Microbiome State Transitions: Insights from Rat Diet Experiments

Abstract

Understanding how the gut microbiome shifts between distinct states is crucial for uncovering its role in health and disease. While advances in 16S rRNA sequencing and metagenomics have revealed associations between the microbiome and various conditions, including inflammatory bowel disease and neurodegenerative disorders, the underlying mechanisms of microbiome state transitions remain poorly understood. Diet is one of the primary external drivers of these transitions, but its effects are shaped by microbial diversity, functional redundancy, and the microbiome's capacity to respond to environmental perturbations. To investigate the interplay of these factors, we performed diet intervention experiments in rats fed three distinct diets, coupled with fecal microbiome profiling. The resulting data will inform the development of a gut microbiome simulator capable of reproducing state transitions under varying dietary and environmental conditions. This work aims to provide a quantitative framework for studying microbiome dynamics, with potential applications in both basic research and personalized nutrition.