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Pooled DNA was used as template for amplification of the full-length 16S rRNA gene with 27 F (5��-AGAGTTTGATCCTGGCTCAG-3��) and 1492R (5��-GGTTACCTTGTTACGACTT-3��) primers [30]. To limit [http://en.wikipedia.org/wiki/Diglyceride diglyceride] PCR bias, gradient PCR was performed with 5 units/��L of TaKaRa Ex Taq? (Takara Bio Inc., Otsu, Japan) across 7 different annealing temperatures with the following reaction: 1 minute at 94��C; 35 cycles of 1 minute at 94��C, 30 s at 48��C to 58��C (7��C temperature gradient) and 1 minute at 72��C; and a final extension for 7 minutes at 72��C. Amplicons were combined across gradients and cleaned with the QIAquick PCR Purification Kit (Qiagen, Hilden, Germany) as directed by the manufacturer. Cleaned amplicons were quantified via Qubit (Life Technologies, Carlsbad, CA, USA) and input into an Illumina library preparation pipeline. [http://www.selleckchem.com/products/a-1210477.html A-1210477 nmr] Sequencing preparation and sequencing Illumina library construction followed standard protocols at the University of California Davis DNA Technologies Core Facility (http://dnatech.genomecenter.ucdavis.edu) as previously described [29]. Briefly, amplicons were fragmented to an average size of 225 bp using the Bioruptor NGS (Diagenode, Seraing, Belgium), and sheared fragments were used in a robotic library preparation protocol using the Appollo 324 robot (Integenx, Pleasanton, CA, USA) following the manufacturer��s instructions. Each sample was tagged with unique barcodes consisting of six nucleotides internal to the adapter read as a separate indexing read, and ligated to each fragment. There were 12 cycles of PCR enriched for adapter-ligated fragments before library quantification and validation. Fecal samples underwent the same preparation with two exceptions: (1) genomic DNA was used and (2) DNA was fragmented to 550 bp. Libraries were added, in equimolar amounts, to the Illumina HiSeq 2000 platform. Paired-end sequences were obtained with 100 cycles and the data processed with Casava [http://www.selleckchem.com/products/ldn193189.html selleck compound] version 1.8.2. Raw read data has been deposited in the NCBI Short Read Archive (accession number SRP033353). EMIRGE assembly of full-length 16S rRNA gene amplicons EMIRGE is an iterative template-guided assembler that relies on a database of 16S rRNA gene sequences to probabilistically generate full-length 16S rRNA gene sequences and provide the relative abundance of these sequences in the assayed consortia [31]. For the reference database, we used version 108 of the SILVA SSU database, filtered to exclude sequences