A genome is a related collection of DNA. In most cases, a genome represents the DNA for a single sequenced strain of a particular organism; however, metagenomes? and environmental samples contain DNA for multiple organisms, and these can be stored in the SproutDatabase as genomes.

A genome is identified by a Genome ID that consists of an NCBI organism number followed by a version number. So, for example, the 1313 in the genome ID 1313.4 indicates Streptococcus pneumoniae and the 4 indicates the INV200 strain. Genome ID 1313.5, which differs only in the version number, is the OXC141 strain. On occasion, a new version of a genome will be put into the system that represents a more accurate sequencing of an existing strain. When this happens, the new version replaces the old one, and a record is made of the fact that the old genome has a new ID.