Continuum modeling of transport and microbial dynamics in an idealized intestinal geometry

The small intestine engineers fluid flow and the host bacterial population for efficient absorption of nutrients; however, the precise role of gut peristalsis and the intestinal surface geometry in modulating bacterial retention and nutrient absorption is not fully understood. The research aims to numerically quantify how the complex interplay between fluid flow and intestinal geometry controls microbial dynamics and nutrient absorption in the small intestine. We use direct numerical simulation of the unsteady Navier-Stokes equation in an idealized axisymmetric geometry with radially protruding villi. A pulsatile inlet boundary condition will be used to model gut motility. Nutrient and bacterial dynamics are solved using coupled nonlinear reaction-advection-diffusion equations with Monod kinetics. We map bacterial retention for a range of Péclet and Damköhler numbers to find that crypts in the small intestine play an important role in retaining bacteria when advection is strong, and reaction is weak – conditions unfavorable for bacterial growth. We further explore how diet composition (protein, carbohydrates, water intake, and more) and flow conditions affect bacterial growth and nutrient absorption. Our flexible numerical approach can be adapted to model a range of intestinal flow conditions and reaction kinetics for nutrients and the gut microbiome.