Lactococcus lactis is a primary constituent of many starter cultures used for the manufacturing of fermented dairy products but the species also occurs in various non-dairy niches. The strains that are used in most scientific studies typically originate from dairy fermentations and three genome sequences of such model strains are publicly available (Bolotin et al., 2001; Makarova et al., 2006; Wegmann et al., 2007). In recent years there has been growing interest in isolates from non-dairy sources such as (fermented) plant material. Several reports have shown that these strains may have phenotypes of industrial interest, such as a unique flavour-forming potential (Van Hylckama Vlieg et al., 2006). We performed an extensive molecular and phenotypic diversity analysis on a highly diverse strain collection consisting of dairy and non-dairy strains. Two non-dairy isolates, strains KF147 and KF282, were chosen for further study and their genomes were sequenced to 3× coverage. Numerous genes were identified that do not have orthologs in the published genome sequences of dairy L. lactis strains. Adaptation to growth on substrates derived from plant cell walls is evident from the presence of gene sets for the uptake and conversion of complex polysaccharides and plant cell-wall degradation products. Comparative genome hybridisation with high-density multistrain DNA microarrays (nimblegen platform) allowed a high-resolution analysis of the genomic diversity within a collection of 40 strains from dairy and non-dairy origin. The results reveal the distribution of the L. lactis gene pool over strains and niches and illustrate the high genomic flexibility of the species. The impact on our view on metabolic diversity and evolutionary relationships within L. lactis as well as biotechnological implications will be discussed.

Exploring genomic diversity of Lactococcus lactis by comparative genome hybridisation with multistrain DNA microarrays.

FELIS, Giovanna;
2007-01-01

Abstract

Lactococcus lactis is a primary constituent of many starter cultures used for the manufacturing of fermented dairy products but the species also occurs in various non-dairy niches. The strains that are used in most scientific studies typically originate from dairy fermentations and three genome sequences of such model strains are publicly available (Bolotin et al., 2001; Makarova et al., 2006; Wegmann et al., 2007). In recent years there has been growing interest in isolates from non-dairy sources such as (fermented) plant material. Several reports have shown that these strains may have phenotypes of industrial interest, such as a unique flavour-forming potential (Van Hylckama Vlieg et al., 2006). We performed an extensive molecular and phenotypic diversity analysis on a highly diverse strain collection consisting of dairy and non-dairy strains. Two non-dairy isolates, strains KF147 and KF282, were chosen for further study and their genomes were sequenced to 3× coverage. Numerous genes were identified that do not have orthologs in the published genome sequences of dairy L. lactis strains. Adaptation to growth on substrates derived from plant cell walls is evident from the presence of gene sets for the uptake and conversion of complex polysaccharides and plant cell-wall degradation products. Comparative genome hybridisation with high-density multistrain DNA microarrays (nimblegen platform) allowed a high-resolution analysis of the genomic diversity within a collection of 40 strains from dairy and non-dairy origin. The results reveal the distribution of the L. lactis gene pool over strains and niches and illustrate the high genomic flexibility of the species. The impact on our view on metabolic diversity and evolutionary relationships within L. lactis as well as biotechnological implications will be discussed.
2007
Lactococcus lactis; Comparative Genomic hybridization; microarray; diversity
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11562/315992
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