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

Click one of the links below to read more: