The quality of raw milk is a key factor influencing the whole dairy processing chain. The richness and diversity of bacteria in raw milk affect its quality and safety. However, traditional microbial detection methods mainly depend on the known microbe culture and are often time consuming. Thus, the development of efficient ways for supervising any possible microbiological contamination is desiderated. In the current work, single-molecule real-time (SMRT) sequencing, developed by Pacific Biosciences (PacBio), was applied to acquire long reads and applied for discrimination of bacteria at species level. Forty samples of raw milk obtained from Beijing, Hebei, Inner Mongolia, Shanghai, and Guangdong in China during summer, autumn, and winter were investigated. Among 35 bacteria species identified in these samples, Acinetobacter albensis, Pseudomonas gessardii, Pseudomonas weihenstephanensis, and Rahnella inusitata were the bacteria with the highest relative abundance in the overall sample, whereas the bacteria with the highest relative abundance in raw milk samples of different origins and seasons are different. Significant differences in bacterial richness and bacterial community diversity in raw milk grouped according to different production areas and different sampling seasons were confirmed by Welch's t-test. Interestingly, the transport distance and transport time positively correlated with the relative abundance of Pseudomonas weihenstephanensis, suggesting that the content of this bacteria was expected to be a standard for evaluating the freshness of raw milk. Pathogens Bacillus cereus and Klebsiella pneumoniae were detected in most samples, indicating that the raw milk was at risk of contamination by pathogenic bacteria. Moreover, the findings of this study provide important evidence for quality and safety monitoring and biological control of raw milk.

This study was undertaken to investigate the prevalence, antimicrobial resistance, and virulence gene profiles of Bacillus cereus in different brands of infant formula in Beijing supermarkets. Eighty-eight Bacillus cereus isolates were recovered in sixty-eight infant formulas of five domestic brands and fourteen imported brands. The prevalence rate in domestic and imported samples were 70.6% and 52.9%, respectively. Lower mean prevalence level was found in domestic samples (1.17 MPN/g) compared with the imported samples (3.52 MPN/g). Twenty-four virulence gene profiles were found, and most strains carried at least one virulence gene. The prevalence of nheA, nheB, nheC, cytK, bceT, and entFM in domestic and imported brand samples was similar. The occurrence of enterotoxin genes hblA, hblC, and hblD in domestic samples were 22.2%, 27.8%, and 22.2%, respectively, which was significantly higher than imported samples. Antimicrobial drugs-susceptibility analysis showed that all isolates were susceptible to gentamincin, amikacin, and ciprofloxacin; 38%, 7%, and 2.3% were resistant to rifampin, tetracycline, and chloramphenicol, respectively; and only one isolate was resistant to trimethoprim-sulfamethoxazole. Moreover, the cell numbers of Bacillus cereus in prepared infant formula increased rapidly at room temperature. Thus, monitoring guidelines are needed for accepted levels of Bacillus cereus in infant formula.