Herbivore and carnivore microbial signatures indicate diet and health variation in human gut microbiota

Diet is a key factor shaping gut microbiota in mammals, with herbivores and carnivores harboring distinct microbial communities. However, despite humans being highly omnivorous, it remains unclear whether their gut microbiota more closely resembles that of herbivores or carnivores or how individual-level variations along this spectrum are associated with human health status. We compared gut microbiota profiles of 858 samples from 109 mammalian species and constructed a Herbivore-Carnivore (HC) index based on bacterial groups characteristic of each diet. The HC-index positioned humans between herbivores and carnivores and showed that traditional hunter-gatherers and nonhuman apes retained herbivore-leaning profiles, whereas urbanized humans exhibited a shift toward a carnivore-leaning state. By applying the HC-index to >72,000 participants across multiple cohorts worldwide, we found that elevated HC-index values were associated with plant-based and fiber-rich diets, greater microbial diversity, enhanced potential to degrade plant-derived carbohydrates, favorable clinical measures, and lower prevalence of self-reported disease. We demonstrated that the HC balance of gut microbiota captures a conserved diet-related gradient across mammals and provides an interpretable framework linking human diet, microbial function, and health.