Illumina MiSeq paired end sequencing
Goal:  To determine the inherent variability of the gut microbiota between samples obtained from two different areas of the intestinal tract (rectal faeces (RF) and terminal ileum content (TIC) in six identically treated sheep.  Setup of individual library:  Pooled PCR amplicons were sequenced at Edinburgh Genomics, University of Edinburgh, using Illumina miSeq platform. Paired-end sequencing (2x250 bp) was run on the Illumina MiSeq platform. Three separate sequencing primers were used for sequencing; two used to read sequences from either end: Read 1 primer (TATGGTAATT GT GTGCCAGCMGCCGCGGTAA) to yield the 5� read; Read 2 primer (AGTCAGTCAG CC GGACTACHVGGGTWTCTAAT) to yield the 3� read and a third as the indexing primer (ATTAGAWACCCBDGTAGTCCGGCTGACTGACT) used to read the barcode sequence.