The role of intestinal microbiota is becoming ever more important in the context of obesity, type II diabetes (T2D), and infectious disorders as represented by the emerging discipline therapeutic microbiology. The gut microbiota is strictly interconnected with obesity and T2D playing also an important role in immune system regulation. Obesity and diabetes can lead to chronic inflammation, which results in the secretion of pro-inflammatory cytokines like IL-6, IL-1, and TNF-alpha, causing immune system alteration which predisposes patients with obesity and T2D to chronic infections. Therefore, the principal aim of the study is to investigate changes in gut microbiota composition between patients with chronic infections or not, so as to attribute to specific phyla the formation of the infections in these patients.