Differentiation of Milk and Whey Protein Concentrates by Microbiome Profiling Using 16S Metagenomics

Protein powder identification presents a challenge in quality control. There is current deliberation of the specificity of methods for the identification of milk proteins, and the consensus identification method of whey protein from the United States Pharmacopeia Food Chemical Codex relies on a combined analysis of the testing of ash, fat, lactose, loss on drying, and protein. These methods are non-specific. Milk and whey proteins both contain background DNA content. Both milk and whey proteins retain source DNA (cow), but also have bacterial DNA from natural flora, the dairy plant, and in whey protein, the cheesemaking process. The DNA in these materials is retained post-processing, even after the pasteurization process.

By utilizing 16S metagenomics, the bacterial DNA in protein powders can be sequenced and cross-referenced to a curated library to ultimately create a microbiome profile of these raw materials. This microbiome can be measured for alpha and beta diversity, specifically how many and which species of bacteria are present.

Using 16S metagenomics, we measure alpha and beta diversity of the microbiome profile of each protein powder and use principle coordinate analysis to produce differential groupings, providing a novel identification method for raw materials.

In this study, we demonstrate that the microbiome of cow proteins can be used for raw material identification, as the microbiome of milk and whey proteins differ significantly. We also demonstrate that the microbiome of whey protein concentrate can differ from supplier to supplier.

Microbiome profiling by 16S metagenomics can be an important forensic tool for quality control.

Principle Coordinate Analysis can be used as a statistical tool for protein differentiation using the protein microbiome.