In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis

Jessica J. Saw; Mayandi Sivaguru; Elena M. Wilson; Yiran Dong; Robert A. Sanford; Chris J. Fields; Melissa A. Cregger; Annette C. Merkel; William J. Bruce; Joseph R. Weber; John C. Lieske; Amy E. Krambeck; Marcelino E. Rivera; Timothy Large; Dirk Lange; Ananda S. Bhattacharjee; Michael F. Romero; Nicholas Chia; Bruce W. Fouke

doi:10.34067/KID.0006942020

In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis

Jessica J. Saw, Mayandi Sivaguru, Elena M. Wilson, Yiran Dong, Robert A. Sanford, Chris J. Fields, Melissa A. Cregger, Annette C. Merkel, William J. Bruce, Joseph R. Weber, John C. Lieske, Amy E. Krambeck, Marcelino E. Rivera, Timothy Large, Dirk Lange, Ananda S. Bhattacharjee, Michael F. Romero, Nicholas Chia, Bruce W. Fouke

Integrative Microbiomics

Research output: Contribution to journal › Article › peer-review

15 Scopus citations

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.

Original language	English
Pages (from-to)	298-311
Number of pages	14
Journal	Kidney360
Volume	2
Issue number	2
DOIs	https://doi.org/10.34067/KID.0006942020
State	Published - Feb 1 2021

Funding

This research was supported by the Mayo Clinic and University of Illinois Strategic Alliance for Technology-Based Healthcare, Mayo Clinic Center for Individualized Medicine and Mayo Clinic O’Brien Urology Research Center (DK100227), Mayo Nephrology/Urology Summer Undergraduate Research Fellowship (DK101405), and the National Aeronautics and Space Administration Astrobiology Institute (Cooperative Agreement NNA13AA91A). A. Krambeck reports consultancy agreements with Boston Scientific, Lumenis, Sonomotion, and Virtuoso; receiving research funding from Boston Scientific, Lumenis; receiving honoraria from Boston Scientific, Lumenis, Sonomotion, and Virtuoso; reports having patents and inventions b7h1 and Survivin as a marker for Renal Cell Carcinoma; and reports being a scientific advisor or member of Boston Scientific, Sonomotion, and Virtuoso. B. Fouke reports receiving research funding from Dornier MedTech. D. Lange reports having consultancy agreements with AdvaTec, BD/Bard, Boston Scientific, Cook Medical, and Kisolite; having an ownership interest in Kisolite Corp; reports receiving research funding from AdvaTec, BD/Bard, Boston Scientific, and Cook Medical; and reports scientific advisor or membership of Kisolite Corp. J. Lieske reports having consultancy agreements with Alnylam, Allena, American Board of Internal Medicine, Dicerna, Orfan, OxThera, Retrophin, and Siemens; reports receiving research funding from Allena, Alnylam, Dicerna, OxThera, Retrophin, and Siemens; reports receiving honoraria from Alnylam, Allena, American Board of Internal Medicine, Dicerna, Retrophin, Novobiome, Orfan, OxThera, and Synlogic; scientific advisor or membership of American Board of Internal Medicine, Hyperoxaluria Foundation, Kidney International, and Oxalosis. M. Rivera reports consultancy agreements with Boston Scientific, Cook Medical and Lumenis. M. Romero reports scientific advisor or membership of Kidney360 - Associate Editor, American Journal of Physiology-Renal Physiology, Hyperoxaluria Foundation, Oxalosis, National Institute of Diabetes and Digestive and Kidney Diseases study sections, ad hoc. N. Chia reports receiving research funding from Archer Daniels Midland. T. Large reports having consultancy agreements with Boston Scientific and Lumenis. Y. Dong reports being a scientific advisor or member of Frontiers in Microbiology. All remaining authors have nothing to disclose. All remaining authors have nothing to disclose.

