title: MiSeq of chicken: cecum
design: 16S metagenomic libraries from chicken cecal contents were constructed following the Illumina protocol as modified by Kozich, 2013.   Extracted genomic DNA was amplified with Illumina indexed adaptor primers (V4 primers). Each PCR reaction contained 12.5 l Paq5000 Master Mix (Agilent Technologies, Mississauga, Canada) , 1.0 l of each 10 M primer, 8.5 l of molecular grade water, and 2.0 l of bacterial community DNA.   Size selection and purification was completed using AMPure XP beads (Beckman Coulter, Mississauga, Canada) following manufacturers recommendations.  Quantification was confirmed with a Qubit (Thermo Fisher Scientific, Mississauga, Canada) and size selection evaluated using a Bioanalyzer (Agilent Technologies). Indexed DNA libraries were normalized to 1.5 ng/l and pooled together. A PhiX control (20%) was run with the normalized DNA library, and both were denatured and diluted to 4 pM prior to loading into the MiSeq Reagent Kit v2 500-cycle (Illumina, San Diego, CA).