MiSeq replaces 454 in Microbiome projects

One of my Bioinformatics students, Laura Cox, is working on a Human Microbiome Project  study with Martin Blaser. Yesterday, she presented a lab report to a standing room only crowd about her sequencing work on bacterial populations using the Illumina MiSeq machine. Up till now, HMP work was about the only sequencing that we consistently ran on the 454 machine. Laura showed that with the MiSeq paired-end 150 bp sequencing protocol, it was possible to sequence 16S amplicons (in the V4 region) from both ends and stitch them together using the ea-utils FASTQ-join [Erik Aronesty (2011). ea-utils : "Command-line tools for processing biological sequencing data"; http://code.google.com/p/ea-utils] to get about 260 bp reads on each amplicon. Laura used a custom multiplex scheme to get 192 different samples into one MiSeq run, which after demultiplexing, gave about 2,000 P-E reads per sample. 


She also demonstrated that the resulting sequence data could be processed with QIIME [http://www.qiime.org] to get reasonable taxonomy information, build phylogenetic trees, and apply all the cute tools to calculate diversity and compare groups of samples by PCA and UNIFRAC [http://bmf2.colorado.edu/unifrac].


The economics of MiSeq are persuasive. It is giving amplicon data at about 40X less cost than 454. As our HMP protocols shift over to MiSeq, this will be the last year that we keep the 454 machine in the Genomics Core Lab.