This research article explores the relationship between gut physiology (transit time and pH) and the human gut microbiome's composition and metabolism. A nine-day observational study of 61 healthy adults utilized multi-omics to profile microbiome and metabolite changes, correlating these with gut environmental factors. The study revealed significant individual variations in gut environment stability and found that stool moisture and fecal pH were key factors explaining daily microbiome fluctuations. Inter-individual variations were linked to whole-gut and segmental transit times and pH, with specific metabolites showing correlations to these factors and dietary components. The findings highlight the importance of considering gut physiology when studying the human microbiome.