Distinct compositional changes but shared quantitative microbiome and anti-inflammatory modulations by diet

Gut microbiome composition has been frequently but inconsistently associated with human disease. Using a food dye-based gastrointestinal (GI) passage assay to measure GI transit time, stool production (fecal mass), fecal microbiota density (microbial load), and absolute microbiota proliferation (fecal microbiota excretion) in mice, we show quantitative microbiome parameters (QMPs) to be controlled by diet, feeding pattern, and IL-10 deficiency, with food intake and GI transit time acting as separate modulators. High-fiber diet (HFiD) and time-restricted feeding (TRF) reduce GI transit time and induce convergent QMP reductions, whereas high-fat diet (HFaD) produces contrary effects. Intestinal gene expression signatures are consistent with the described shared anti-inflammatory effects of HFiD and TRF, which sharply contrast differences in fecal taxonomic microbiota profiles that are explained by ecological and experimental confounders. Similar QMP and gene expression modulations by distinct diet and feeding interventions warrant exploration of a diagnostic and therapeutic QMP potential for microbiome-mediated disease.