**5. Conclusions**

Under the conditions of model experiments, the effect of bacteria that are present in human urine (*Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae* and *Staphylococcus aureus*) on the formation of the renal stone mineral phases, such as brushite, struvite, vitlocite, octacalcium phosphate, apatite, whewellite, and weddellite, was studied in systems simulating the composition of human urine and using two types of nutrient media (Muller–Hinton Broth and Meat–Peptone Broth). Multidirectional changes in the pH values of the solutions were analyzed, which are the result of all system components' interactions with the crystallization process.

It was shown that the presence of bacteria has a different effect on the phosphate and oxalate phases' formation. The presence of pathogens and nutrient media significantly affect the precipitant phase composition and the position of the resulting phosphate phase's crystallization boundaries, which can shift both to more acidic (struvite, apatite) and more alkaline (brushite) areas. Under conditions of oxalate mineralization, bacteria accelerate the nucleation of calcium oxalates by almost two times and also increase the amount of oxalate precipitates along with phosphates and stabilize the calcium oxalate dihydrate to weddellite.

As it can be seen from the reported results and the available literature data, the bacterial effect on oxalate and phosphate phase formation is different. Thus, in the case of oxalate mineralization, primarily (most likely), the inflammatory process will contribute to the decrease of oxalate supersaturation in urine due to calcium oxalate crystallization. In the case of phosphate mineralization, the change in urine pH and the products of bacterial metabolism will be of major importance. Studies aimed at identifying the specific action of certain microorganisms on the crystallization of certain mineral phases should serve to develop individual methods of treatment and prevention of urolithiasis.

The obtained results could be regarded as the scientific basis for understanding the mechanisms of bacterial participation stone formation in the human urinary system and the creation of biotechnological methods for the prevention of this disease.

**Author Contributions:** Conceptualization, A.R.I., O.V.F.-K., and V.V.M.; methodology, A.R.I., M.A.K., and O.V.F.-K.; investigation, A.R.I., A.M.N., M.A.K., and V.V.M.; writing—original draft preparation, A.R.I., M.A.K., and A.M.N.; writing—review and editing, A.R.I., O.V.F.-K., and V.V.M.; visualization, A.R.I. and A.M.N.

**Funding:** This research was funded by the Russian Science Foundation (grant 18-77-00026 to A.R.I.).

**Acknowledgments:** The XRD have been performed at the X-ray Diffraction Centre of the St. Petersburg State University. We are grateful to reviewers for useful comments.

**Conflicts of Interest:** The authors declare no conflict of interest.
