EnteroBase¶

A Powerful, User-Friendly Online Resource for Analyzing and Visualizing Genomic Variation within Enteric Bacteria

Click here to get started (registering and logging in.)
Click here to see the tutorials.

Gallery¶

GrapeTree of cgMLST (3,002 loci) from 1,082 Salmonella enterica serovar Agona genomes in EnteroBase	Core SNP phylogeny of ancient (red) and modern genomes of Para C Lineage in Salmonella eneterica

Alikhan et al. 2018	Zhou et al. 2018a

Visualization of 3,902 legacy Salmonella MLST STs from 99,722 genomic assemblies

Zhou et al. 2018b

Databases¶

EnteroBase aims to establish a world-class, one-stop, user-friendly, backwards-compatible but forward-looking genome database, Enterobase – together with a set of web-based tools, EnteroBase Backend Pipeline – to enable bacteriologists to identify, analyse, quantify and visualise genomic variation principally within the genera:

Misc¶

Click here to Post an issue or bug about EnteroBase

Funded by BBSRC research grant BB/L020319/1.

Citation¶

If you use data/metadata from the website, or the analysis based on these data, please cite EnteroBase as:

Zhou Z., Alikhan NF, Mohamed K, the Agama Study Group, Achtman M (2020), “The EnteroBase user’s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny and Escherichia core genomic diversity”, Genome Res. 2020. 30: 138-152, https://doi.org/10.1101/gr.251678.119

Please cite Salmonella database as:

Achtman M, Zhou Z, Alikhan NF, et al. (2020) “Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project”, Wellcome Open Research 5, 223, https://doi.org/10.12688/wellcomeopenres.16291.1

or

Alikhan NF, Zhou Z, Sergeant MJ, Achtman M (2018) “A genomic overview of the population structure of Salmonella”, PLoS Genet 14 (4): e1007261, https://doi.org/10.1371/journal.pgen.1007261

Please cite Clostridioides database as:

Frentrup M, Zhou Z, Steglich M, et al. (2020) “A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics”, Microb Genom. 6(8). doi: http://dx.doi.org/10.1099/mgen.0.000410

If you use GrapeTree please cite the following paper:

Zhou Z, Alikhan NF, Sergeant MJ, Luhmann N, Vaz C, Francisco AP, Carrico JA, Achtman M (2018) “GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens”, Genome Research. 28(9): 1395–1404, https://doi.org/10.1101/gr.232397.117

If you use Hierarchical Clustering please cite the following paper:

Zhou Z, Charlesworth J and Achtman M (2021) “HierCC: A multi-level clustering scheme for population assignments based on core genome MLST” Bioinformatics, Vol37, 20:3645–3646

3rd Party acknowledgements¶

If you use data generated by 3rd party tools in EnteroBase, please cite both EnteroBase and the paper describing the specific tool.

rMLST is Copyright 2010-2016, University of Oxford. rMLST is described in: Jolley et al. 2012 Microbiology 158:1005-15.
Serovar predictions (SISTR) have been calculated using the pipeline developed by the SISTR team and is described in Yoshida et al. 2016 PLoS ONE 11(1): e0147101 and evaluated in Robertson et al. 2018 M Gen 4(2):e000151
SeqSero2 is described in Zhang et al. 2019 Appl Environ Microbiol 85:e01746-19
ClermonTyping is described in Beghain et al. 2018 M Gen 4(7): e000192
EzClermont is described in: Waters et al. 2020 DOI 10.1099/acmi.0.000143
FimTyper is described in: Roer et al. 2017 J Clin Microbiol 55(8):2538-2543

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