Intestinal Structure Regulates Bacterial Colonization Patterns
Faculty Mentor Information
Dr. Kevin Roche, Boise State University
Presentation Date
7-16-2026
Abstract
Many incurable gastrointestinal diseases are linked to gut dysbiosis, an imbalance in the gut microbiome, motivating better understanding of what allows pathogenic bacteria to colonize the gut's spatially complex environment. Along the gut wall, the epithelial tissue is folded to form “crypts”. These dead-end pockets vary in depth, creating diverse microenvironments that support bacterial colonization. In this study, we explore how gut geometry influences crypt colonization of a fluorescently-labeled strain of Escherichia coli, a common gut occupant. We inoculated the E. coli strain into an in vitro “gut on a chip” microfluidic device with a main flow channel and branching crypts that vary in depth from 10-350μm, then flowed a nutrient solution through the device for two days to promote colonization. Fluorescent microscopy to quantify bacterial colonization patterns. A zone of habitation is observed in crypts with a minimum depth of 90μm, where quantified fluorescence intensity shows colonization concentrated above a depth threshold of approximately 120μm, with signal intensity declining sharply beyond this threshold. These results suggest that gut structure regulates whether, and where, bacteria colonize the intestinal tract, making crypt shape a potential target for pharmaceuticals and a possible factor in susceptibility to disease and microbial virulence.
Intestinal Structure Regulates Bacterial Colonization Patterns
Many incurable gastrointestinal diseases are linked to gut dysbiosis, an imbalance in the gut microbiome, motivating better understanding of what allows pathogenic bacteria to colonize the gut's spatially complex environment. Along the gut wall, the epithelial tissue is folded to form “crypts”. These dead-end pockets vary in depth, creating diverse microenvironments that support bacterial colonization. In this study, we explore how gut geometry influences crypt colonization of a fluorescently-labeled strain of Escherichia coli, a common gut occupant. We inoculated the E. coli strain into an in vitro “gut on a chip” microfluidic device with a main flow channel and branching crypts that vary in depth from 10-350μm, then flowed a nutrient solution through the device for two days to promote colonization. Fluorescent microscopy to quantify bacterial colonization patterns. A zone of habitation is observed in crypts with a minimum depth of 90μm, where quantified fluorescence intensity shows colonization concentrated above a depth threshold of approximately 120μm, with signal intensity declining sharply beyond this threshold. These results suggest that gut structure regulates whether, and where, bacteria colonize the intestinal tract, making crypt shape a potential target for pharmaceuticals and a possible factor in susceptibility to disease and microbial virulence.