16S rRNA amplicon sequencing of broiler intestinal tract following antibiotic use
16S rRNA genes of interest were amplified using the primer set 16S V3/V4: 515F-806R  with the barcode included in the PCR product (Yu et al., 2005). PCR products were mixed with 1X loading buffer containing SYBR green in a 1:1 ratio and electrophoresed on a 2% agarose gel. Samples with a bright band at the 400  450bp marker were excised using the Qiagen Gel Extraction Kit (Qiagen, Germany). DNA libraries were prepared using the NEBNext UltraTM DNA Library Prep Kit (New England Biolabs, United States) for Illumina and quantified via Qubit and qPCR.