title: U1_Site1_day_2
design: Two sets of fusion primers were used: the first set generated the primary 16S amplicons and the second converted the primary amplicons into libraries for sequencing (Glenn et al. in prep).  Primers targeting 16s rRNA hypervariable V4 region were selected to capture the diversity of fecal-associated bacteria (Forward: 5’-CAGCMGCCGCGGTAATWC -3’; Reverse: 5’-CCGTCAATTCCTTTRAGGTT-3’(20)).  Forward primers also contained the Illumina Nextera Read 1 sequence (5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3’), whereas reverse primers had the Illumina Nextera Read 2 sequence (5’-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-3’). Unique sequence tags of varying lengths (5-8 nt) were synthesized between the Nextera and 16S sequences.  A total of eight forward and 12 reverse fusion primers were synthesized.