Influence of butyrate, host immune response, and antibiotics on gut microbiota
This project investigates how diet, antibiotic exposure (Abx), and immune status shape the microbiome across multiple host compartments over time. Using a controlled experimental design, microbial communities were sampled from urine, stool, kidney, and bladder at defined timepoints and across distinct housing cages representing structured treatment groups.Microbial diversity was assessed using both alpha diversity (richness) and beta diversity (community composition; weighted UniFrac). Statistical frameworks including non-parametric tests, PERMANOVA, and multivariate modeling were applied to evaluate the effects of diet, antibiotics, and their interactions within and across timepoints. In parallel, differential abundance analysis (DESeq2) was used to identify taxa associated with specific experimental conditions.This integrative approach enables a comprehensive characterization of how environmental (diet), pharmacological (antibiotics), and host factors (immune status) interact to influence microbiome structure and function. The findings aim to clarify context-dependent microbiome responses and identify microbial signatures associated with specific treatment conditions.