['We established a bacterial reconstitution model to investigate epithelial cell-luminal bacteria interaction. The aim of the study was to identify the known genes directly or indirectly modulated by non-pathologic bacterial flora in the colonic epithelia of germ-free mice.', 'Germ-free mice were orally given a bacterial suspension prepared from specific pathogen-free counterparts (bacterial reconstitution). Colonic epithelial cells were isolated, then total and poly (A) RNA were extracted. We investigated differential gene expression in colonic epithelial cells among germ-free, bacteria-reconstituted, and specific pathogen-free mice by DNA microarray. Finally, differential expression was confirmed by Northern blot or quantitative RT-PCR.', 'Thirty genes were initially selected as differentially expressed genes in DNA microarray analysis. We confirmed that genes associated with growth (Reg IIIbeta, Reg IIIgamma, guanylate nucleotide binding protein 2), apoptosis (Bcl-associated death promotor), cytoskeleton (tubulin alpha4, erythrocyte protein band 7.2), and immune response (lymphocyte antigen complex 6) were induced by bacterial reconstitution. In contrast, genes possibly participating in extracellular oxidant defence (selenoprotein P, metallothionein 1) and cellular metabolism (cytochrome P450, HMGCoA synthase 2, alcohol dehydrogenase 1 complex, aldehyde dehydrogenase family 1, carbonic anhydrase 1, glycoprotein galactosyltransferase alpha1,3) were down-regulated by bacterial challenge.'] Do non-pathogenic bacteria modulate colonic epithelial gene expression in germ-free mice?