Long-term adherence to the carnivore diet and its impact on the gut microbiota: a cross-sectional study

Objective This study aimed to characterize the gut microbiota composition and predicted metabolic functionality of healthy individuals adhering long-term to a carnivore diet and to compare those with confounder-matched omnivore controls. Methods A cross-sectional analysis was conducted including ten healthy individuals following a carnivore diet for an average of 36±11·9 months and 874 confounder-matched controls. 16S rRNA sequencing was used to assess composition and predicted functionality. Diversity metrics, differential abundance testing and multivariate regression modelling were applied to evaluate the associations. Results Carnivore diet adherence was a dominant independent predictor of microbiota composition and predicted functionality. Alpha-diversity metrics did not differ significantly between groups, whereas carnivores exhibited higher Chao1 richness. Several low-abundance phyla, including Synergistetes and Desulfobacterota, were enriched. Functional profiling revealed substantial metabolic differences, with significant differences in over 300 metabolic pathways and 13 functional modules, including those related to amino-acid degradation, B-vitamin synthesis, energy metabolism, gut barrier integrity and protein fermentation. Modules associated with cytotoxicity, inflammation and constipation were also elevated. Regression analyses confirmed that these taxonomic and functional shifts were primarily attributable to the diet itself. Conclusions Long-term carnivore diet adherence leads to distinct taxonomic changes and profound functional alterations of the gut microbiota. Significance These findings challenge the assumption that dietary fiber is essential for maintaining microbiota diversity, suggesting the potential prebiotic effects of certain nutrients in the animal-based diet, while highlighting potential long-term risks associated with an exclusively animal-based diet.