Access to over 40,000 Bacterial Genomes

Ensembl Bacteria

Ensembl Bacteria hosts the annotation of over 44,000 prokaryotic (bacterial and archaeal) genomes that have been submitted to the databases of the International Nucleotide Sequence Database Collaboration (INSDC), i.e. the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan.

Non-redundant genomes

The ENA houses over 90,000 prokaryotic genome assemblies, including multiple strains of many species. To reduce redundancy, we have adopted a policy (as of release 35 (April 2017)) of only loading in new sequences that are relatively non-redundant with the existing data set, according to the criteria of the UniProt Knowledgebase (DOI: 10.1093/database/baw139). All strains that were present in the INSDC archives prior to this release have already been included in Ensembl Bacteria (regardless of whether they meet the new criteria) and will remain available in future.

Data access

Data can be visualised through the Ensembl genome browser and accessed programmatically via our Perl and RESTful APIs. Data is also accessible through public MySQL databases and our FTP site containing full data dumps in FASTA, EMBL, GTF, GFF3, JSON and RDF formats.

There are no BioMarts currently available for Ensembl Bacteria,, but we are developing new, more powerful data mining tools. A selection of over 100 key bacterial genomes has been included in the pan-taxonomic Compara, and genes from all genomes have been classified into families using HAMAP and PANTHER (more details).

Citing Ensembl Genomes

If you've used Ensembl Genomes in your work, please cite the most recent overview article below and the Ensembl Genomes release you retrieved your data from (currently 35). References for the specific genome assembly can be found on the More information and statistics page for each species (e.g.Escherichia coli).

Kersey PJ, et al. Ensembl Genomes 2016: more genomes, more complexity. Nucleic Acids Res. 2016 Jan;44(D1) D574-80. doi:10.1093/nar/gkv1209. PMID: 26578574; PMCID: PMC4702859.

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. For information on how to cite Ensembl Genomes click here.