title: 16S sequencing of gut microbiome
design: Microbial DNA from SI aspirate and fecal samples was extracted using phenol chloroform method. Microbial DNA was sent to the University of Minnesota Genomics Center for 16S rRNA sequencing. Amplicons were generated from the 16S rRNA V4 hypervariable region using barcoded primers ([forward overhang] + 515 F: [TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG]GTGCCAGCMGCCGCGGTAA; and [reverse overhang] + 806R: [GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG] GGACTACHVGGGTWTCTAAT). Samples were sequenced using Illumina MiSeq using 2x300 bp chemistries. Sequencing reads were annotated essentially as described by Callahan et al. (2016) (3). Briefly, Atropos was used to remove primers, DADA2 for trimming, denoising, taxonomy assignment (with Silva v132 16S sequence database), SortMeRNA and Infernal for filtering, and FastTree for generating phylogenetic trees.
identifiers.namespace: SUB15547581
identifiers.id: SB106