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Updated: Mar 16, 2026
A Method for Targeted 16S Sequencing of Human Milk Samples
Published on: March 23, 2018
Using PacBio Long-Read High-Throughput Microbial Gene Amplicon Sequencing To Evaluate Infant Formula Safety
Yi Zheng1, Xiaoxia Xi1, Haiyan Xu1
1Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University , Hohhot 010018, People's Republic of China.
Insights
Infant formula (IF) bacterial contamination was profiled using PacBio SMRT sequencing. Distinct microbial communities were found between domestic and imported IF, with preheating affecting Bacillus levels, aiding quality control.
Area of Science:
- Microbiology
- Food Science
- Genomics
Background:
- Infant formula (IF) requires stringent microbiological standards due to infant vulnerability to foodborne illnesses.
- Assessing bacterial contamination in IF is crucial for ensuring infant safety and product quality.
- Traditional methods may not fully capture the complex bacterial profiles in IF.
Purpose of the Study:
- To characterize the bacterial microbiota of Chinese domestic and imported infant formula using advanced sequencing technology.
- To identify differences in bacterial profiles between domestic and imported IF samples.
- To explore the relationship between processing parameters, like preheating (whey protein nitrogen index - WPNI), and bacterial contamination.
Main Methods:
- Utilized PacBio single-molecule real-time (SMRT) sequencing for full-length 16S rRNA gene analysis.
- Analyzed 30 samples of Chinese domestic and imported infant formula.
- Employed principal coordinate analysis (PCoA) and multivariate analysis of variance (MANOVA) for statistical comparison of bacterial profiles.
Main Results:
- Identified a total of 600 bacterial species, with Streptococcus thermophilus, Lactococcus lactis, and Lactococcus piscium being dominant.
- Observed significant differences in bacterial profiles between domestic and imported IF samples.
- Found a negative correlation between the whey protein nitrogen index (WPNI) and the abundance of the Bacillus genus, indicating preheating impacts bacterial load.
Conclusions:
- PacBio SMRT sequencing is an effective tool for comprehensive assessment of bacterial contamination in infant formula.
- The study highlights distinct microbial characteristics of domestic versus imported IF, informing safety assessments.
- Findings provide valuable insights for the dairy industry to enhance microbial quality monitoring and safety protocols during IF production.
Abstract:
Infant formula (IF) requires a strict microbiological standard because of the high vulnerability of infants to foodborne diseases. The current study used the PacBio single-molecule real-time (SMRT) sequencing platform to generate full-length 16S rRNA-based bacterial microbiota profiles of 30 Chinese domestic and imported IF samples. A total of 600 species were identified, dominated by Streptococcus thermophilus, Lactococcus lactis, and Lactococcus piscium. Distinctive bacterial profiles were observed between the two sample groups, as confirmed with both principal coordinate analysis and multivariate analysis of variance. Moreover, the product whey protein nitrogen index (WPNI), representing the degree of preheating, negatively correlated with the relative abundances of the Bacillus genus. This study has demonstrated the application of the PacBio SMRT sequencing platform in assessing the bacterial contamination of IF products, which is of interest to the dairy industry for effective monitoring of microbial quality and safety during production.