Keywords

Raman spectroscopy
bacteria
basic science
fungi entombment
geomicrobiology
kidney stone mineralogy
microbiome
nephrolithiasis
super-resolution autofluorescence (SRAF) microscopy
urolithiasis

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.34067/KID.0006942020

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Saw, J. J., Sivaguru, M., Wilson, E. M., Dong, Y., Sanford, R. A., Fields, C. J., Cregger, M. A., Merkel, A. C., Bruce, W. J., Weber, J. R., Lieske, J. C., Krambeck, A. E., Rivera, M. E., Large, T., Lange, D., Bhattacharjee, A. S., Romero, M. F., Chia, N., & Fouke, B. W. (2021). In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis. Kidney360, 2(2), 298-311. https://doi.org/10.34067/KID.0006942020

@article{d6b6acba82cb457b86541d6973134513,

title = "In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis",

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.",

keywords = "Raman spectroscopy, bacteria, basic science, fungi entombment, geomicrobiology, kidney stone mineralogy, microbiome, nephrolithiasis, super-resolution autofluorescence (SRAF) microscopy, urolithiasis",

author = "Saw, {Jessica J.} and Mayandi Sivaguru and Wilson, {Elena M.} and Yiran Dong and Sanford, {Robert A.} and Fields, {Chris J.} and Cregger, {Melissa A.} and Merkel, {Annette C.} and Bruce, {William J.} and Weber, {Joseph R.} and Lieske, {John C.} and Krambeck, {Amy E.} and Rivera, {Marcelino E.} and Timothy Large and Dirk Lange and Bhattacharjee, {Ananda S.} and Romero, {Michael F.} and Nicholas Chia and Fouke, {Bruce W.}",

note = "Publisher Copyright: Copyright {\textcopyright} 2021 by the American Society of Nephrology.",

year = "2021",

month = feb,

day = "1",

doi = "10.34067/KID.0006942020",

language = "English",

volume = "2",

pages = "298--311",

journal = "Kidney360",

issn = "2641-7650",

publisher = "Wolters Kluwer",

number = "2",

}

Saw, JJ, Sivaguru, M, Wilson, EM, Dong, Y, Sanford, RA, Fields, CJ, Cregger, MA, Merkel, AC, Bruce, WJ, Weber, JR, Lieske, JC, Krambeck, AE, Rivera, ME, Large, T, Lange, D, Bhattacharjee, AS, Romero, MF, Chia, N & Fouke, BW 2021, 'In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis', Kidney360, vol. 2, no. 2, pp. 298-311. https://doi.org/10.34067/KID.0006942020

TY - JOUR

T1 - In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis

AU - Saw, Jessica J.

AU - Sivaguru, Mayandi

AU - Wilson, Elena M.

AU - Dong, Yiran

AU - Sanford, Robert A.

AU - Fields, Chris J.

AU - Cregger, Melissa A.

AU - Merkel, Annette C.

AU - Bruce, William J.

AU - Weber, Joseph R.

AU - Lieske, John C.

AU - Krambeck, Amy E.

AU - Rivera, Marcelino E.

AU - Large, Timothy

AU - Lange, Dirk

AU - Bhattacharjee, Ananda S.

AU - Romero, Michael F.

AU - Chia, Nicholas

AU - Fouke, Bruce W.

PY - 2021/2/1

Y1 - 2021/2/1

N2 - 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.

AB - 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.

KW - Raman spectroscopy

KW - bacteria

KW - basic science

KW - fungi entombment

KW - geomicrobiology

KW - kidney stone mineralogy

KW - microbiome

KW - nephrolithiasis

KW - super-resolution autofluorescence (SRAF) microscopy

KW - urolithiasis

UR - http://www.scopus.com/inward/record.url?scp=85110165869&partnerID=8YFLogxK

U2 - 10.34067/KID.0006942020

DO - 10.34067/KID.0006942020

M3 - Article

AN - SCOPUS:85110165869

SN - 2641-7650

VL - 2

SP - 298

EP - 311

JO - Kidney360

JF - Kidney360

IS - 2

ER -

In Vivo Entombment of Bacteria and Fungi during Calcium Oxalate, Brushite, and Struvite Urolithiasis

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UN SDGs

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