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A niche is a spatial organization in which the microbiome interacts with the host (microbiome-host niche), e.g., with the host's immune system
The interaction is via secondary metabolites, foreign molecular patterns (MAMPs, PAMPs), and antigens.
The residence time of microbial stimuli in discrete spatial niches determines the strength and duration of host stimulation
The biochemical milieu within niches is dynamic and dictates the dose and timing of host exposure to conditioning stimuli from the microbiome
It is now clear that many different niches exist along all axes of the intestine (proximal-distal, luminal-mucosal)
An example of a unique microbiome host niche is Akkermansia muciniphila. A. muciniphila occupies a unique host niche that promotes the delivery of multiple stimuli to the host, including foreign molecular patterns and antigens, thus cooperatively conditioning homeostatic immunity
Oxygen gradients, nutrient availability, and the presence of antimicrobial molecules provide selection pressures within shared microbiome–host tissue niches
Segmented filamentous bacteria are mouse pathobionts that invade epithelial cells within a unique niche in the small intestine that promotes the development of antigen-specific Th17 cell responses, as evidenced by colonization experiments