DNA of the biopsy specimens was extracted with the QIAamp DNA Mini Kit, and RNA of biopsy specimens and cultured cells were extracted with TRIzol reagent. The RNA samples were reverse-transcribed into complementary DNA with the PrimeScript RT Reagent Kit. Real-time PCR was performed on an iQ5 (Bio-Rad) with Real-time PCR Master Mix according to the manufacturer’s specifications. The mRNA expression of 16S rDNA, cagA, MMP-10, IL-22, chemokine, β-defensin, and Reg3 genes was measured using the TaqMan and/or SYBR green method with the relevant primers (table S3). For mice, mouse β2-microglobulin mRNA level served as a normalizer, and its level in the stomach of uninfected or WT mice served as a calibrator. For human, human β-actin mRNA level served as a normalizer, and its level in the unstimulated cells or stomach of uninfected donors served as a calibrator. The relative gene expression was expressed as fold change of relevant mRNA calculated by the ΔΔCt method.

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