The concept of an ideal protein refers to the amino acid profile that precisely meets the nutritional requirements of animals. Achieving a diet aligned with the ideal protein concept enhances protein absorption and reduces the energy cost associated with excretion. This leads to better nutritional utilization and positively impacts the animal's success. This success can be understood as increased production -in the case of productive animals- or improved adaptive success -in the context of wild animals-. To determine the ideal protein profile, it is necessary to understand both the amino acid requirements of the animal and the nutritional value of the available foods.

Determining the ideal protein profile of feed or the food provided by an ecosystem is challenging. The constantly changing conditions of nutritional requirements—which are not linear—and the complex interactions between amino acids, among other factors, make the concept of ideal protein highly dynamic, akin to the Red Queen hypothesis, where constant adaptation is required to maintain the status quo.

In this changing scenario, finding tools to approach the concept of ideal protein is an interesting goal in both animal production and biodiversity fields. Metabolomics, understood as the study of the metabolome—the complete set of metabolites within an animal—can be a powerful tool to achieve this goal. Through multivariate analysis, it is possible to identify metabolites that differentiate between two distinct populations.

In the study we present—Biomarkers for Ideal Protein: Rabbit Diet Metabolomics Varying Key Amino Acids—we analyze potential biomarkers to refine the concept of ideal protein using the rabbit as a model through two distinct experiments.

In the first experiment, we analyzed the effects on the metabolome of a diet with an amino acid profile according to current recommendations (Diet B) and an identical diet with a significant reduction of an essential amino acid, lysine, causing a deficiency and making it a limiting amino acid (Diet U). To enhance the model, the same animal was fed both diets. Metabolomic analysis of the two diets revealed a clear distinction in the metabolomic profile (Figure 1) and identified three metabolites responsible for these differences.

 Figure 1: The Principal component analyzed (PC) plot derived from multivariate analysis demonstrates a clear separation between the two experimental diets, with no overlap observed.  Blue squares : animals fed Diet B and red circles: Animals fed Diet U.

The second experiment aimed to go a step further and analyze potential interaction effects between several amino acids. Diets with different combinations of amino acids—three variable levels (low, medium, and high) and three distinct amino acids (lysine, sulfur-containing amino acids, and threonine)—were analyzed. The metabolome of five different diets was assessed. Our results again showed a clear separation in the metabolome and identified ten distinct metabolites.

The overall perspective of the study suggests that metabolomics can be a sensitive and useful tool for developing the concept of ideal protein using the rabbit as a model. It also identifies candidate metabolites to refine nutritional requirements and deepen the understanding of the ideal protein concept.

These findings are expanded upon in the full study: https://doi.org/10.1038/s42003-024-06322-2