Microbial Community Analysis of Biopsy Samples

DNA was extracted from biopsy specimens using the QIAamp DNA minikit (Qiagen, CA, USA). Details of amplification, sequencing, raw data processing, and differential taxon selection were described previously (7 (link)). Briefly, the V3-V4 region of microbial 16S rRNA gene was amplified using universal primers (341F, 5′-CCTACGGGNBGCASCAG-3′; 805R, 5′-GACTACNVGGGTATCTAATCC-3′) and sequenced on the Illumina HiSeq 2500 PE250 platform. Sequence reads were processed and clustered into operational taxonomic units (OTUs) using IMNGS (www.imngs.org). Differential microbial taxa with relative abundances of >1% after eradication were selected by paired t tests when P values adjusted by FDR were less than 0.05.