-1984; Published in Advance June 4, 2012, doi:10.1101/gr.138198.112
...genes in a phylogenetically diverse collection of 15 enteric pathogens, including unrelated Clostridia (C. difficile, C. perfringens, and C. tetani), Enterobacteria (pathogenic Escherichia coli and Salmonella enterica), Streptococcus sanguinis, Campylobacter jejuni, Helicobacter hepaticus, Lawsonia...
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Next-Generation DNA Sequencing/Review: Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
- Micah Hamady and
- Rob Knight
Genome Res. July 2009 19: 1141-1152; Published in Advance April 21, 2009, doi:10.1101/gr.085464.108
...of Escherichia coli as a classic gut bacterium, but the entire Gamma-proteobacteria phylum that contains it typically comprises much less than 1% of gut bacteria—rather, E. coli grows extremely well in culture and can thus be detected at low abundance. Most species found in the gut of a given individual are rare...

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