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Open Access Research article

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

Hela El Kafsi12, Johan Binesse12, Valentin Loux3, Julien Buratti3, Samira Boudebbouze12, Rozenn Dervyn12, Sean Kennedy124, Nathalie Galleron124, Benoît Quinquis124, Jean-Michel Batto12, Bouziane Moumen12, Emmanuelle Maguin12 and Maarten van de Guchte12*

Author Affiliations

1 INRA, UMR1319 Micalis, Jouy en Josas, France

2 AgroParisTech, UMR Micalis, Jouy en Josas, France

3 INRA, UR1077 Mathématique Informatique et Génome, Jouy en Josas, France

4 Present address: INRA, US1367 Metagenopolis, Jouy en Josas, France

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BMC Genomics 2014, 15:407  doi:10.1186/1471-2164-15-407

Published: 28 May 2014

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.

Keywords:
Lactobacillus delbrueckii; Bulgaricus; Lactis; Genome; Comparative genomics; Adaptation; Evolution