Comparative Genome Analysis of Lactococcus lactis Indicates Niche Adaptation and Resolves Genotype/Phenotype Disparity

Abstract

Lactococcus lactis is one of the most important micro-organisms in the dairy industry for the fermentation of cheese and buttermilk. Besides the conversion of lactose to lactate it is responsible for product properties such as flavor and texture, which are determined by volatile metabolites, proteolytic activity and exopolysaccharide production. While the species Lactococcus lactis consists of the two subspecies lactis and cremoris their taxonomic position is confused by a group of strains that, despite of a cremoris genotype, display a lactis phenotype. Here we compared and analyzed the (draft) genomes of 43 L. lactis strains, of which 19 are of dairy and 24 are of non-dairy origin. Machine-learning algorithms facilitated the identification of orthologous groups of protein sequences (OGs) that are predictors for either the taxonomic position or the source of isolation. This allowed the unambiguous categorization of the genotype/phenotype disparity of ssp. lactis and ssp. cremoris strains. A detailed analysis of phenotypic properties including plasmid-encoded genes indicates evolutionary changes during niche adaptations. The results are consistent with the hypothesis that dairy isolates evolved from plant isolates. The analysis further suggests that genomes of cremoris phenotype strains are so eroded that they are restricted to a dairy environment. Overall the genome comparison of a diverse set of strains allowed the identification of niche and subspecies specific genes. This explains evolutionary relationships and will aid the identification and selection of industrial starter cultures.

Abundance, diversity and plant‐specific adaptations of plant‐associated lactic acid bacteria

“…To this regard, all 74 isolates of Streptococcus thermophilus from vegetable, fodder crop and flowering plant sources were able to produce EPS (Umamaheswari et al ., ). Additionally, although numerous strains of L. lactis contain chromosomal gene clusters for cell wall polysaccharide biosynthesis, only one gene cluster ( epsXABCDEFGHIJKL ) has been found exclusively in plant‐associated L. lactis isolates (Wels et al ., ).…”

“…heat shock proteins, chaperonins, USP proteins) as compared to when that strain was incubated in standard laboratory culture medium (Filannino et al ., ). Lastly, the analysis of whole genomes from 44 strains of L. lactis found that plant‐associated strains cluster separately from dairy‐associated strains (Wels et al ., ). Lactococcus lactis isolates from plants were found to have fewer amino acid requirements necessary for growth relative to L. lactis isolated from other sources (Ayad et al ., ).…”

Precise Populations’ Description in Dairy Ecosystems Using Digital Droplet PCR: The Case of L. lactis Group in Starters

“…As reported in the literature, the large metabolic capabilities of the lactis species, particularly in carbohydrate metabolism, may promote faster growth rate than the cremoris species (Kelleher et al, 2017). However, as lactose is the main carbohydrate in milk, this dairy environment is very well adapted to the cremoris species strains which have the necessary ability to break down this sugar (Wels et al, 2019). Moreover, several studies have shown that strains of the lactis species initially produce acid slowly (Herreros et al, 2003;Fusieger et al, 2020) and that, conversely, strains of the cremoris species usually produce better acidification than lactis species, both at the beginning and at the end of the fermentation (Nomura et al, 2006;Fernández et al, 2011).…”

“…The use of this new denomination is now well admitted. In the lactis group, both species are associated with well described growth characteristics (Wels et al, 2019). However, cremoris species have different phenotypes (Cavanagh et al, 2015a), with strains identified as "true" cremoris, and strains showing a Lactis phenotype (growth at 40 • C, in the presence of 4% NaCl and pH 9.2, and the ability to degrade arginine).…”

Onward and [K + ]Upward: a New Potassium Importer under the Spell of Cyclic di-AMP

“…cremoris strains are also osmoresistant (27). Recent analyses using genotype-phenotype matching approaches with 43 L. lactis genomes have been unable to a identify specific gene(s), based on a presence/absence analysis, that is responsible for differences in osmoresistance between strains (28).…”