Multivariate statistical analysis of the 16S rRNA pyrosequencing data showed that there were significant differences in bacterial community profiles between the Pacific and Sydney Rock oysters (Global R = 0.988,P = 0.001), irrespective of storage time. Furthermore, significant differences (Global R = 1, P = 0.001) in bacterial profiles associated with storage time were also observed regardless of the oyster species, with significant pair-wise differences noted among each of the three time points investigated (P = 0.001). This distinct separation in bacterial communities associated with oyster species and storage time is demonstrated in the PCO presented in Fig. 5. SIMPER analysis showed that the overall bacterial profiles of Pacific and Sydney Rock oysters were 34.7% similar. For each time point investigated, bacterial profiles within oyster species were 30.2–32.7% similar. As the oysters spoiled, their bacterial profiles became distinct from those observed in fresh oysters. Bacterial communities between the Day 0 and 3 oysters were 47.9–53.7% similar, while those of Day 0 and 7 oysters were only 16.2–18.1% similar. Furthermore, as the oysters spoiled, the bacterial profiles between oyster species became more similar indicating a common spoilage profile. Pacific and Sydney Rock oysters showed 17.5%, 35.4% and 51.1% similarity at Days 0, 3 and 7 respectively.