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Cardiometabolic impairments that begin early in life are particularly critical, because they often predict metabolic dysfunction in adulthood. Obesity, high-fat diet (HFD), and inactivity are all associated with adipose tissue (AT) inflammation and insulin resistance (IR), major predictors of metabolic dysfunction. Recent evidence has also associated the gut microbiome with cardiometabolic health.The objective of this study is to compare equal energy deficits induced by exercise and caloric reduction on cardiometabolic disease risk parameters including AT inflammation, IR, and gut microbiota changes during HFD consumption.Obesity-prone rats fed HFD were exercise trained (Ex, n = 10) or weight matched to Ex via caloric reduction although kept sedentary (WM, n = 10), and compared with ad libitum HFD-fed (Sed, n = 10) rats for IR, systemic energetics and spontaneous physical activity (SPA), adiposity, and fasting metabolic parameters. Visceral, subcutaneous, periaortic, and brown AT (BAT), liver, aorta, and cecal digesta were examined.Despite identical reductions in adiposity, Ex, but not WM, improved IR, increased SPA by approximately 26% (P < 0.05 compared with WM and Sed), and reduced LDL cholesterol (P < 0.05 compared with Sed). WM and Ex both reduced inflammatory markers in all AT depots and aorta, whereas only Ex increased indicators of mitochondrial function in BAT. Ex significantly increased the relative abundance of cecal Streptococcaceae and decreased S24-7 and one undefined genus in Rikenellaceae; WM induced similar changes but did not reach statistical significance.Both Ex and WM reduced AT inflammation across depots, whereas Ex caused more robust changes to gut microbial communities, improved IR, increased fat oxidation, increased SPA, and increased indices of BAT mitochondrial function. Our findings add to the growing body of literature indicating that there are weight-loss–independent metabolic benefits of exercise.