Abstract
BackgroundStrains of Lactobacillus paracasei are present in many diverse environments, including dairy and plant materials and the intestinal tracts of humans and animals. Their adaptation to various niches is correlated to intra-species diversity at the genomic and metabolic level. In this study, we compared the genome sequences of three L. paracasei strains isolated from mature Cheddar cheeses, two of which (DPC4206 and DPC4536) shared the same genomic fingerprint by PFGE, but demonstrated varying metabolic capabilities.ResultsGenome sizes varied from 2.9 Mbp for DPC2071, to 3.09 Mbp for DPC4206 and 3.08 Mpb for DPC4536. The presence of plasmids was a distinguishing feature between the strains with strain DPC2071 possessing an unusually high number of plasmids (up to 11), while DPC4206 had one plasmid and DPC4536 harboured no plasmids. Each of the strains possessed specific genes not present in the other two analysed strains. The three strains differed in their abundance of sugar-converting genes, and in the types of sugars that could be used as energy sources. Genes involved in the metabolism of sugars not usually connected with the dairy niche, such as myo-inositol and pullulan were also detected, but strains did not utilise these sugars. The genetic content of the three strains differed in regard to specific genes for arginine and sulfur-containing amino acid metabolism and genes contributing to resistance to heavy metal ions. In addition, variability in the presence of phage remnants and phage protection systems was evident.ConclusionsThe findings presented in this study confirm a considerable level of heterogeneity of Lactobacillus paracasei strains, even between strains isolated from the same niche.
Highlights
Strains of Lactobacillus paracasei are present in many diverse environments, including dairy and plant materials and the intestinal tracts of humans and animals
The comparative genomic analysis of L. casei and L. paracasei genomes has revealed that, as in other Lactobacillales, there is an evolutionary trend towards minimisation of genome size through the decay of genes coding for functions not required for strains inhabiting specific niches
L. casei and L. paracasei pangenome studies have confirmed the wide range of ecological niches that can be inhabited by strains of the L. casei group [4, 7, 9], arising from the variability of genes supporting utilisation of numerous energy sources and other specific genes contributing to efficient survival in habitats with differing environmental conditions
Summary
Strains of Lactobacillus paracasei are present in many diverse environments, including dairy and plant materials and the intestinal tracts of humans and animals Their adaptation to various niches is correlated to intra-species diversity at the genomic and metabolic level. The comparative genomic analysis of L. casei and L. paracasei genomes has revealed that, as in other Lactobacillales, there is an evolutionary trend towards minimisation of genome size through the decay of genes coding for functions not required for strains inhabiting specific niches. This loss of redundant genes has been shown to be followed by the acquisition of genes by horizontal gene transfer (HGT) as a response to niche adaptation [6]. L. casei and L. paracasei pangenome studies have confirmed the wide range of ecological niches that can be inhabited by strains of the L. casei group [4, 7, 9], arising from the variability of genes supporting utilisation of numerous energy sources and other specific genes contributing to efficient survival in habitats with differing environmental conditions
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