Defining the Food Microbiome for Authentication, Food Safety, and Probiotic Validation

In light of recent revelations surrounding the veracity of claims regarding supplements and probiotic additives and foods, it is clear that culture independent methods for the validation and authentication of these products is needed. In this whitepaper we propose and outline a strategy that leverages high throughput sequencing (HTS) technologies, curated and annotated reference whole genome sequences, bacterial strain banks, previously described and novel informatics techniques, and a scalable computing platform to provide a solution that will be robust and extendable to encompass the supply chain. Through this work we propose to:

• Measure a baseline microbiome for raw products that commonly have probiotic cultures added to them during process, which will serve as a reference database of microbiomes.
• Measure the shift in the microbiome after the addition of probiotics to raw material. We propose carrying out experiments to generate data required to create predictive models that capture the effects of time, environment, and dose in order to significantly change the foundational microbiome.
• Characterize the resulting, steady state, or time varying microbiome in finished products. These measurements will be crucial in providing input data for developing assays for food authentication, validation of live probiotic organisms, and determine the robustness of the predictions for finished products.