title: 16S amplicon analysis of human gut microbiome
design: We compared microbial composition and diversity between fecal samples from individuals who had diarrhea but were negative for Clostridium difficile, individuals who were C. difficile positive, and healthy individuals.  DNA was extracted from human stool samples (0.25g stool per extractions) a using a MoBio PowerSoil Kit (MoBio Laboratories, Carlsbad, CA, USA).  The V4 region (515F, 806R) of the 16S rRNA gene was amplified and sequenced using an Illumina MiSeq (Illumina, San Diego, CA) at the Mayo Clinic Medical Genome Facility (Mayo Clinic, Rochester, MN). Demultiplexing and quality filtering was performed in QIIME 1.9.1.  Operational taxonomic unit (OTU) clustering at 97% sequence similarity and taxonomic assignment was performed with UCLUST, RDP classifier, and Greengenes (DeSantis et al. 2006). OTUs were picked closed-reference and de novo.