Potential application of ribosomal intergenic spacer analysis to the microbial community analysis of agronomic products

Ribosomal intergenic spacer analysis (RISA) has been applied to the microbial community analysis of agronomic products in combination with a simple and rapid DNA extraction method, consisting of a one-step extraction and two-step purification, for a variety of agronomic products. RISA appears to be a useful tool for the study of the community structures of food-associated microbes and their use as a unique fingerprinting signature for each agronomic product. Sequencing analyses of amplicons generated from RISA suggest that this method can detect conventional microbes. In the case of RISA of wasabi paste DNA, the sequences of the amplicons showed high similarity to the plant pathogen Xanthomonas campestris and the soil bacterium Bacillus subtilis, whereas several food-associated bacteria (Lactococcus lactis, Lactococcus raffinolactis, and Lactococcus sakei) were detected using this technique in sausage DNA. Unexpectedly, the sequencing analyses also revealed the presence of several microbes that possessed high similarity to human bacterial pathogens such as Weissella confusa and Yersinia pestis. The results suggest that RISA will be a useful method for routine microbial community analysis in agronomic products.