Genome‐scale diversity and niche adaptation analysis of Lactococcus lactis by comparative genome hybridization using multi‐strain arrays

Abstract

SummaryLactococcus lactis produces lactic acid and is widely used in the manufacturing of various fermented dairy products. However, the species is also frequently isolated from non‐dairy niches, such as fermented plant material. Recently, these non‐dairy strains have gained increasing interest, as they have been described to possess flavour‐forming activities that are rarely found in dairy isolates and have diverse metabolic properties. We performed an extensive whole‐genome diversity analysis on 39 L. lactis strains, isolated from dairy and plant sources. Comparative genome hybridization analysis with multi‐strain microarrays was used to assess presence or absence of genes and gene clusters in these strains, relative to all L. lactis sequences in public databases, whereby chromosomal and plasmid‐encoded genes were computationally analysed separately. Nearly 3900 chromosomal orthologous groups (chrOGs) were defined on basis of four sequenced chromosomes of L. lactis strains (IL1403, KF147, SK11, MG1363). Of these, 1268 chrOGs are present in at least 35 strains and represent the presently known core genome of L. lactis, and 72 chrOGs appear to be unique for L. lactis. Nearly 600 and 400 chrOGs were found to be specific for either the subspecies lactis or subspecies cremoris respectively. Strain variability was found in presence or absence of gene clusters related to growth on plant substrates, such as genes involved in the consumption of arabinose, xylan, α‐galactosides and galacturonate. Further niche‐specific differences were found in gene clusters for exopolysaccharides biosynthesis, stress response (iron transport, osmotolerance) and bacterial defence mechanisms (nisin biosynthesis). Strain variability of functions encoded on known plasmids included proteolysis, lactose fermentation, citrate uptake, metal ion resistance and exopolysaccharides biosynthesis. The present study supports the view of L. lactis as a species with a very flexible genome.

Lactococcus lactis Metabolism and Gene Expression during Growth on Plant Tissues

“…Genes for arabinose degradation were induced on average 7.6-fold during KF147 growth in ATL compared to GM17 (see Table S2). Notably, the capacity for arabinose metabolism is not found in dairy lactococci, including strain IL1403 (15). Finally, ribose uptake (rbsABC) and metabolism (rbsD and rbsK) genes were also induced 2.7-fold on average (see Table S2).…”

“…Although such "experimental evolution" experiments were not the purpose of the study here, it is intriguing to consider the possible genetic and physiological outcomes of growth of the dairy-originating L. lactis strains on plant tissues over many generations. It seems unlikely that significant increases in growth rate and yield would be achieved by dairy-associated strains because of the variety of unique genes found among plantassociated L. lactis strains that are relevant for adaptation and growth on plant tissues (15). This possibility is supported by the current understanding that L. lactis originated on plants and was domesticated for growth in milk through reductive evolution and horizontal gene transfer (15).…”

“…It seems unlikely that significant increases in growth rate and yield would be achieved by dairy-associated strains because of the variety of unique genes found among plantassociated L. lactis strains that are relevant for adaptation and growth on plant tissues (15). This possibility is supported by the current understanding that L. lactis originated on plants and was domesticated for growth in milk through reductive evolution and horizontal gene transfer (15). ⌬xylA mutant were inoculated into XM17.…”

“…In this regard, genes coding for arabinose, D-galacturonate, and D-glucuronate transporters and degradative enzymes were induced during L. lactis KF147 growth in ATL. KF147 is the only sequenced Lactococcus strain to possess genes annotated for D-galacturonate catabolism, although other plant-isolated lactococci have also been demonstrated to consume this compound (15). Similarly strain KF147, and not the dairyassociated strains L. lactis subsp.…”

“…Comparative genomics studies indicate that the L. lactis species originated in association with plants, and through anthropogenic forces, members of this species adapted to the dairy niche (14,15). Compared to their dairy-isolated counterparts, L. lactis isolates collected from plants have a greater genetic potential as reflected by traits such as the capacity to consume a broader array of carbohydrates, especially those derived from plants, increased biosynthetic capacity for nonribosomal peptides and polyketides, and fewer amino acid auxotrophies (15,16). The transition to the experiments in triplicate into 5 ml of either GM17 or ATL at a cell density of 10 5 CFU/ml.…”