Raw FASTQ files were demultiplexed and quality-filtered using QIIME (version 1.17; http://qiime.org/). The 250–base pair (bp) reads were truncated at any site of more than three sequential bases receiving an average quality score of <20. Reads shorter than 50 bp, containing ambiguous base calls or barcode/primer errors, were discarded. Chimeric sequences were checked by UCHIME (www.drive5.com/usearch/manual/uchime_algo.html) and removed from subsequent analyses. The remaining high-quality sequences were clustered into OTUs at 97% similarity using USEARCH (version 7.0; www.drive5.com/usearch/manual/). To assess adequacy of sequencing depth, rarefaction analysis was performed using the RDP Rarefaction tool based on the number of sequences and OTUs for each sample. α-Diversity was assessed using the species richness indices (Ace and Chao) and species diversity indices (Shannon) (12). Partial least-squares discriminant analysis (PLS-DA) was performed to visually evaluate the difference and similarity of bacterial communities between groups (β-diversity) (32). The differentially expressed bacterial taxa between SCZ and HC samples were identified using LEfSe (33). Taxonomy was assigned to OTU representatives using the RDP classifier against the SILVA database. A Venn diagram was generated to describe the common and unique OTUs between groups.

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