Background: Symbiotic interactions of microorganisms are widespread in nature, and support fundamentally important processes linking health and disease to the bacterial ecology. Intestinal microbiota is the largest source of microbial stimulation that exerts both harmful and beneficial effects on human health. It participates in the development of the postnatal immune system as well as oral tolerance and immunity. The recently explored impact of the microbiota on energy metabolism, gut hormone regulation and the gut-brain axis was judged to be a fascinating topic and of great value in the future, and can have a clinical role in the management of obesity and diabetes. Objective: To assess the impact of the gut microbe, Lactobacillus acidophilus, in patients with type 2 Diabetes Mellitus (controlled and uncontrolled) compared to healthy individuals, as a preliminary approach to future treatment with probiotics, prebiotics or diet modulation. Methods: A case control study was conducted on 30 diabetic patients and 10 control individuals. All patients were subjected to full history, thorough clinical examination, and laboratory measurement of fasting blood sugar, 2 hours post prandial, Glycosylated Hemoglobin (HbA1C), CRP (C-Reactive Protein), Lipid profile, and Identification of stool Lactobacillus acidophilus by PCR (polymerase chain reaction) technique. Results: Significantly lower Stool Lactobacillus acidophilus PCR count among diabetic patients when compared to healthy control individuals. Conclusion: Stool Lactobacillus acidophilus PCR count was lower among type 2 diabetic patients, which may show relationship of lactobacillus with type 2 diabetes mellitus. However, further studies are needed to determine correlation or causation of this relationship.