The contribution of dysbiotic gut microbiota configuration is essential when making reference to the metabolic disorders by increasing energy. It is important to understand that the gut microbiota induced metabolic disease mechanisms and inflammations. Thus it is imperative to have an insight into the state of all chronic subclinical inflammations influencing disease outcomes. However, from the emerging studies, there still exist inconsistencies in the findings of such studies. While making the best out of the reasons for inconsistencies of the findings, this review is designed to make a clear spell out as to the inconsistence of gut microbiota with respect to diabetes. It considered gut-virome alterations and diabetes and gut-bacteriome-gut-virome-alterations and diabetes as confounding factors. The review further explained some study design strategies that will spontaneously eliminate any potential confounding factors to lead to a more evidence based diabetic-gut microbiota medicine. Lipopolysaccharide (LPS) pro-inflammatory, metabolic endotoxemia and diet/gut microbiota insulin-resistance and low-grade systemic inflammation induced by gut microbiota can trigger pro-inflammatory cytokines in insulin-resistance, consequently, leading to the diabetic condition. While diet influences the gut microbiota, the consequences are mainly the constant high levels of pro-inflammatory cytokines in the circulatory system. Of recent, dietary natural products have been shown to be anti-diabetic. The effects of resveratrol on the gut showed an improved lipid profile, anti-inflammatory properties and ameliorated the endotoxemia, tight junction and glucose intolerance.