Short Communication

Subject Category: Microbial ecology and functional diversity of natural habitats

The ISME Journal (2012) 6, 1621–1624; doi:10.1038/ismej.2012.8; published online 8 March 2012

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

J Gregory Caporaso1, Christian L Lauber2, William A Walters3, Donna Berg-Lyons2, James Huntley4, Noah Fierer2,5, Sarah M Owens6, Jason Betley7, Louise Fraser7, Markus Bauer7, Niall Gormley7, Jack A Gilbert6,8, Geoff Smith7 and Rob Knight9,10

  1. 1Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
  2. 2Cooperative Institute for Research in Environmental Sciences, UCB 216, University of Colorado, Boulder, CO, USA
  3. 3Department of Molecular, Cellular and Developmental Biology, UCB 347, University of Colorado, Boulder, CO, USA
  4. 4Colorado Initiative in Molecular Biotechnology, UCB 347, University of Colorado, Boulder, CO, USA
  5. 5Department of Ecology and Evolutionary Biology, UCB 334, University of Colorado, Boulder, Colorado, USA
  6. 6Argonne National Laboratory, Argonne, IL, USA
  7. 7Illumina Cambridge Ltd., Chesterford Research Park, Saffron Walden, Essex, UK
  8. 8Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
  9. 9Department of Chemistry and Biochemistry, UCB 215, University of Colorado, Boulder, CO, USA
  10. 10Howard Hughes Medical Institute, University of Colorado at Boulder, UCB 215, Boulder, CO, USA

Correspondence: R Knight, Howard Hughes Medical Institute, University of Colorado at Boulder, UCB 215, Boulder, CO 80309, USA. E-mail:

Received 12 September 2011; Revised 13 January 2012; Accepted 19 January 2012
Advance online publication 8 March 2012



DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600Gb 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.


illumine; barcoded sequencing; QIIME