Under intense scrutiny for safety and authenticity, our food supply encompasses probiotic supplementation, fermentation organisms, pathogenic bacteria, and microbial toxins - in short, the microbiome and metabolome of food. Recent claims regarding probiotic supplements, additives, and cultured foods highlight the need for widely accepted protocols for evidence-based oversight of such products, as well as specific methods to assess their safety and authenticity. Rapid improvements in high-throughput sequencing technologies, curated and annotated reference databases of whole genome sequences, bacterial strain banks, and novel informatics techniques coupled to a scalable computing platform are poised to provide a robust solution extendable to encompass systematic authentication of the microbiome and its variations up and down the supply chain. Members of the Sequence the Food Supply Chain Consortium are working to characterize and quantify the microbiome at a baseline and after processing. They are also working to create reference databases and develop a Metagenomics Computation and Analytics Workbench, capable of verifying the effectiveness of good manufacturing practices and monitoring control measures highlighted in a site's Hazard Analysis Critical Control Point plan. In this paper, we propose how microbial ecology, evolvability, and phylogenetic diversity exhort the application of new molecular techniques to assure safety, authenticity, and traceability for wholesome food.