Background Helicobacter pylori (H. pylori) is well-known for its role in chronic gastritis and gastric cancer. Eradication of these carcinogenic bacteria from the gut is one of the major challenges for the clinicians. The complexity of treatment is mainly owing to, antibiotic resistance and relapse due to extra gastric reservoir in the oral cavity. Our study focuses on the isolation of H. pylori from distinct habitats (gastric biopsy and gastric juice) of the gut microenvironment and its subsequent characterization. Further, we have also evaluated the effect of various plaque control agents on isolated strains of H. pylori.Results The strains isolated from two different habitats of the same subject shows a striking difference in their growth pattern. Promisingly, some included chemicals are effective in growth inhibition after recommended 30 sec treatment. The subsequent evaluation shows that chemical B (out of chemical A, B, C, D and E) is the most effective and downregulate the expression of CagA in the infected AGS cells.Conclusion For the fast time, in our study the pylori isolated from different habitat of the same subject shows differential growth pattern. Nowadays, antibiotic resistance and relapse of H. pylori make it difficult to eradicate the bacteria from gastric as well as oral reservoir. Thus, this study may help to reduce the bacteria in their oral reservoir and also control the H. pylori migration from oral to gastric compartment.