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

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 5 and 3-prime reads from each lane. These sets of reads were treated as independent replicates to assess the reproducibility of the results.