Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action

• Published in: BMC genomics Vol. 15; no. 1; p. 407
• Main Authors: El Kafsi, Hela, Binesse, Johan, Loux, Valentin, Buratti, Julien, Boudebbouze, Samira, Dervyn, Rozenn, Kennedy, Sean, Galleron, Nathalie, Quinquis, Benoît, Batto, Jean-Michel, Moumen, Bouziane, Maguin, Emmanuelle, van de Guchte, Maarten
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 28.05.2014; BioMed Central
• Subjects: Amino acids; Amino Acids - biosynthesis; Bacterial Proteins - genetics; Biochemistry, Molecular Biology; Carbohydrate Metabolism; Carbohydrates; Evolution, Molecular; Fermentation; Gene Transfer, Horizontal; Genes; Genes, Bacterial; Genetic aspects; Genome, Bacterial; Genomes; Genomics; Lactobacillus delbrueckii; Lactobacillus delbrueckii - genetics; Life Sciences; Milk; Multilocus Sequence Typing; Phylogenetics; Physiological aspects; Proteins; Proteome - genetics; RNA, Bacterial - genetics; RNA, Ribosomal, 16S - genetics; Sequence Analysis, DNA; lactis; bulgaricus; Comparative genomics; Evolution; Lactobacillus delbrueckii; Genome; Adaptation
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/1471-2164-15-407

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. 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. 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.