Intra-species variations of Lactobacillus sakei
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This project launched in 2007 is a survey of intraspecies genomic variations of the meat born lactic acid bacterium Lactobacillus sakei, through studies of variable chromosomal loops and plasmids genetic repertoire. We aim at understanding the relationship between the genomic biodiversity of the L. sakei species with the bacterium’s adaptation to meat food products and to assess its potential role in fresh meat biopreservation. The figure on the right displays the relationship between the major genotypic clusters of L. sakei strains. This project involves three laboratories and two institutes:
If you wish to collaborate to this project, please contact Stéphane Chaillou |
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INRA Unité de Flore Lactique Environnement Carné (FLEC)
Description of the project:
Lactobacillus sakei strains display a large genomic diversity with more than 25% variation in genome size between isolates, ranging from 1,815 kb to 2,310 kb. Ten different genotypic clusters can be identified within the species and they show noticeable differences in their average genome size reflecting the natural population structure (Chaillou et al., 2009. Appl. Environ. Microbiol. 75: 970-980). Furthermore, most L. sakei isolates harbor several plasmid population (our unpublished data). The L. sakei intra-species diversity project (as described in the figure below) is aiming at the identification of the intraspecies gene pool variations (estimated to be around ~800-1,000 genes). The project can be divided in several parts. The first consisting of a 454 sequencing of individual plasmids isolated from the species repertoire ; The second is based on Sanger sequencing of strain-specific DNA obtained after genomic subtraction of a collection of strains (at least 10) selected from our biodiversity analysis and representing several individuals within the major genomic lineages of the species. A combination of several methods are planned in such a way that this project is to be considered as a whole shotgun sequencing of the variable genetic pool of the species. The whole project is planned to produce ~30,000 sequencing reads. The third part is consisting of sequence assembly and subsequent annotation of the gene clusters using an updated version of the AGMIAL software. Finally, newly identified genes will be added to the already existing 70-mers oligoset-based L. sakei DNA microarrays to produce a tool further coined L. sakei species-wide DNA microarrays.
Blue and red loops are schematic views of genomic islands that may vary between strains. Such variations also occur in the plasmid population with possible exchanges with the chromosome of strains (central arrow).
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Perspectives (toward pangenomic studies of L. sakei species): Our goal is to take advantage of recent flow cell sequencing technologies to fully sequence the genome of the 10 strains selected in our project. Once the sequence information of these 10 reference strains obtained, a very good tool will be available to investigate the genetic traits of this industrially important organism (such as cDNA sequencing quantification for instance). |