Culture Independent Analysis of Contaminated Yogurt via Next Generation Sequencing

Introduction:  In September 2013, select lots of Greek yogurt in US marketplaces were suspected of being contaminated with an unknown biological agent.  Consumer complaints ranged from odd taste and smell from their yogurts to a few reported that they became ill after consuming this product. The suspected lots were recalled by the manufacturer and further investigation led to the identity of the contamination a mold, Mucor circinelloides.  The company stated that this mold is commonly found in plants and it not harmful for human consumption.

Purpose:  We have developed a culture-free analytical tool in order to detect unknown contaminants in foods containing live microbials.  In addition to identifying unknown biologics, we can explore the known contents of these products and ensure proper safety and labeling in rapid time.

Methods:  Utilizing whole genome sequencing, we have developed a pipeline that includes DNA isolation, data production, and in-house data analyses for identification of microbes in dietary supplements and functional foods.  Analyses performed on this food commodity included strain identification from the yogurt samples sent from FDA’s Office of Regulatory Affairs Pacific Regional Lab (PRL).

Results:  From the analytical work, two types of mold, Mucor circinelloides and Rhizopus, were identified. This result is different from what was provided by the company in their reported analysis.  In addition, the presence of the mold in these samples caused a shift in their bacterial population.

Significance:  This project determined the identity of mold in a contaminated food product using whole genome sequencing and also determined a shift in the microbes present in the yogurt when contaminated. This method will be very useful for identification of contaminants in foods containing live microbials to ensure proper labeling and safety of our food supply.