Detailed study design and study procedures have been reported previously (22 (link)). In brief, four-week-old A/J, C57BL/6J, FVB/NJ, and NOD/ShiLtJ mice (The Jackson Laboratory, Bar Harbor, ME) were acclimated for two weeks and then randomized to one of five diets: traditional Mediterranean diet (MeD), Japanese diet (JD), typical American diet (mentioned as Western diet (WD) hereafter), ketogenic diet (KD), or control mouse chow with five mice per diet, sex, and strain (Supplementary Figure 1). Mice were housed five per cage and maintained at 22°C under a 12-h light cycle. The mice were maintained on the experimental human and mouse control diets from 6 to 30 weeks of age. Fecal samples were collected at 30 weeks of age and stored at −80°C until further processing. The final dataset had 16S rRNA gene amplicon sequencing data from 149 mice (n = 27–34 per diet, 27–44 per strain, and 3–10 per diet-strain, Supplementary Table 1). The study protocol was approved by Texas A&M University Institution Animal Care and Use Committee (IACUC) protocol number 2017-0076. All experiments were performed in accordance with relevant guidelines and regulations.
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