Jessica J Saw1,2,3, Mayandi Sivaguru1, Elena M Wilson1,4, Yiran Dong1, Robert A Sanford1,5, Chris J Fields6, Melissa A Cregger1,7, Annette C Merkel1,4, William J Bruce1,4, Joseph R Weber1,4, John C Lieske8,9, Amy E Krambeck10,11, Marcelino E Rivera11, Timothy Large11, Dirk Lange12, Ananda S Bhattacharjee1, Michael F Romero13,14, Nicholas Chia9,10, Bruce W Fouke1,4,5,6,15. 1. Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois. 2. Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, Illinois. 3. Mayo Clinic Alix School of Medicine, Mayo Clinic, Rochester, Minnesota. 4. School of Molecular and Cellular Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois. 5. Department of Geology, University of Illinois at Urbana-Champaign, Urbana, Illinois. 6. Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois. 7. Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee. 8. Department of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota. 9. Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota. 10. Department of Urology, Mayo Clinic, Rochester, Minnesota. 11. Department of Urology, Indiana University School of Medicine, Indianapolis, Indiana. 12. The Stone Centre at Vancouver General Hospital, Department of Urologic Sciences, University of British Columbia, Jack Bell Research Centre, Vancouver, British Columbia, Canada. 13. Department of Individualized Medicine, Mayo Clinic, Rochester, Minnesota. 14. Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota. 15. Department of Evolution, Ecology and Behavior, University of Illinois at Urbana-Champaign, Urbana, Illinois.
Abstract
Background: Human kidney stones form via repeated events of mineral precipitation, partial dissolution, and reprecipitation, which are directly analogous to similar processes in other natural and manmade environments, where resident microbiomes strongly influence biomineralization. High-resolution microscopy and high-fidelity metagenomic (microscopy-to-omics) analyses, applicable to all forms of biomineralization, have been applied to assemble definitive evidence of in vivo microbiome entombment during urolithiasis. Methods: Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, whereas one patient formed each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from seven of these 20 patients (five CaOx, one brushite, and one struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, super-resolution autofluorescence (SRAF), and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions. Results: Bulk-entombed DNA was sequenced from stone fragments in 11 of the 18 patients who formed CaOx stones, and the patients who formed brushite and struvite stones. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Aspergillus niger. Bacterial cells approximately 1 μm in diameter were also optically observed to be entombed and well preserved in amorphous hydroxyapatite spherules and fans of needle-like crystals of brushite and struvite. Conclusions: These results indicate a microbiome is entombed during in vivo CaOx stone formation. Similar processes are implied for brushite and struvite stones. This evidence lays the groundwork for future in vitro and in vivo experimentation to determine how the microbiome may actively and/or passively influence kidney stone biomineralization.
Background: Human kidney stones form via repeated events of mineral precipitation, partial dissolution, and reprecipitation, which are directly analogous to similar processes in other natural and manmade environments, where resident microbiomes strongly influence biomineralization. High-resolution microscopy and high-fidelity metagenomic (microscopy-to-omics) analyses, applicable to all forms of biomineralization, have been applied to assemble definitive evidence of in vivo microbiome entombment during urolithiasis. Methods: Stone fragments were collected from a randomly chosen cohort of 20 patients using standard percutaneous nephrolithotomy (PCNL). Fourier transform infrared (FTIR) spectroscopy indicated that 18 of these patients were calcium oxalate (CaOx) stone formers, whereas one patient formed each formed brushite and struvite stones. This apportionment is consistent with global stone mineralogy distributions. Stone fragments from seven of these 20 patients (five CaOx, one brushite, and one struvite) were thin sectioned and analyzed using brightfield (BF), polarization (POL), confocal, super-resolution autofluorescence (SRAF), and Raman techniques. DNA from remaining fragments, grouped according to each of the 20 patients, were analyzed with amplicon sequencing of 16S rRNA gene sequences (V1-V3, V3-V5) and internal transcribed spacer (ITS1, ITS2) regions. Results: Bulk-entombed DNA was sequenced from stone fragments in 11 of the 18 patients who formed CaOx stones, and the patients who formed brushite and struvite stones. These analyses confirmed the presence of an entombed low-diversity community of bacteria and fungi, including Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Aspergillus niger. Bacterial cells approximately 1 μm in diameter were also optically observed to be entombed and well preserved in amorphous hydroxyapatite spherules and fans of needle-like crystals of brushite and struvite. Conclusions: These results indicate a microbiome is entombed during in vivo CaOx stone formation. Similar processes are implied for brushite and struvite stones. This evidence lays the groundwork for future in vitro and in vivo experimentation to determine how the microbiome may actively and/or passively influence kidney stone biomineralization.
Authors: Yiran Dong; Robert A Sanford; William P Inskeep; Vaibhav Srivastava; Vincent Bulone; Christopher J Fields; Peter M Yau; Mayandi Sivaguru; Dag Ahrén; Kyle W Fouke; Joseph Weber; Charles R Werth; Isaac K Cann; Kathleen M Keating; Radhika S Khetani; Alvaro G Hernandez; Chris Wright; Mark Band; Brian S Imai; Glenn A Fried; Bruce W Fouke Journal: Astrobiology Date: 2019-04-30 Impact factor: 4.335
Authors: Aaron W Miller; Kristina L Penniston; Kate Fitzpatrick; José Agudelo; Gregory Tasian; Dirk Lange Journal: Nat Rev Urol Date: 2022-09-20 Impact factor: 16.430