A total of 0.5 g lumen contents and mucosal scraps of ileum, cecum, and colon were used to extract total bacterial genomic DNA using the QIAamp R Fast DNA Stool Mini Kit (QIAGEN Ltd., Hilden, Germany) according to the manufacturer’s protocol. The V3–V4 region of the 16S rRNA gene was amplified using universal primers 338F (5′-ACTCCTACGGGAGGCAGCAG-3′) and 806R (5′-GGACTACHVGGGTWTCTAAT-3′). The PCR reactions were conducted using the following program: denaturation at 95 °C for 3 min, 27 cycles of 95 °C for 30 s, annealing at 55 °C for 30 s, elongation at 72 °C for 45 s, and a final extension at 72 °C for 10 min. The PCR components, the extraction and purification of PCR products were the same with previous study [29 (link)]. Purified PCR products were pooled into equimolar amounts and sequenced on the Illumina MiSeq platform according to the standard protocols by Shanghai Majorbio Bio-pharm Technology Co., Ltd. (Shanghai, China). The raw reads were deposited into the NCBI Sequence Read Archive (SRA) database (Accession Number: PRJNA694358).
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