Search for a gene
Search for a genome
e.g. type esc to find Escherichia
- Search for a gene - type the name of a gene or other identifier into the search box above
- Find a genome - click in the 'browse a genome' box above and start typing your genome name to find matching genomes
- View full list of all Ensembl Bacteria species
- Access Ensembl Bacteria programmatically
What's New in Release 62
Did you know...?
To access Ensembl Genomes data from any programming language, try our REST service. For full documentation, including examples from a wide range of languages, visit http://rest.ensembl.org
In June 2023, Ensembl Bacteria released new gene predictions for almost all of the genomes it hosts. This was done in collaboration with the EMBL-EBI metagenomics team and utlised a pipeline using Prokka, combined with results from cmscan, EggNOG and InterProScan. We have retained the community-submitted annotation for 115 species that are in our pan-taxonomic comparative analysis.
Genomes
- A total of 31,332 non-redundant bacterial and archaeal genomes
Data
- Updated annotation of molecular interactions involving bacterial genes
- Updated protein features for all species using InterProScan
- Updated pan-taxonomic compara (which includes key bacterial species)
The New Ensembl Site
The new Ensembl provides access to over 4700 genomes: http://beta.ensembl.org
There are over 4100 animal, 470 plant, and 100 fungal genomes ready to explore. We provide pangenomes for many species including human (565 haplotypes), barley (69 cultivars), and pig (27 breeds).
Genomes from projects such as Darwin Tree of Life, the Human Pangenome Reference Consortium, the Vertebrate Genomes Project and the European Reference Genome Atlas are regularly added.
We are in the process of migrating our existing prokaryotic genomes, with a target of moving all ~36,000 by July 2026. Prokaryotic releases will be phased, with batches migrating from Feb 2026 onwards.
From the summer of 2026, all new data will only be available through this new Ensembl site. Important info for programmatic access is available on this blog.
Archive sites
The following archive sites are available to access previous versions of data: - Release 59, May 2024 eg59-bacteria.ensembl.org - Release 56, February 2023 eg56-bacteria.ensembl.org - Release 52, December 2021 eg52-bacteria.ensembl.org - Release 49, December 2020 eg49-bacteria.ensembl.org
Ensembl Bacteria
Ensembl Bacteria is a browser for bacterial and archaeal genomes. The assemblies for these are taken from the databases of the International Nucleotide Sequence Database Collaboration, the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan).
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. A selection of over 100 key bacterial genomes have been included in the pan-taxonomic compara, and genes from all genomes have been classified into families using HAMAP and PANTHER more details.
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.
Ensembl Bacteria release 62 - September 2025 © EMBL-EBI EMBL-EBI
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