Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms (MiSeq)

Twenty-four samples were sequenced on three paired-end Illumina HiSeq2000 lanes, and in one paired-end MiSeq run. The samples represented soil (source: USA; n=8) and several host-associated environment types: human feces (source: USA; n=2), mouth (source: USA; n=2) and skin (source: USA; n=6); canine feces (source: USA; n=1) mouth (source: USA; n=1) and skin (source: USA; n=4). These four paired-end lanes (three on HiSeq and one on MiSeq) resulted in eight sets of reads, corresponding to 5prime and 3prime reads from each lane. These sets of reads were treated as independent replicates to assess the reproducibility of the results.