Intragenomic 16S rRNA gene heterogeneity in Lactococcus lactis subsp cremoris

Partial 16S rRNA gene sequencing of Lactococcus lactis subsp. cremoris strains from our collection identified strains containing sequences diagnostic of both subspecies L lactis subsp. lactis and L lactis subsp. cremoris together in the same strain. The presence of a plasmid-encoded 16S rRNA pseudogene partly explained this result. Twenty-four out of 46 L lactis subsp. cremoris strains tested by PCR contained this pseudogene. However, further analysis showed that five of these 24 strains also contained chromosomal 16S rRNA genes with sequences typical of L lactis subsp. lactis. Genetic and phenotypic tests indicated these strains were otherwise normal L lactis subsp. cremoris strains. Past recombination events between the 16S rRNA pseudogene and chromosomal 16S rRNA genes may explain this phenomenon. Genomic heterogeneity for both 16S rRNA and other gene sequences was observed for L lactis subsp. cremoris SK11 from different laboratories, indicating caution is needed when integrating data from diverse sources for nominally the same strain. (C) 2008 Elsevier Ltd. All rights reserved.