Antibiotic perturbation of kidney microbiome

Molecular and culture-based clinical studies of the urinary tract (UT) microbiome suggest a direct, antibiotic-dependent, impact on kidney physiology. However, evidence for a consistent kidney microbiome is based on studies of kidney stones and kidney urine and no such studies exist for kidney tissue itself, except in cases of disease. Here, we describe the impact of a commonly used perioperative antibiotic, cefazolin, on the resident renal microbiome towards promoting a lithogenic environment. Cefazolin led to a loss of uroprotective Lactobacillus spp. and proliferation of Enterobacteriaceae, which includes many known uropathogens. The effects of cefazolin were dependent on the duration of administration and recovery of the microbiome was apparent. Experiments on uroprotective L. crispatus and stone-associated E. coli reveal that these clinically divergent strains differentially influence calcium oxalate (CaOx) lithogenesis through the incorporation of CaOx inhibitors or promoters, respectively, in a recently discovered, non-canonical pathway of CaOx crystallization.