Molecular Identification of Isolated from Korean Water Deer () and Striped Field Mouse () Feces by Using an SNP-Based 16S Ribosomal Marker.

Ambiguous, heterogeneous, endospore-forming species, notably , often produce fatal toxins that threaten human health. We identified from wild animal fecal samples ( = 80), including the Korean water deer ( = 25) and striped field mouse ( = 55). Using traditional culture-based methods, 25 animal fecal samples (31.25%; 25/80) were found to be positive for species, whereas using molecular techniques, 19 samples (23.75%; 19/80) were found to be positive for the same. In addition, we designed a species-specific 16S ribosomal RNA (rRNA) gene marker and utilized it to identify 19 samples by means of PCR amplification and sequencing, using at least one colony from the 19 positive samples. The recovered sequences were matched to sequences of three species (, and ) from the GenBank database. Moreover, the phylogenetic tree generated in this study established specific clades for the group. In addition, to differentiate between , , and , we designed a single nucleotide polymorphism (SNP)-based primer by identifying SNPs in the alignment of 16S rRNA gene sequences of group strains. The SNPs were used to design primer sets for discrimination between highly similar species from the group. The study could be used in surveillance of agricultural fresh-produce-associated outbreaks, for accurate identification of each species, and in the development of control measures.