 dna sequencing continues to decrease in cost with the illumina hiseq2000 generating up to 600  gb of paired - end 100 base reads in a ten - day run . here 
 we present a protocol for community amplicon sequencing on the hiseq2000 and miseq illumina platforms , and apply that protocol to sequence 24 microbial communities from host - associated and free - living environments . a critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform . 
 we show that the protocol developed for these instruments successfully recaptures known biological results , and additionally that biological conclusions are consistent across sequencing platforms ( the hiseq2000 versus the miseq ) and across the sequenced regions of amplicons . 
Supplementary Material