Segmental patterning of microbiota and immune cells in the murine intestinal tract

Abstract

The intestine exhibits distinct characteristics along its length, with a substantial immune cell reservoir and diverse microbiota crucial for maintaining health. This study investigates how anatomical location and regional microbiota influence intestinal immune cell abundance. Using conventionally colonized and germ-free mice, segment-specific immune cell composition and microbial communities were assessed. Metagenomic sequencing analyzed microbiome variations, while flow cytometry and immunofluorescence examined immune cell composition. Microbiome composition varied significantly along the intestine, with diversity and abundance increasing from upper to lower segments. Immune cells showed distinct segment-specific patterning influenced by microbial colonization and localization. T cell subsets displayed varied dependence on microbiome presence and anatomical location. This study highlights locoregional differences in intestinal immune cell and microbiome composition, identifying immune subsets susceptible to microbiota presence. The findings provide context for understanding immune cell alterations in disease models.

Keywords: Microbiome; germ-free vs colonized; immune cells; segmental patterning.

Figure 1.

Overview of the segment-specific bacterial colonization and associated immune cells of the mouse intestine.

Figure 2.

Absolute immune cell abundances and gut morphology in conventional and germ-free mice.

Figure 3.

Intestinal immune cell clusters and composition of conventional and germ-free mice.

Figure 4.

Microbiome variation along the small and large intestines of mice.

Figure 5.

Influence of microbial colonization and segment on the abundance of intestinal immune cells.

Figure 6.

Summary of the segment-specific T cell distribution across the mouse intestine.