DNA sequencing
Obesity
OBESITY, DISEASE, POSITIVE
Fecal sample processing, nucleic acid extraction, library preparation, and whole genome shotgun sequencing were performed at the University of North Carolina at Chapel Hill Microbiome Core (Chapel Hill, NC, USA), which is supported by the following grants: Gastrointestinal Biology and Disease (CGIBD P30 DK034987) and the UNC Nutrition Obesity Research Center (NORC P30 DK056350). DNA was extracted using the QIAamp Fast DNA Stool Mini Kit and library was prepared using the Swift 2S Turbo DNA library kit. DNA was sequenced on the Illumina HiSeq 4000 PE 150 platform. Positive controls included ZymoBIOMICS Microbial Community Standard (Cat. No. D6300), Microbial Community DNA standard (Cat. No. D6305), and Gut Microbiome Standard (Cat. No. D6331). DNA-free deionized water was used as a negative control and to detect possible contamination. To avoid batch effects, fecal samples were randomized prior to nucleic acid extraction and all samples were sequenced at the same time. Mean total reads were 18,339,758, with similar read depth on each diet (19,475,004 for the WD and 17,204,513 for the MBD).