Riboprinting and 16S rRNA gene sequencing for identification of brewery Pediococcus isolates

A total of 46 brewery and 15 ATCC Pediococcus isolates were ribotyped using a Qualicon RiboPrinter. Of these, 41 isolates were identified as Pediococc us damnosus using EcoRI digestion. Three ATCC reference strains had pattern s similar to each other and matched 17 of the brewery isolates. Six other b rewing isolates were similar to ATCC 25249. The other 18 P. damnosus brewer y isolates had unique patterns. Of the remaining brewing isolates, one was identified as P. parvulus, two were identified as P. acidilactici, and two were identified as unique Pediococcus species. The use of alternate restric tion endonucleases indicated that PstI and PvuII could further differentiat e some strains having identical EcoRI profiles. An acid-resistant P. damnos us isolate could be distinguished from non-acid-resistant varieties of the same species using PstI instead of EcoRI. 16S rRNA gene sequence analysis w as compared to riboprinting for identifying pediococci. The complete 16S rR NA gene was PCR amplified and sequenced from seven brewery isolates and thr ee ATCC references with distinctive riboprint patterns. The 168 rRNA gene s equences from six different brewery P. damnosus isolates were homologous wi th a high degree of similarity to the GenBank reference strain but were ide ntical to each other and one ATCC strain with the exception of 1 bp in one strain. A slime-producing, beer spoilage isolate had 16S rRNA gene sequence homology to the P. acidilactici reference strain, in agreement with the ri boprint data. Although 168 rRNA gene sequencing correctly identified the ge nus and species of the test Pediococcus isolates, riboprinting proved to be a better method for subspecies differentiation.