The impact of variable high pressure treatments and/or cooking of rice on bacterial populations after storage using culture-independent analysis

Food processing treatments can alter the microbial biodiversity which can significantly affect shelf-life and safety. These changes in biodiversity can be analysed using culture-independent community profiling methods to provide a better understanding of which bacteria are resistant to the process. In this study, we used rice as a model food that contains a rich bacterial biodiversity to determine what effect variable high pressure processing (HPP) parameters and/or cooking has on the bacterial population. Two samples of milled rice each from two harvest years were pressured at 0, 200, 400 or 600 MPa for 10 min at 25 °C, then either cooked at 100 °C or left uncooked. Samples were stored at 25 °C for up to 8 weeks or until spoilage was detected by total aerobic plate count. Bacterial DNA was extracted and the community composition was analysed by Illumina sequencing of 250 bp of 16S rDNA. Pressured, uncooked samples spoiled after one day of storage at 25 °C and it was found that pressures at and above 400 MPa selected for aerobic sporeformers namely Bacillaceae being the dominant group. Of these, Bacillus cereus, Bacillus subtilis or Paenibacillus amylolyticus groups were the most abundant in samples. The untreated rehydrated rice control and rice treated at 200 MPa contained spoilage populations consisting of a mix of primarily Enterobacteriaceae and Bacillaceae suggesting that 200 MPa treatment was not severe enough to eliminate Gram-negative bacteria. Cooked rice samples spoiled after three days storage at 25 °C and contained almost exclusively Bacillus spp. with B. subtilis and B. cereus groups dominating the populations. With pressures of 400 and 600 MPa, cooked samples remained unspoilt after eight weeks of storage at 25 °C with sequences representing DNA from a highly heterogeneous mix of non-viable bacterial cells. The lower pressure treatment (200 MPa) combined with cooking resulted in one out of four samples spoiling due to growth of Bacillus flexus group bacteria. In summary, the culture-independent method used here demonstrates that higher HPP (400 and 600 MPa) treatment or cooking alone selected for sporeforming bacterial spoilage profiles. A combination of HPP (400 and 600 MPa) with cooking resulted in ambient temperature stable rice, with no growth of potentially hazardous sporeformers observed.