title: 16S amplicon analysis of mouse gut microbiome
design: We compared fecal microbial composition and diversity between mice humanized by stool from dysbiotic" human donors and healthy-like human donors with diarrhea before and after exposure to C. difficile.  Dysbiotic donors had diarrhea and gut microbial communities that were more similar to microbial communities of patients with Clostridium difficile infections.  Healthy-like donors also had diarrhea but had gut microbial communities more similar to healthy individuals. Mice humanized from the same human sample were co-housed in covered cages, and animals humanized with like communities (dysbiotic or healthy-like) were co-housed in the same isolator. Human derived communities were allowed 4 weeks to adapt to the mouse gut; then, the mice were challenged by oral gavage with 300?l of overnight liquid culture growth of C. difficile strain 630. Fecal pellets were collected before and at day 1, day 2, and day 6 post-challenge for C. difficile colony counts.  DNA was extracted from mouse pellets 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.
library_name: MouseStudy1_healthy-like_Healthy-like_C_Week4.PreCdiff