The genomic analysis conducted on the 54 strains confirmed the finding that L. plantarum is highly adapted to grow on a large variety of carbohydrates with a preference for beta-glucosides. A total of 429 OGs was assigned to sugar import and metabolism in the L. plantarum pan-genome, of which 371 are predicted to be present on the chromosome and 58 are presumably plasmid-encoded. The complete list of OGs belonging to sugar metabolism category is reported in Table 12.
The majority of the 429 OGs is organized in 83 sugar utilization cassettes, of which only 14 belong to the core genome of L. plantarum (Table 12). Notably, 42 of the chromosomal carbohydrate cassettes are clustered in a so-called sugar island (or life-style island), corresponding to genes lp_3131–3661 in the reference genome WCFS1. These results are in agreement with the previous CGH analyses performed with this species (2,44), but the present analysis identified an additional 32 carbohydrate cassettes (18 chromosomal and 14 plasmid-encoded) that are absent in WCFS1 (Table 12). These newly identified cassettes predominantly encode import and metabolism of fructose, mannose and maltose, which are carbohydrates present in plants and fruits and may contribute to the fitness of L. plantarum in a plant-associated environment.
L. plantarum genomes contain a large number of phosphotransferase (PTS) systems with specificity for beta-glucosides, at least according to their annotation (Table 12). Beta- glucosides are di- and oligosaccharides with β1->4 bonds linking two glucose or glucose-substituted molecules, e.g. cellobiose (2 glucose moieties) or chitobiose (2 glucosamine moieties). At least 16 PTS systems for beta-glucosides were found, or which 4 systems are fully conserved in all L. plantarum genomes, and each individual strain has 6-12 beta-glucosides PTS systems.
There are 5 systems for maltose/maltodextrin utilization, with ABC or MFS transporters, but only one of these is fully conserved (cs3), and 3 others are fairly rare (cs42, cs72, cs81). The conserved cassette cs3 is found in two variants that use a different maltose ABC transporter.
There is one conserved PTS for lactose (cs40; only absent in strain NIZO2259), while a second lactose PTS (cs37) is absent in 15 strains. There are 7 PTS systems annotated as specific for fructose (or sorbose/mannose/mannitol). Their presence is highly variable, with individual strains having 0-5 fructose PTS (Table 12).
The two consecutive cassettes for myo-inositol utilization (cs60, cs61) are only present in 9 strains.
2. Siezen RJ, Tzeneva VA, Castioni A, Wels M, Phan HTK, Rademaker JLW, et al. Phenotypic and genomicdiversity of Lactobacillus plantarum strainsisolatedfromvariousenvironmental niches. Environ Microbiol. 2010 Mar;12(3):758–73.
44. Molenaar D, Bringel F, Schuren FH, de Vos WM, Siezen RJ, Kleerebezem M. Exploring Lactobacillus plantarum genomediversity by usingmicroarrays. Journal of Bacteriology. 2005 Aug 31;187(17):6119–27.