Editing BioMicroCenter:Research (section)

=== High Throughput Metagenomics Using Illumina Sequencing - [http://almlab.mit.edu/l ALM LAB] - [http://web.mit.edu/be BE] - [http://web.mit.edu/cehs CEHS] === 
Understanding the role of the human microbiome in health and disease is an emerging field, and has been targeted as a major NIH Roadmap Initiative. Microbial community analysis by 16S rRNA sequencing is a key component of microbiome studies, together with whole genome sequencing and metagenomics. The BioMicro Center has worked with the Alm lab to establish and optimize an experimental approach to generating partial 16S rRNA sequences that is orders of magnitude less expensive than conventional methods, thus enabling unprecedented resolution in microbiome comparisons using the Illumina Genome Analyzers. <BR><BR>
The use of Illumina sequencing for assay microbiomes has been limited by read length and by financial considerations. In addition, homopolymeric sequences are very difficult to process using the standard Illumina image analysis software. Improvements to read length introduced by Illumina and careful selection of priming sites have addressed the former issue. The expense of the reads has been solved by using very highly multiplexed lanes. While each lane of Illumina sequence costs $3,300 for the read lengths needed for this project, multiplexing the samples (up to 96x) dramatically lowers the cost per sample. Barcoding the sample also allowed the Alm lab to bypass the lack of complexity in ribosomal reads as the highly diverse sequences meet the criteria needed for spot finding. Data from this project has been used in an NIH grant application and in a patent application.