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A Powerful, User-Friendly Online Resource for Analyzing and Visualizing
Genomic Variation within bacterial enteric pathogens

Mark Achtman | Zhemin Zhou | Nabil-Fareed Alikhan | Khaled Mohamed | Yulei Fan


EnteroBASE EnteroBase 1 is a Powerful, User-Friendly Online Resource for Analyzing and Visualizing Genomic Variation within Enteric Bacteria

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 visualize genomic variation principally within the genera:

  • Escherichia
  • Salmonella
  • Yersinia
  • Clostridiodes (Clostridium difficile)
  • Moraxella

EnteroBase is populated with over 200,000 of genomic assemblies derived from publicly available complete genomes, sequence read archives and user uploads. Enterobase implements core genome MLST schemes to catalogue these genomic assemblies into biological population, and visualize the genetic relationships using GrapeTree 2,3, which supports facile manipulations of both tree layout and metadata. It calculates phylogenies using the neighbor-joining (NJ) algorithm, the classical minimal spanning tree algorithm (MSTree), or an improved minimal spanning tree algorithm which we call MSTree V2.


GrapeTree is named after the clusters of related bacterial strains that tends to be presented in minimal spanning trees. Our GrapeTree GUI is available within EnteroBase once you have created a workspace or connected to somebody else’s workspace.

To start using EnteroBase please click this link, for documentations please click here

This project is funded by BBSRC research grant BB/L020319/1.

  1. 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.
  2. Alikhan NF, Zhou Z,Sergeant MJ, Achtman M (2018) “A genomic overview of the population structure of Salmonella.” PLoS Genet 14 (4): e1007261.
  3. Zhou, Z., Alikhan, N., Sergeant, M.J., Luhmann, N., Vaz, C., Francisco, A.P., Carriço, J.A., & Achtman, M. (2018). GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens. Genome research.
  4. Z Zhou et al. (2018) “Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.”, Current Biology, VOLUME 28, ISSUE 15, P2420-2428.E10