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.

Figure 1

Genome atlas of L. delbrueckii ssp. lactis CNRZ327. The ten circles (outer to inner) show: Circles 1 and 2, CDS (excluding pseudogenes and transposases) on positive (red) or negative (blue) strand; Circle 3, transposases of the IS30 family (yellow); Circle 4, transposases of the IS256 family (green); Circle 5, transposases of the ISL3 family (orange); Circle 6, transposases of the IS110 family (red); Circle 7, transposases of the IS3 family (blue); Circle 8, transposases of the IS4 family (purple); Circle 9, transposases of ISL30 family (black) Circle 10, transposases of unkown family (grey).

Figure 2

Core proteomes of L. delbrueckii ssp. lactis and ssp. bulgaricus . Ovals represent the core proteomes of L. delbrueckii ssp. lactis and L. delbrueckii ssp. bulgaricus. The overall core of the 5 ssp. lactis and the 5 ssp. bulgaricus strains in this study consists of 989 proteins. A, 65 proteins are present in all ssp. lactis strains and absent from all 5 ssp. bulgaricus strains; B, 104 proteins are present in all ssp. lactis strains and absent from 1 to 4 ssp. bulgaricus strains; C, 25 proteins are present in all ssp. bulgaricus strains and absent from all 5 ssp. lactis strains; D, 112 proteins are present in all ssp. bulgaricus strains and absent from 1 to 4 ssp. lactis strains.

Figure 3

Metabolic capacities of L. delbrueckii ssp. lactis CNRZ327 and L. delbrueckii ssp. bulgaricus ATCC 11842. Metabolic pathway analysis was performed using KEGG [12, 13]. Graphs were generated using ipath [14]. A, L. delbrueckii ssp. lactis CNRZ327; B, L. delbrueckii ssp. bulgaricus ATCC 11842; red, enzyme functions identified in the respective genomes; highlighted in blue, carbohydrate metabolism pathways; highlighted in green, amino acid biosynthesis pathways.

Figure 4

Lactose transport and metabolism pathways in L. delbrueckii and its ancestors. In L. delbrueckii ssp. bulgaricus, lactose uptake relies on a lactose-galactose antiporter which has been acquired by horizontal gene transfer while the ancestral lactose PTS system has been lost. L. delbrueckii ssp. lactis contains both transport systems. In L. delbrueckii ssp. bulgaricus, lactose metabolism relies on a β-galactosidase which has been acquired by horizontal gene transfer while the ancestral β-galactosidases have been lost. L. delbrueckii ssp. lactis contains the same horizontally acquired β-galactosidase and, in addition, the pathways to completely metabolize lactose-6-P generated by the lactose PTS-system. PEP, phosphoenolpyruvate; Pyr, pyruvate.