The human gut microbiome activity is resilient and stable for up to six months: a large stool metatranscriptomic study

The human microbiome influences health and disease through diverse biochemical and functional outputs (e.g. enzymes, structural proteins, metabolites, and other cellular components) that affect nearly every aspect of human physiology. Metatranscriptomics (MT), an unbiased RNA sequencing approach, is a high-throughput and high-content method that quantifies both gut microbial taxonomy and active biochemical functions. Because microbial community composition and gene expression are dynamic, understanding temporal variation in the gut metatranscriptome across multiple time scales is essential. Here, we report the temporal dynamics of gut microbiome species and functions using a large cohort (n=6,157) with a clinically validated stool MT test. We quantified microbiome stability from hours to years and assessed taxonomic and functional resilience to major luminal perturbations, such as colonoscopy bowel preparation. Longitudinal analyses of samples collected within the same day, and across days, weeks, months, and years, revealed significant stability in both composition and gene expression within a single day and over six months. Among individuals reporting stable diets and no antibiotic exposure, taxonomic and functional profiles remained stable for up to three years. Following colonoscopy preparation, the microbiome demonstrated strong resilience, returning to its pre-procedure state within one week. These findings support the robustness of stool-based MT profiling for species-level and pathway-resolved functional analysis in longitudinal research and health applications.