title: Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms.
abstract: 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.
authors.affiliation: Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA.
authors.forename: J Gregory
authors.initials: JG
authors.lastname: Caporaso
authors.forename: Christian L
authors.initials: CL
authors.lastname: Lauber
authors.forename: William A
authors.initials: WA
authors.lastname: Walters
authors.forename: Donna
authors.initials: D
authors.lastname: Berg-Lyons
authors.forename: James
authors.initials: J
authors.lastname: Huntley
authors.forename: Noah
authors.initials: N
authors.lastname: Fierer
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Owens
authors.forename: Jason
authors.initials: J
authors.lastname: Betley
authors.forename: Louise
authors.initials: L
authors.lastname: Fraser
authors.forename: Markus
authors.initials: M
authors.lastname: Bauer
authors.forename: Niall
authors.initials: N
authors.lastname: Gormley
authors.forename: Jack A
authors.initials: JA
authors.lastname: Gilbert
authors.forename: Geoff
authors.initials: G
authors.lastname: Smith
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
mesh_terms: D001419:Bacteria / Q000235:genetics*; D017753:Ecosystem; D004783:Environmental Microbiology; D059014:High-Throughput Nucleotide Sequencing / Q000191:economics / Q000295:instrumentation* / Q000379:methods*; D015203:Reproducibility of Results