16S amplicon sequencing of manufactured diet
DNA was extracted using the QIAmp PowerFecal DNA Kit (Qiagen, Valencia, CA, USA) according to manufacturers instructions. The V1-V3 region of the bacterial 16S rRNA gene was amplified using the 27F/534R primer set to produce amplicons for Illumina sequencing via a two-step PCR. PCR1 amplified the target sequences and then PCR2 added barcodes and Illumina adapters. PCR products from individual samples were visualized, cleaned, quantified, and pooled for 2 x 300bp paired-end sequencing.