title: Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation.
abstract: 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.
authors.affiliation: Department of Nutrition, Dietetics, and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT 84322-8700, USA. jeff.broadbent@usu.edu
authors.forename: Jeff R
authors.initials: JR
authors.lastname: Broadbent
authors.forename: Eric C
authors.initials: EC
authors.lastname: Neeno-Eckwall
authors.forename: Buffy
authors.initials: B
authors.lastname: Stahl
authors.forename: Kanokwan
authors.initials: K
authors.lastname: Tandee
authors.forename: Hui
authors.initials: H
authors.lastname: Cai
authors.forename: Wesley
authors.initials: W
authors.lastname: Morovic
authors.forename: Philippe
authors.initials: P
authors.lastname: Horvath
authors.forename: Jessie
authors.initials: J
authors.lastname: Heidenreich
authors.forename: Nicole T
authors.initials: NT
authors.lastname: Perna
authors.forename: Rodolphe
authors.initials: R
authors.lastname: Barrangou
authors.forename: James L
authors.initials: JL
authors.lastname: Steele
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D005075:Biological Evolution; D016000:Cluster Analysis; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D044404:Genomic Islands; D007780:Lacticaseibacillus casei / Q000235:genetics*; D010802:Phylogeny