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Background    Lactococcus lactis  is among the most widely studied lactic acid bacterial species due to its long history of safe use and economic importance to the dairy industry, where it is exploited as a starter culture in cheese production.    Results  In the current study, we report on the complete sequencing of 16  L. lactis  subsp.  lactis  and  L. lactis  subsp.  cremoris  genomes. The chromosomal features of these 16  L. lactis  strains in conjunction with 14 completely sequenced, publicly available lactococcal chromosomes were assessed with particular emphasis on discerning the  L. lactis  subspecies division, evolution and niche adaptation. The deduced pan-genome of  L. lactis  was found to be closed, indicating that the representative data sets employed for this analysis are sufficient to fully describe the genetic diversity of the taxon.    Conclusions  Niche adaptation appears to play a significant role in governing the genetic content of each  L. lactis  subspecies, while (differential) genome decay and redundancy in the dairy niche is also highlighted.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3650-5) contains supplementary material, which is available to authorized users.

Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation