LBA01-01: Fungi and Bacteria Entombed within Human Calcium Oxalate-Apatite Kidney Stones
Friday, May 15, 2020
7:00 AM – 9:00 AM
Jessica Saw, Mayandi Sivaguru, Elena Wilson, Yiran Dong, Rob Sanford, Christopher Fields, Melissa Cregger, William Bruce, Annette Merkel, John Lieske, Amy Krambeck, Marcelino Rivera, Tim Large, Nicholas Chia, Michael Romero, Dirk Lange, Joe Weber, Bruce Fouke
Introduction: Fungi and Bacteria Entombed within Human Calcium Oxalate-Apatite Kidney Stones
Methods: Kidney stones composed of both calcium oxalate and apatite (n=18) were removed from patients undergoing percutaneous nephrolithotomy. Bacterial and fungal 16S rRNA gene sequences and internal transcribed spacer (ITS) regions were amplified from whole stone genomic DNA on a FluidigmTM system and then paired-end sequenced on an IlluminaTM MiSeq. The datasets were denoised and analyzed with DADA2 software. Phylogenetic diversity estimates and statistical analysis were completed using Phyloseq v1.22.3 and R. Doubly polished petrographic 25 µm-thick thin sections were analyzed using brightfield, confocal and super-resolution autofluorescence microscopy to identify crystalline architecture and entombed organic matter.
Results: A low-diversity community of entombed microbes were detected in all 18 stones, including bacterial sequences affiliated with the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and fungal sequences affiliated with Aspergillus niger. Fungal sequences were entombed in 9 of 18 stones and correlated with higher urine calcium concentrations (335 ± 131 mg, p=0.01). Thin section petrography identified one calcium oxalate-apatite stone (of a total of 30 stones analyzed) that contained distinct and well-preserved fungal borings within apatite spherules (Fig. 1).
Conclusions: A role for Aspergillus niger in human kidney stone mineral precipitation, secondary erosion and biogeochemical recycling is consistent with documented fungal activity in all natural environmental systems. These unexpected observations suggest a possible role for an entombed microbiome in human stone pathogenesis. Source of
Funding: Mayo Clinic and University of Illinois Strategic Alliance for Technology-Based Healthcare; Mayo Clinic O’Brien Urology Research Center (No. DK100227); Mayo Clinic Center for Individualized Medicine; National Aeronautics and Space Administration (NASA) Astrobiology Institute (Cooperative Agreement No. NNA13AA91A)