title: Evaluating microbiome patterns, microbial species, and leg health associated with reused litter in a commercial broiler barn
design: Fresh cecal contents from six TR and six CL birds was aseptically collected from flocks in Y1 and Y2 into whirl pak bags on ice, and were immediately transported to be lab for DNA extraction using a Bacterial Genomic DNA Isolation Kit (Norgen Biotek, Corp., ON, Canada) per manufacturer's instructions. Extracted DNA was sent to the Iowa State University DNA Facility for library preparation and sequencing. The V4-V5 region of the 16S rRNA gene (515F, 926R) was amplified and sequenced using Illumina MiSeq sequencing technology generating 2x250bp reads.