Draft Genome Sequences of 11 Lactococcus lactis subsp.
            <i>cremoris</i>
            Strains

Wels, Michiel; Backus, Lennart; Boekhorst, Jos; Dijkstra, Annereinou; Beerthuyzen, Marke M.; Siezen, Roland J.; Bachmann, Herwig; Hijum, Sacha A. F. T. van

doi:10.1128/genomea.01739-16

Cited by 5 publications

(6 citation statements)

References 13 publications

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“…The strains were mainly isolated from either a dairy environment or plant material with the exception of one isolate each from human, leafhopper, soil and sink drain water. The draft genomes of 34 strains were recently described (Backus et al, 2017; Wels et al, 2017) while complete genome sequences are available for the other strains.…”

Section: Resultsmentioning

confidence: 99%

“…This can only be overcome by using genome sequencing data. The draft genomes of the L. lactis strains used by Siezen et al (2011) were recently sequenced (Backus et al, 2017; Wels et al, 2017) and here we analyzed and compared these strains plus several publicly available fully sequenced L. lactis genomes. We used machine-learning algorithms (Bayjanov et al, 2013) to identify orthologous groups of protein sequences (OGs) that are predictors for either the taxonomic position or the source of isolation.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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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.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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“…Subsequently, the identified KF147 competence protein sequences were used as a reference 83 set for identification and comparison to the orthologous groups (OGs) of genes encoded by 42 other 84 L. lactis strains (20,21,(25)(26)(27)(28)(29)(30)(31)(32)(33)(34). Full length protein sequence identity relative to the KF147 OGs was 85 calculated for all 42 L. lactis strains ( Fig.…”

Section: Genomic Analyses Show Complete Sets Of Competence Genes In Smentioning

confidence: 99%

“…Such an approach has been 60 successful in S. thermophilus (24), but failed in L. lactis IL1403 (19). Nevertheless, the observation 61 that complete sets of late competence genes are apparently present in some of the L. lactis genomes 62 (25,26) and that their expression can be induced under specific conditions (22,23), deserves a more 63 dedicated bioinformatic and experimental effort. 64…”

Section: Introduction 27mentioning

confidence: 99%

“…The strains used in this study can be found in Table S1. The 295 publicly available draft genome sequences of 43 L. lactis strains (20,21,(25)(26)(27)(28)(29)(30)(31)(32)(33)(34) were used for 296 comparative genomics of late competence genes, by employing OrthoMCL to obtain orthologous 297 group (OG) sequences in order to construct an orthologous gene matrix (61,Wels et al,manuscript 298 in preparation). L. lactis strains were routinely cultivated in M17 (Tritium, Eindhoven, the 299 Netherlands) supplemented with 1 % (w/v) glucose (Tritium, Eindhoven, the Netherlands), at 30 °C 300 without agitation.…”

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Unleashing natural competence inLactococcus lactisby induction of the competence regulator ComX

Mulder

Wels

Kuipers

et al. 2017

Preprint

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In biotechnological work horses like Streptococcus thermophilus and Bacillus subtilis natural competence can be induced, which facilitates genetic manipulation of these microbes. However, in strains of the important dairy starter Lactococcus lactis natural competence has not been established to date. However, in silico analysis of complete genome sequences of 43 L. lactis strains revealed complete late-competence gene-sets in 2 L. lactis subspecies cremoris strains (KW2 and KW10) and 8 L. lactis subspecies lactis strains, including the model strain IL1403 and the plant-derived strain KF147. The remainder of the strains, including all dairy isolates, displayed genomic decay in one or more of the late competence genes. Nisin-controlled expression of the competence regulator comX in L. lactis subsp. lactis KF147 resulted in the induction of expression of the canonical competence regulon, and elicited a state of natural competence in this strain. By contrast, comX expression in L. lactis NZ9000, predicted to encode an incomplete competence gene-set, failed to induce natural competence. Moreover, mutagenesis of the comEA-EC operon in strain KF147, abolished the comX driven natural competence, underpinning the involvement of the competence machinery. Finally, introduction of nisin-inducible comX expression into nisRK-harboring derivatives of strains IL1403 and KW2 allowed the induction of natural competence also in these strains, expanding this phenotype to other L. lactis strains of both subspecies.Significance statementSpecific bacterial species are able to enter a state of natural competence in which DNA is taken up from the environment, allowing the introduction of novel traits. Strains of the species Lactococcus lactis are very important starter cultures for the fermentation of milk in the cheese production process, where these bacteria contribute to the flavor and texture of the end-product. The activation of natural competence in this industrially relevant organism can accelerate research aiming to understand industrially relevant traits of these bacteria, and can facilitate engineering strategies to harness the natural biodiversity of the species in optimized starter strains.

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A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota

Ederveen

Smits

Hajo

et al. 2019

Sci Rep

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We present TaxPhlAn, a new method and bioinformatics pipeline for design and analysis of single-locus sequence typing (SLST) markers to type and profile bacteria beyond the species-level in a complex microbial community background. TaxPhlAn can be applied to any group of phylogenetically-related bacteria, provided reference genomes are available. As TaxPhlAn requires the SLST targets identified to fit the phylogenetic pattern as determined through comprehensive evolutionary reconstruction of input genomes, TaxPhlAn allows for the identification and phylogenetic inference of new biodiversity. Here, we present a clinically relevant case study of high-resolution Staphylococcus profiling on skin of atopic dermatitis (AD) patients. We demonstrate that SLST enables profiling of cutaneous Staphylococcus members at (sub)species level and provides higher resolution than current 16S-based techniques. With the higher discriminative ability provided by our approach, we further show that the presence of Staphylococcus capitis on the skin together with Staphylococcus aureus associates with AD disease.

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Draft Genome Sequences of 11 Lactococcus lactis subsp. cremoris Strains

Abstract: The lactic acid bacterium Lactococcus lactis is widely used for the fermentation of dairy products. Here, we present the draft genome sequences of 11 L. lactis subsp. cremoris strains isolated from different environments.

Cited by 5 publications

References 13 publications

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

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

Unleashing natural competence inLactococcus lactisby induction of the competence regulator ComX

A generic workflow for Single Locus Sequence Typing (SLST) design and subspecies characterization of microbiota

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