*Purpose: Kidney ischemia reperfusion injury (IRI) leads to changes in gut microbiome, and pre-IR microbiome changes can modify course of experimental tissue injury. There is limited data targeting microbiota after injury to improve renal IRI, important since most patients are diagnosed after IR. We hypothesized that modification of gut microbiome after IR can accelerate the course of kidney repair after experimental IRI in mice.

*Methods: B6 mice underwent 50 min unilateral IRI. After inducing IRI, mice were divided into 4 groups: control (no antibiotics -ABXs), amoxicillin, metronidazole and combination of ABXs (ampicillin, metronidazole, neomycin, and vancomycin) groups. Glomerular filtration rate (GFR) was measured by gold-standard inulin clearance at baseline, 24 h, 1, 2, 3, and 4 weeks. Plasma short chain fatty acid (SCFA) levels were measured. Stool DNA was analyzed with 16s sequencing. Mice were sacrificed after 4 weeks. Kidney fibrosis was assessed with Masson’s trichrome staining and Col1α1, TGFβ, and αSMA profibrotic genes expression were measured with quantitative RT-PCR. Kidney T cell numbers and activation were measured with flow cytometry. To evaluate role of CD4 T cells and microbiota, CD4 KO mice and germ free (GF) mice were studied.

*Results: Amoxicillin treated mice had significantly (P<0.01) higher GFR compared to control 4 weeks after IR (931 vs 758 μL/min/100g). Control mice had significantly higher percentage of necrotic tubules in both cortex (12.1 vs 5.5%, P<0.01) and outer medulla (13.9 vs 6.6%, P<0.01) compared to amoxicillin treated mice. Pro-fibrotic TGFβ mRNA expression was significantly increased (P<0.01) in the kidneys of control mice compared to amoxicillin treated mice (4.5 vs 1.8-fold changes). No significant differences were detected in expression of Col1α1 and αSMA genes. No differences were observed in SCFA levels between control and amoxicillin group. Flow analysis showed significantly reduced (P<0.01) CD4 T cells and increased (P<0.01) CD8 T cells in amoxicillin group. Amoxicillin treated CD4 KO mice had higher GFR at 4 weeks (1028 vs 802 μL/min/100g, P=0.01) compared to vehicle treated CD4 KO mice. No significant differences were detected in GFR level and fibrosis gene expression in GF mice treated with amoxicillin compared with GF control. Other antibiotic treated groups showed variable responsiveness.

*Conclusions: Amoxicillin given after IRI accelerates kidney repair. The mechanism appears dependent on gut bacteria but independent of CD4 T cells. SCFA levels did not correlate, and 16s sequencing to identify possible candidate gut bacteria is in progress. Modification of gut bacteria is a promising novel approach to accelerate repair from IRI, which could improve the quality and quantity of deceased donor organ transplants.

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