Dataset Information

Draft genome sequence of Lactococcus lactis subsp. lactis RTIII518: a potent dairy starter isolated from traditional lait caille in Burkina Faso.

ABSTRACT: Lactococcus lactis subsp. lactis RTIII518 was isolated from lait caillé, a traditional fermented milk product from Burkina Faso. The draft genome size is 25,554,260 base pairs with 76 contigs, 34.26% average content of GC, 50 tRNAs, 4 rRNA, and 2,498 coding genes.

SUBMITTER: Bayili GR

PROVIDER: S-EPMC10793282 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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Draft genome sequence of Lactococcus lactis subsp. lactis RTIII518: a potent dairy starter isolated from traditional lait caillé in Burkina Faso.

Bayili Geoffroy Romaric GR Diaz Maria M Parkouda Charles C Sawadogo-Lingani Hagrétou H

Microbiology resource announcements 20231204 1

Lactococcus lactis subsp. lactis RTIII518 was isolated from lait caillé, a traditional fermented milk product from Burkina Faso. The draft genome size is 25,554,260 base pairs with 76 contigs, 34.26% average content of GC, 50 tRNAs, 4 rRNA, and 2,498 coding genes. ...[more]

PMID: 38047684

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Project description:Twenty Lactococcus lactis strains with an L. lactis subsp. lactis phenotype isolated from five traditional cheeses made of raw milk with no added starters belonging to the L. lactis subsp. lactis and L. lactis subsp. cremoris genotypes (lactis and cremoris genotypes, respectively; 10 strains each) were subjected to a series of phenotypic and genetic typing methods, with the aims of determining their phylogenetic relationships and suitability as starters. Pulsed-field gel electrophoresis (PFGE) analysis of intact genomes digested with SalI and SmaI proved that all strains were different except for three isolates of the cremoris genotype, which showed identical PFGE profiles. Multilocus sequence typing (MLST) analysis using internal sequences of seven loci (namely, atpA, rpoA, pheS, pepN, bcaT, pepX, and 16S rRNA gene) revealed considerable intergenotype nucleotide polymorphism, although deduced amino acid changes were scarce. Analysis of the MLST data for the present strains and others from other dairy and nondairy sources showed that all of them clustered into the cremoris or lactis genotype group, by using both independent and combined gene sequences. These two groups of strains also showed distinctive carbohydrate fermentation and enzyme activity profiles, with the strains in the cremoris group showing broader profiles. However, the profiles of resistance/susceptibility to 16 antibiotics were very similar, showing no atypical resistance, except for tetracycline resistance in three identical cremoris genotype isolates. The numbers and concentrations of volatile compounds produced in milk by the strains belonging to these two groups were clearly different, with the cremoris genotype strains producing higher concentrations of more branched-chain, derived compounds. Together, the present results support the idea that the lactis and cremoris genotypes of phenotypic Lactococcus lactis subsp. lactis actually represent true subspecies. Some strains of the two subspecies in this study appear to be good starter candidates.

Project description:BackgroundImportant industrial traits have been linked to plasmids in Lactococcus lactis.ResultsThe dairy isolate L. lactis subsp. lactis biovar diacetylactis FM03P was sequenced revealing the biggest plasmidome of all completely sequenced and published L. lactis strains up till now. The 12 plasmids that were identified are: pLd1 (8277 bp), pLd2 (15,218 bp), pLd3 (4242 bp), pLd4 (12,005 bp), pLd5 (7521 bp), pLd6 (3363 bp), pLd7 (30,274 bp), pLd8 (47,015 bp), pLd9 (15,313 bp), pLd10 (39,563 bp), pLd11 (9833 bp) and pLd12 (3321 bp). Structural analysis of the repB promoters and the RepB proteins showed that eleven of the plasmids replicate via the theta-type mechanism, while only plasmid pLd3 replicates via a rolling-circle replication mechanism. Plasmids pLd2, pLd7 and pLd10 contain a highly similar operon involved in mobilisation of the plasmids. Examination of the twelve plasmids of L. lactis FM03P showed that 10 of the plasmids carry putative genes known to be important for growth and survival in the dairy environment. These genes encode technological functions such as lactose utilisation (lacR-lacABCDFEGX), citrate uptake (citQRP), peptide degradation (pepO and pepE) and oligopeptide uptake (oppDFBCA), uptake of magnesium and manganese (2 mntH, corA), exopolysaccharides production (eps operon), bacteriophage resistance (1 hsdM, 1 hsdR and 7 different hsdS genes of a type I restriction-modification system, an operon of three genes encoding a putative type II restriction-modification system and an abortive infection gene) and stress resistance (2 uspA, cspC and cadCA). Acquisition of these plasmids most likely facilitated the adaptation of the recipient strain to the dairy environment. Some plasmids were already lost during a single propagation step signifying their instability in the absence of a selective pressure.ConclusionsLactococcus lactis FM03P carries 12 plasmids important for its adaptation to the dairy environment. Some of the plasmids were easily lost demonstrating that propagation outside the dairy environment should be minimised when studying dairy isolates of L. lactis.

Dataset Information

Draft genome sequence of Lactococcus lactis subsp. lactis RTIII518: a potent dairy starter isolated from traditional lait caille in Burkina Faso.

Publications

Draft genome sequence of <i>Lactococcus lactis</i> subsp. <i>lactis</i> RTIII518: a potent dairy starter isolated from traditional <i>lait caillé</i> in Burkina Faso.

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