Complete Genome Sequence of
            <i>Lactococcus lactis</i>
            subsp.
            <i>lactis</i>
            KF147, a Plant-Associated Lactic Acid Bacterium

Siezen, Roland J.; Bayjanov, Jumamurat R.; Renckens, Bernadet; Wels, Michiel; Hijum, Sacha A. F. T. van; Molenaar, Douwe; Vlieg, Johan E. T. van Hylckama

doi:10.1128/jb.00276-10

Cited by 101 publications

(102 citation statements)

References 9 publications

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“…cremoris (Makarova et al, 2006) and KF147 L. lactis ssp. lactis (Siezen et al, 2010) were subjected to orthology prediction using the orthoMCL algorithm V2.0.2 (Li et al, 2003). Orthologous groups (OGs) were subsequently used for core-and pan-genome analyses.…”

Section: Methodsmentioning

confidence: 99%

Multifactorial diversity sustains microbial community stability

et al. 2013

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Maintenance of a high degree of biodiversity in homogeneous environments is poorly understood. A complex cheese starter culture with a long history of use was characterized as a model system to study simple microbial communities. Eight distinct genetic lineages were identified, encompassing two species: Lactococcus lactis and Leuconostoc mesenteroides. The genetic lineages were found to be collections of strains with variable plasmid content and phage sensitivities. Kill-the-winner hypothesis explaining the suppression of the fittest strains by density-dependent phage predation was operational at the strain level. This prevents the eradication of entire genetic lineages from the community during propagation regimes (back-slopping), stabilizing the genetic heterogeneity in the starter culture against environmental uncertainty.

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Section: Methodsmentioning

confidence: 99%

Multifactorial diversity sustains microbial community stability

et al. 2013

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“…Sequence alignment against the reference genome of KF147 was performed with standard settings using the ELAND software package of the Illumina analysis pipeline. To increase the accuracy of Single Nucleotide Polymorphism (SNP) and INsertion/DELetion (INDEL) identification, the reference genome was also resequenced with the same technology and confirmed the sequence previously published for this strain (Siezen et al 2010). SNPs and INDELs were identified with an in-house Perl script by GATC-Biotech.…”

Section: Genotypic Characterizationmentioning

confidence: 99%

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution

Bachmann¹,

Starrenburg²,

Molenaar³

et al. 2011

Genome Res.

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149

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Experimental evolution is a powerful approach to unravel how selective forces shape microbial genotypes and phenotypes. To this date, the available examples focus on the adaptation to conditions specific to the laboratory. The lactic acid bacterium Lactococcus lactis naturally occurs on plants and in dairy environments, and it is proposed that dairy strains originate from the plant niche. Here we investigate the adaptation of a L. lactis strain isolated from a plant to a dairy niche by propagating it for 1000 generations in milk. Two out of three independently evolved strains displayed significantly increased acidification rates and biomass yields in milk. Genome resequencing, revealed six, seven, and 28 mutations in the three strains, including point mutations in loci related to amino acid biosynthesis and transport and in the gene encoding MutL, which is involved in DNA mismatch repair. Two strains lost a conjugative transposon containing genes important in the plant niche but dispensable in milk. A plasmid carrying an extracellular protease was introduced by transformation. Although improving growth rate and growth yield significantly, the plasmid was rapidly lost. Comparative transcriptome and phenotypic analyses confirmed that major physiological changes associated with improved growth in milk relate to nitrogen metabolism and the loss or down-regulation of several pathways involved in the utilization of complex plant polymers. Reproducing the transition from the plant to the dairy niche through experimental evolution revealed several genome, transcriptome, and phenotype signatures that resemble those seen in strains isolated from either niche.

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“…In addition, L. lactis contributes to the texture and formation of flavor in cheese, which are key determinants of the product's sensory quality (1,2). Next to these industrial food fermentation applications, L. lactis is frequently found in other environments, such as (decaying) plant material, especially when nutrients become available as a consequence of primary degradation of plant polymers by other microorganisms, including yeasts and fungi (3).…”

mentioning

confidence: 99%

Genome-Wide Transcriptional Responses to Carbon Starvation in Nongrowing Lactococcus lactis

Ercan

Wels

Smid

et al. 2015

Appl Environ Microbiol

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f This paper describes the transcriptional adaptations of nongrowing, retentostat cultures of Lactococcus lactis to starvation. Near-zero-growth cultures ( ‫؍‬ 0.0001 h ؊1 ) obtained by extended retentostat cultivation were exposed to starvation by termination of the medium supply for 24 h, followed by a recovery period of another 24 h by reinitiating the medium supply to the retentostat culture. During starvation, the viability of the culture was largely retained, and the expression of genes involved in transcription and translational machineries, cell division, and cell membrane energy metabolism was strongly repressed. Expression of these genes was largely recovered following the reinitiation of the medium supply. Starvation triggered the elevated expression of genes associated with synthesis of branched-chain amino acids, histidine, purine, and riboflavin. The expression of these biosynthesis genes was found to remain at an elevated level after reinitiation of the medium supply. In addition, starvation induced the complete gene set predicted to be involved in natural competence in L. lactis KF147, and the elevated expression of these genes was sustained during the subsequent recovery period, but our attempts to experimentally demonstrate natural transformation in these cells failed. Mining the starvation response gene set identified a conserved cis-acting element that resembles the lactococcal CodY motif in the upstream regions of genes associated with transcription and translational machineries, purine biosynthesis, and natural transformation in L. lactis, suggesting a role for CodY in the observed transcriptome adaptations to starvation in nongrowing cells.L actococcus lactis has a long history of use in the manufacturing of fermented foods. In particular, dairy starter cultures containing L. lactis are important for primary acidification of cheese milk. In addition, L. lactis contributes to the texture and formation of flavor in cheese, which are key determinants of the product's sensory quality (1, 2). Next to these industrial food fermentation applications, L. lactis is frequently found in other environments, such as (decaying) plant material, especially when nutrients become available as a consequence of primary degradation of plant polymers by other microorganisms, including yeasts and fungi (3).In nature, microbial populations mostly live in nutrient-limiting conditions due to low carbon and energy source availability (4). Under these environmental conditions, microbes either develop adaptive responses to high-affinity substrate acquisition or scavenge the ecosystem for alternative nutrients, resulting in a survival advantage (5). Similarly, in industrial fermentation applications, microbes may encounter restricted access to carbon sources for longer periods of time. For example, lactic acid bacteria (LAB) encounter long periods of low or no carbon availability during the ripening of dried sausages (6) and cheese (1), but they are able to survive under these conditions during months of ripening (6,7,...

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Complete Genome Sequence of Lactococcus lactis subsp. lactis KF147, a Plant-Associated Lactic Acid Bacterium

Cited by 101 publications

References 9 publications

Multifactorial diversity sustains microbial community stability

Multifactorial diversity sustains microbial community stability

Microbial domestication signatures of Lactococcus lactis can be reproduced by experimental evolution

Genome-Wide Transcriptional Responses to Carbon Starvation in Nongrowing Lactococcus lactis

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