Prebiotic fructooligosaccharides are noted for their intestinal immunodulating effects, and theidentification of markers for the effects is a matter of great concern. This study aimed to identifymarker genes for physiological effects of a particular fructooligosaccharide (FOS) on a host animaland also to define the target of its function in the small intestine. DNA microarray technology wasused to screen candidate marker genes, and comprehensive changes in gene expressions in theileum of mice fed with FOS were investigated. One of the major physiological effects of FOS wasintestinal immunomodulation. Marker genes were then identified for major histocompatibility complexclasses I and II, interferon, and phosphatidylinositol metabolites. Also, the ileum was segmented intoPeyer's patch (PP) and the other ileal organ (
PP), and these were analyzed by quantitative RT-PCR method, with the result that the site for recognizing the FOS function was the
PP rather thanthe PP. This is the first paper showing the markers for the physiological effects of FOS in the smallintestine at gene expression level. Applying these marker genes would make it possible to clarify themechanisms of how the administration of dietary FOS and associated changes in the intestinalenvironment are recognized by host organisms as well as how its immunomodulating effects areexpressed in the body.