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The aetiology of obesity is multi-factorial. Recent research has identified a novel association between endotoxaemia (circulating lipopolysaccharide in the systemic circulation) and low-grade inflammation in the adipose organ, which may contribute to obesity. The mechanisms for the low-grade elevation of circulating lipopolysaccharide in obesity are poorly understood. Vitamin D has been increasingly recognised for its pleiotropic actions beyond maintenance of musculoskeletal health. The parathyroid-vitamin D axis is altered in obesity. Circulating vitamin D levels are lower in obese individuals. The regulatory role of vitamin D in the immune system and colonic mucosa may explain the under-appreciated contribution of vitamin D deficiency in the obese to the pathogenesis of endotoxaemia and adipose inflammation. We propose a hypothetical model linking metabolic endotoxaemia with vitamin D deficiency in obesity. A therapeutic approach involving the use of probiotics and vitamin D metabolites in the obese is described.