Purpose: The objective of this work was to develop a whole genome sequencing (WGS)-based protocol to identify microbial ingredients in dietary supplements as to verify label content information as well as the identification of any putative pathogen present. This culture-free method allows for a rapid turnaround time and the potential to be a very powerful analytical tool.
Methods: Seventeen top selling probiotic supplements have been sequenced without any enrichment. The sequences were analyzed using a unique K-mer analysis to determine the bacterial content within these samples. The analysis identifies signature 25-mers and calculates the percentage of reads matched to that unique sequence.
Results: Based on this method, we found labeled probiotic ingredients missing from nine of the 17 surveyed supplements while twelve had additional probiotic strains not included on the label. Lot-to-lot variations were also detected in ten samples. One product was found to contain a potentially pathogenic strain of Enterococcus. In addition, there were instances of taxonomic discrepancies between strains of high genotypic similarity within five products.
Significance: Our data suggest that our culture-free, WGS-based identification protocol could enable the FDA to monitor these supplements to ensure accuracy of manufacturer labeling and product safety in an effort to protect the consumer.