INSDC members assign strain-level taxonomy IDs to microbes whose genomes are submitted to the INSDC. The INSDC is, however, going to stop assigning strain-level taxonomy ID in February, 2014, and BioSample IDs will be defined microbial genomes instead of strain-level taxonomy ID.
For more details, please refer to "Planned change in bacterial strain-level information management".
Assigning strain-level TaxID will be discontinued in February 2014. However, existing strain-level TaxIDs will remain, and we will continue to add informal strain-specific names for genomes from specimens that have not yet been identified to the species level.
If a genome assembly is derived from an unidentified/unpublished organism, species-level informal names will still be generated which use strain identifiers in form of "Genus sp. strain".
DDBJ Center will start to accept new BioSample submissions in February 2014. Submitters of genome sequences will be required to register sample metadata in the BioSample database for each organism that they are sequencing. The BioSample submission will include the strain information and other metadata, such as culture collection and isolation information, as appropriate.
Submitters of genome sequences are already required to register metadata about the research project in the BioProject database. We no longer require a one-to-one relationship between a BioProject accession and a genome. Instead, a research effort examining multiple strains of a species or multiple species of drug-resistant bacteria, for example, could be registered as a single BioProject.