title: Gut microbial changes associated with obesity in youth with type 1 diabetes
design: We characterized the gut microbiome in participant stool samples using whole genome shotgun (WGS) sequencing. DNA was extracted using the Qiagen MagAttract PowerSoil DNA KF kit (Formerly MOBio PowerSoil DNA Kit) using a KingFisher robot. DNA quality was evaluated visually via gel electrophoresis and quantified using a Qubit 3.0 fluorometer (Thermo-Fischer, Waltham, MA, USA). Libraries were prepared using an Illumina Nextera library preparation kit with an in-house protocol (Illumina, San Diego, CA, USA). Paired-end sequencing (150 bp x 2) was done on a NextSeq 500 in medium-output mode at Microbiome Insights.