Quantitative_Microbiome_Parameters
The gut microbiome is widely implicated in host health and disease, yet microbiome–disease associations based on fecal taxonomic composition remain inconsistent across studies, cohorts, and interventions. Here, previously described gastrointestinal dye-based passage assays to measure gastrointestinal transit time were expanded, enabling quantitative measurement of novel gut microbiome parameters, including fecal mass, microbial load, and microbiota excretion. Quantitative microbiome parameters were strongly modulated by diet, feeding pattern, and IL-10 deficiency, reflecting changes in food intake and gastrointestinal transit. Microbiota excretion emerged as an integrative parameter determined by fecal mass and microbial load, with microbial load itself positively associated with gastrointestinal transit time. High-fiber diet (HFiD) and time-restricted feeding (TRF) induced convergent reductions in microbial load, microbiota excretion, and transit time, whereas high-fat diet (HFaD) produced opposing effects. These quantitative microbiome changes were associated with overlapping intestinal gene expression signatures, consistent with anti-inflammatory effects of HFiD and TRF, indicating relevance for host physiology. In contrast, fecal taxonomic microbiota profiles were dominated by ecological and experimental confounders, showing limited reproducibility across studies. By uncovering shared quantitative gut microbiome patterns, the study highlights alternative mechanisms for host-microbiome interactions, which may help resolve inconsistencies in reported taxonomy-based microbiome-disease associations and provide new diagnostic and therapeutic opportunities in microbiome-mediated diseases.
The gut microbiome is widely implicated in host health and disease, yet microbiome–disease associations based on fecal taxonomic composition remain inconsistent across studies, cohorts, and interventions. Here, previously described gastrointestinal dye-based passage assays to measure gastrointestinal transit time were expanded, enabling quantitative measurement of novel gut microbiome parameters, including fecal mass, microbial load, and microbiota excretion. Quantitative microbiome parameters were strongly modulated by diet, feeding pattern, and IL-10 deficiency, reflecting changes in food intake and gastrointestinal transit. Microbiota excretion emerged as an integrative parameter determined by fecal mass and microbial load, with microbial load itself positively associated with gastrointestinal transit time. High-fiber diet (HFiD) and time-restricted feeding (TRF) induced convergent reductions in microbial load, microbiota excretion, and transit time, whereas high-fat diet (HFaD) produced opposing effects. These quantitative microbiome changes were associated with overlapping intestinal gene expression signatures, consistent with anti-inflammatory effects of HFiD and TRF, indicating relevance for host physiology. In contrast, fecal taxonomic microbiota profiles were dominated by ecological and experimental confounders, showing limited reproducibility across studies. By uncovering shared quantitative gut microbiome patterns, the study highlights alternative mechanisms for host-microbiome interactions, which may help resolve inconsistencies in reported taxonomy-based microbiome-disease associations and provide new diagnostic and therapeutic opportunities in microbiome-mediated diseases.
University of Hohenheim