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

Abstract

BackgroundLactobacillus 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.ResultsBoth 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-407) contains supplementary material, which is available to authorized users.

Unprecedented large inverted repeats at the replication terminus of circular bacterial chromosomes suggest a novel mode of chromosome rescue

“…Another possibility is that fold-back DNA synthesis served to generate homologous ends at either side of the break to allow repair by homologous recombination, the principal route of DSB repair in bacteria29. The abundant IS elements in the L. delbrueckii genome45 may have played a role in this process, although no traces of their involvement could be found (anymore) in the present genomes.…”

Determination of the essential nutrients required for milk fermentation by Lactobacillus plantarum

“…For example, Lactobacillus delbrueckii ssp. bulgaricus has lost the majority of amino acid biosynthetic capacities (El Kafsi et al, 2014). Lactobacillus helveticus DPC 4571 and Lactobacillus casei ATCC334 are auxotrophic for sixteen amino acids and three branched-chain amino acids, respectively (Cai, Thompson, Budinich, Broadbent, & Steele, 2009;Callanan et al, 2008).…”

Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats

“…Several studies have depicted the genetic diversity of L. plantarum strains through different phenotypic (Cai et al, 2009;Siezen et al, 2010) and genotypic approaches, such as AFLP, RAPD Torriani et al, 2001;Kleerebezem et al, 2003;Oh et al, 2010;Siezen et al, 2010;Frese et al, 2011;Sun et al, 2015), multi-locus sequence typing (MLST) de Las Rivas et al, 2005;Makarova et al, 2006;Smokvina et al, 2013;Kafsi et al, 2014;Sun et al, 2015), and microarray-based comparative genome hybridization (CGH) (Torriani et al, 2001;Molenaar et al, 2005;Siezen et al, 2010). These approaches allowed the differentiation of L. plantarum at both inter-and intra-species level and investigated a potential link between genome and niche adaptation or fitness (de Las Rivas et al, 2005;Molenaar et al, 2005;De Vuyst et al, 2009;Siezen et al, 2010;Frese et al, 2011;Dutilh et al, 2013;Smokvina et al, 2013).…”