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Access to over 20,000 Bacterial Genomes

What's New in Release 24

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Ensembl Genomes REST ServiceTo access Ensembl Genomes data from any programming language, try our REST service. For full documentation including examples from a wide range of languages, visit

Release 24 of Ensembl Bacteria has been loaded from EMBL-Bank release 120 into 85 multispecies Ensembl v77 databases. The current dataset contains 20,254 genomes (19,980 bacteria and 276 archaea) containing 71,354,364 protein coding genes loaded from 1,765,948 INSDC entries. This release includes 4,994 new genomes, 23 genomes with updated assemblies, 1,435 genomes with updated annotation, 499 genomes where the assigned name has changed, and 10 genomes removed since the last release. Operon and related data from RegulonDB has been loaded for E. coli K12 MG1655.

Note: Those accessing MySQL databases directly should note that the reference bacterial genomes used for the pan-taxonomic compara are now in a separate collection, bacteria_0. This also affects the organisation of our FTP site.

Ensembl Bacteria

Over 20,000 genome sequences from bacteria and archaea have been annotated and deposited in the public archives of the members of the International Nucleotide Sequence Database Collaboration. This site provides access to complete, annotated genomes from bacteria and archaea (present in the European Nucleotide Archive) through the Ensembl graphical user interface (genome browser). More details about the integration are provided here

Programmatic access is available through the Ensembl Perl and REST-ful APIs and through publicly accessible mysql databases, along with full data dumps (including DNA sequence and protein sequence in FASTA format, annotations in GTF format, and mysql dump files). Due to the large number of these databases, there is some modification to the APIs, and database and FTP site structure, compared to that used for other branches of the taxonomy (e.g. the storage of many genomes in one database; the provision of lookup services to identify genomes by INSDC identifiers, taxonomy identifiers, or partial names. Full details are available here.

BioMart access is not available, but we are working on providing new, more powerful data mining tools to allow users to exploit these genomes. A selection of over 100 key bacterial genomes has been included in the pan-taxonomic Compara, and genes from all genomes are classified into families using HAMAP and PANTHER (more details)

Ensembl Bacteria has been developed with the support of the Microme project, a resource for bacterial metabolism.

Ensembl Genomes is developed by EMBL-EBI and is powered by the Ensembl software system for the analysis and visualisation of genomic data. For details of our funding please click here.