title: 16S of mus musculus exposed to stress: fecal pellets
design: This model was adapted from social stress model of traumatic stress,  that uses a "cage-within-cage resident-intruder" protocol where subject mice are exposed to aggressor mice.  We were interested in assessing the16S ribosomal RNA gene from fecal samples collected daily from control and aggressor-exposed mice during a 10-day study.  DNA was extracted using the MoBio PowerSoil DNA Elution Accessory Kit.  For library preparation, we used primers that were previously designed to amplify the V3-V4 hyper-variable regions of the 16S rRNA gene. A limited cycle PCR generated a single amplicon of ~460 bp, and this was followed by addition of Illumina sequencing adapters and dual?index barcodes. Using paired 300 bp reads, and MiSeq v3 reagents, the ends of each read were overlapped to generate high?quality, full?length reads of the V3 and V4 region in a single run. Two MiSeq sequencing runs were performed for each sample to generate reads for metagenomic surveys.