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Kidney Week

Abstract: PO2236

Bacterial and Fungal Communities Entombed Within Calcium Oxalate, Struvite, and Brushite Human Kidney Stones

Session Information

Category: Pathology and Lab Medicine

  • 1601 Pathology and Lab Medicine: Basic

Authors

  • Wilson, Elena Marie, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
  • Saw, Jessica Jia-Wen, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
  • Sivaguru, Mayandi, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
  • Lange, Dirk, Jack Bell Research Centre, Vancouver, British Columbia, Canada
  • Dong, Yiran, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
  • Sanford, Robert A., Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
  • Fields, Christopher J., Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
  • Cregger, Melissa, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
  • Bruce, William J., Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
  • Merkel, Annette, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
  • Lieske, John C., Mayo Clinic Minnesota, Rochester, Minnesota, United States
  • Krambeck, Amy E., Mayo Clinic Minnesota, Rochester, Minnesota, United States
  • Rivera, Marcelino Eduardo, Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Large, Tim, Indiana University School of Medicine, Indianapolis, Indiana, United States
  • Chia, Nicholas L., Mayo Clinic Minnesota, Rochester, Minnesota, United States
  • Romero, Michael F., Mayo Clinic Minnesota, Rochester, Minnesota, United States
  • Weber, Joseph R., Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
  • Fouke, Bruce W., Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States
Background

Mechanisms of human kidney stone formation are poorly understood. More than 70% of stones are composed of calcium phosphate and/or oxalate. Recent studies have shown that kidney stone formation follows a continuum of complex biogeochemical transitions and is strongly influenced by the presence of human host and microbial organic matter.

Methods

Kidney stones, removed via percutaneous nephrolithotomy, were prepared as 25-µm thick doubly polished petrographic thin sections and analyzed using brightfield, confocal and super-resolution autofluorescence microscopy. DNA was extracted from 18 calcium oxalate stones, 1 struvite stone, and 1 brushite stone for FluidigmTM PCR amplification. Paired-end sequencing of bacterial 16S rRNA gene sequences and fungal internal transcribed spacer (ITS) regions was completed using IlluminaTM MiSeq. Reads were correlated with patient metadata and analyzed using DADA2, phyloseq v1.22.3 and R software.

Results

A 153-amplicon sequence variant (ASV) fungal community, dominated by A. niger (92% of total reads), was present in 11 of 20 total sequenced stones and correlated with higher patient urine calcium excretion (335 + 131 vs 175 + 108 mg/day, p=0.01). Petrography of 30 stones documented entombed coccoidal and rod-shaped bacterial cells in the struvite stone and well-preserved fungal borings and hyphae in one calcium oxalate/apatite stone. Entombed bacterial sequences were most closely affiliated with Acinetobacter and Cutibacterium. The brushite stone microbiome community contained Capnocytophaga and Humibacter and the struvite stone microbiome community included Pseudomonas and Staphylococcus.

Conclusion

This study presents the first evidence of a low-diversity fungal and bacterial microbiome community entombed and preserved within calcium oxalate, struvite, and brushite human kidney stones. The macromolecules secreted by the fungal and bacterial communities may play crucial roles in human kidney stone growth, dissolution, and recrystallization, similar to processes that have been documented in natural geologic stone growth.

Funding

  • NIDDK Support