Multi-site microbiota alteration is a hallmark of kidney stone formation

Kait F Al; Benjamin R Joris; Brendan A Daisley; John A Chmiel; Jennifer Bjazevic; Gregor Reid; Gregory B Gloor; John D Denstedt; Hassan Razvi; Jeremy P Burton

doi:10.1186/s40168-023-01703-x

Multi-site microbiota alteration is a hallmark of kidney stone formation

Microbiome. 2023 Nov 25;11(1):263. doi: 10.1186/s40168-023-01703-x.

Authors

Kait F Al^{1

2}, Benjamin R Joris³, Brendan A Daisley⁴, John A Chmiel^{1

2}, Jennifer Bjazevic⁵, Gregor Reid^{1

2

5}, Gregory B Gloor³, John D Denstedt⁵, Hassan Razvi⁵, Jeremy P Burton^{6

7

8}

Affiliations

¹ Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada.
² Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada.
³ Department of Biochemistry, The University of Western Ontario, London, ON, Canada.
⁴ Molecular and Cellular Biology Department, University of Guelph, Guelph, ON, Canada.
⁵ Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada.
⁶ Centre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada. Jeremy.burton@lawsonresearch.com.
⁷ Department of Microbiology and Immunology, The University of Western Ontario, London, ON, Canada. Jeremy.burton@lawsonresearch.com.
⁸ Division of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada. Jeremy.burton@lawsonresearch.com.

Abstract

Background: Inquiry of microbiota involvement in kidney stone disease (KSD) has largely focussed on potential oxalate handling abilities by gut bacteria and the increased association with antibiotic exposure. By systematically comparing the gut, urinary, and oral microbiota of 83 stone formers (SF) and 30 healthy controls (HC), we provide a unified assessment of the bacterial contribution to KSD.

Results: Amplicon and shotgun metagenomic sequencing approaches were consistent in identifying multi-site microbiota disturbances in SF relative to HC. Biomarker taxa, reduced taxonomic and functional diversity, functional replacement of core bioenergetic pathways with virulence-associated gene markers, and community network collapse defined SF, but differences between cohorts did not extend to oxalate metabolism.

Conclusions: We conclude that multi-site microbiota alteration is a hallmark of SF, and KSD treatment should consider microbial functional restoration and the avoidance of aberrant modulators such as poor diet and antibiotics where applicable to prevent stone recurrence. Video Abstract.

Keywords: Gut microbiota; Kidney stones; Microbiota; Shotgun metagenomic sequencing; Urinary microbiota; Urology.

Publication types

Video-Audio Media

MeSH terms

Bacteria
Humans
Kidney Calculi*
Metagenome
Microbiota* / genetics
Oxalates / metabolism

Substances

Oxalates