DNA was extracted from fecal and cecal samples using mechanical disruption (bead-beating with 0.1 mm zirconium beads) in phenol:chloroform:IAA in the same manner as described by McNulty et al. in a previous publication (PMID: 22030749). Libraries were prepared according to a slightly modified version of the protocol accompanying the Illumina Genomic DNA Sample Prep Kit. Briefly, total bacterial gDNA was sonicated in a BioRuptor XL water bath sonicator, cleaned up and concentrated using a Qiagen PCR Purification column, and end-repaired using Klenow DNA polymerase. The blunt DNA was treated with Klenow fragment (exo minus) to add an adenine overhang, and the A-tailed molecules were ligated to the relevant barcoded Illumina adapter sequence.  Adaptered-DNA was then size-selected by agarose gel electrophoresis.  Fragments of the appropriate size were PCR amplified and purified, after which the purified PCR products were loaded on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer I, II or IIx following the manufacturer's protocols.
GEO Accession
GSM1172527