Use of whole genome sequencing (WGS), metagenomics, and metabolomics are robust tools in their own right, but integration of these tools for use in food and health are emerging as a synergistic suite of tools. Single isolate sequences are fruitful in defining outbreaks and subsequent traceability of outbreaks. An explosion in WGS in recent years is now allowing comparison of bacterial genomes at a population scale, something that was not possible until recently. This enables public health and health applications in new ways to understand genomics of infections and transmission of zoonotic microbes. WGS provides exquisite resolution and differentiation accuracy that far exceeds previous methods. However, this still relies on growth and obtaining an isolate from challenging samples. More recently, metagenomes and metaRNAseq techniques applied directly to food, environmental, and animal samples provides encouraging results that a single culture independent method can find define the community and the impactful microbiome members in a single assay that impact safety, health, and disease. The accuracy and determination of the limit of detection remains to be examined and fully explored before this type of tool will be available for use in food and health. Integration of metabolites with microbiome membership is a challenging, but exciting area of exploration that brings a new dimension of biological information that enlightens health and disease. Use of this approach in the placenta and skin provides optimism that multi-factorial diseases will have faster diagnostics, inform better therapies, and perhaps open windows of insight to predict future health. All is dependent on the development of accurate reference databases. The intersection of WGS, metagenomics, and metabolomics to underpin diagnostics and health estimation must meet the demands of accuracy and limit of detection for the most robust and beneficial use at the intersection of food and health.