The Illumina MiSeq sequencing protocol was based on our previous published literature (12). Briefly, microbial DNA was extracted from human and animal stool samples using the QIAamp DNA Stool Mini Kit (QIAGEN, Hilden, Germany). The V3 and V4 regions of the bacteria 16S rRNA gene were amplified by polymerase chain reaction (PCR) using primers 338F and 806R (31). PCR reactions were performed in triplicate 20-μl mixtures. Primers included an eight-base sequence unique to each sample. Amplicons were extracted from 2% agarose gels and purified using the AxyPrep DNA Gel Extraction Kit (Axygen Biosciences, Union City, CA). Purified amplicons were quantified using QuantiFluor-ST (Promega, USA) and paired-end–sequenced (2 × 250) on an Illumina MiSeq platform according to the standard protocols.

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