This study describes the effect of bactofugation (10,000 × g in a continuous flow of 10,000 L/h) of three batches of raw milk on total bacterial count (TBC) and aerobic spore count, and it also shows the effect on the microbial diversity of spore-forming bacteria by analysing their genetic variability through molecular approaches. Given that milk must be preheated to approximately 55 °C before being bactofuged, for comparison, the three batches were evaluated at different stages as refrigerated raw, preheated, and bactofuged milk. For preheated milk, it was found that bactofugation caused a significant reduction (p < 0.05) of 99.52% (from 4.5 × 106 to 2.1 × 104 CFU/mL) in the mean TBC and of 95% (from 333 to 17 CFU/mL) in the aerobic mesophilic spore count. Due to the effect of bactofugation on preheated milk, a reduction of 82% was observed in both TBC and aerobic spore count. With respect to diversity, 107 isolates from raw milk, prior to bactofugation, and 16 isolates from bactofuged milk were recovered and grouped into 40 and 8 clusters, respectively. The predominant species detected in raw and preheated milk were Bacillus toyonensis (63% - 20 clusters) and Lysinibacillus fusiformis (15% - 8 clusters). Proportionally, B. toyonensis (69% - 6 clusters) and L. fusiformis (25% - 1 cluster) were predominant in bactofuged milk. B. pumilus, L. varians, B. flexus, B. invictae, and B. megaterium, bacteria with a known milk spoilage potential, were isolated from milk prior to bactofugation, and they reduced to undetectable levels in bactofuged milk. Bactofugation of milk, therefore, reduces the TBC and aerobic spore count, with a significant effect in reducing the microbial diversity of spore-forming bacteria, proportional to their incidence in raw milk. Therefore, bactofugation can be an alternative to increase the shelf life and technological potential of milk.
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