Cpn60 barcode sequences accurately identify newly defined genera within the Lactobacillaceae.

Abstract

The cpn60 barcode sequence has been established as an informative target for microbial species identification. Applications of cpn60 barcode sequencing are supported by the availability of "universal" PCR primers for amplification and a curated reference database of cpn60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the cpn60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 cpn60 sequences representing 258/269 of the validly named species in Lactobacillus, Paralactobacillus, and the 23 newer genera showed that cpn60-based sequence relationships were generally consistent with whole-genome-based phylogeny. Aligning or mapping full-length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, "universal" barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode makes it a useful target for the detection and identification of lactobacilli, as defined by the latest taxonomic framework.