title: Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action.
abstract: BACKGROUND
  Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus are lactic acid producing bacteria that are largely used in dairy industries, notably in cheese-making and yogurt production. An earlier in-depth study of the first completely sequenced ssp. bulgaricus genome revealed the characteristics of a genome in an active phase of rapid evolution, in what appears to be an adaptation to the milk environment. Here we examine for the first time if the same conclusions apply to the ssp. lactis, and discuss intra- and inter-subspecies genomic diversity in the context of evolutionary adaptation.
  
  
  RESULTS
  Both L. delbrueckii ssp. show the signs of reductive evolution through the elimination of superfluous genes, thereby limiting their carbohydrate metabolic capacities and amino acid biosynthesis potential. In the ssp. lactis this reductive evolution has gone less far than in the ssp. bulgaricus. Consequently, the ssp. lactis retained more extended carbohydrate metabolizing capabilities than the ssp. bulgaricus but, due to high intra-subspecies diversity, very few carbohydrate substrates, if any, allow a reliable distinction of the two ssp. We further show that one of the most important traits, lactose fermentation, of one of the economically most important dairy bacteria, L. delbruecki ssp. bulgaricus, relies on horizontally acquired rather than deep ancestral genes. In this sense this bacterium may thus be regarded as a natural GMO avant la lettre.
  
  
  CONCLUSIONS
  The dairy lactic acid producing bacteria L. delbrueckii ssp. lactis and ssp. bulgaricus appear to represent different points on the same evolutionary track of adaptation to the milk environment through the loss of superfluous functions and the acquisition of functions that allow an optimized utilization of milk resources, where the ssp. bulgaricus has progressed further away from the common ancestor.
authors.forename: Hela
authors.initials: H
authors.lastname: El Kafsi
authors.forename: Johan
authors.initials: J
authors.lastname: Binesse
authors.forename: Valentin
authors.initials: V
authors.lastname: Loux
authors.forename: Julien
authors.initials: J
authors.lastname: Buratti
authors.forename: Samira
authors.initials: S
authors.lastname: Boudebbouze
authors.forename: Rozenn
authors.initials: R
authors.lastname: Dervyn
authors.forename: Sean
authors.initials: S
authors.lastname: Kennedy
authors.forename: Nathalie
authors.initials: N
authors.lastname: Galleron
authors.forename: Benoît
authors.initials: B
authors.lastname: Quinquis
authors.forename: Jean-Michel
authors.initials: JM
authors.lastname: Batto
authors.forename: Bouziane
authors.initials: B
authors.lastname: Moumen
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Maguin
authors.affiliation: INRA, UMR1319 Micalis, Jouy en Josas, France. maarten.vandeguchte@jouy.inra.fr.
authors.forename: Maarten
authors.initials: M
authors.lastname: van de Guchte
mesh_terms: D000596:Amino Acids / Q000096:biosynthesis; D001426:Bacterial Proteins / Q000235:genetics; D050260:Carbohydrate Metabolism; D019143:Evolution, Molecular; D005285:Fermentation; D022761:Gene Transfer, Horizontal; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D048668:Lactobacillus delbrueckii / Q000235:genetics*; D058885:Multilocus Sequence Typing; D020543:Proteome / Q000235:genetics; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins; D020543:Proteome; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S