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

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…

• NS
  National Science Foundation
• HH
  Howard Hughes Medical Institute
• BA
  Bill and Melinda Gates Foundation
• CA
  Crohn's and Colitis Foundation of America
• AW
  Amazon Web Services
• CA
  Crohn's and Colitis Foundation
• NI
  National Institutes of Health