Quantifying Chemical Fluxes Underlying Gut Microbiota-Host Interactions

Abstract

To resolve how the gut microbiota shapes human health, it is essential to quantify the exchange of chemicals between microbes and the host. Much as the dose of a drug determines its pharmacological effect, the magnitude of a specific chemical flux determines its impact. Here, we establish from first principles how fluxes can be estimated by integrating key parameters from human digestive physiology and microbial metabolism. We apply this framework to three cases: the exchange of fermentation products, the production of toxins by bacterial pathogens, and nitrogen homeostasis. Our analysis identifies three directly measurable host-level parameters which, in concert with microbial activity, shape flux magnitudes: intestinal transit time, absolute microbial abundance in feces, and fecal mass loss. The simultaneous quantification of these parameters provides a feasible yet essential step toward a mechanistic and quantitative description of gut microbiota-host interactions across health and disease.