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Background  The broad ecological distribution of  L. casei  makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of  L. casei , we performed comparative analysis of 17  L .  casei  genomes representing strains collected from dairy, plant, and human sources.    Results  Differences in  L .  casei  genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220 accessory genes. Extrapolation of pan-genome data indicates  L .  casei  has a supragenome approximately 3.2 times larger than the average genome of individual strains. Evidence suggests horizontal gene transfer from other bacterial species, particularly lactobacilli, has been important in adaptation of  L .  casei  to new habitats and lifestyles, but evolution of dairy niche specialists also appears to involve gene decay.    Conclusions  Genome diversity in  L .  casei  has evolved through gene acquisition and decay. Acquisition of foreign genomic islands likely confers a fitness benefit in specific habitats, notably plant-associated niches. Loss of unnecessary ancestral traits in strains collected from bacterial-ripened cheeses supports the hypothesis that gene decay contributes to enhanced fitness in that niche. This study gives the first evidence for a  L .  casei  supragenome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible and industrially important lactic acid bacterium. Additionally, our data confirm the Distributed Genome Hypothesis extends to non-pathogenic, ecologically flexible species like  L .  casei .

Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation