Evidence map›Paper›PMID 38007438›Full record

ArticleMicrobiome2023

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

Abstract readVideo-Audio Media
PubMed Full text at PMC Publisher
In one paragraph

Article in Microbiome, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
28citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

28 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  16. Microbiota and kidney disease: the road ahead.Nature reviews. Nephrology · 2025
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  20. TSST-1 promotes colonization ofInfection and immunity · 2025
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Kait F AlCentre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada.
Benjamin R JorisDepartment of Biochemistry, The University of Western Ontario, London, ON, Canada.
Brendan A DaisleyMolecular and Cellular Biology Department, University of Guelph, Guelph, ON, Canada.
John A ChmielCentre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada.
Jennifer BjazevicDivision of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada.
Gregor ReidCentre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada.
Gregory B GloorDepartment of Biochemistry, The University of Western Ontario, London, ON, Canada.
John D DenstedtDivision of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada.
Hassan RazviDivision of Urology, Department of Surgery, The University of Western Ontario, London, ON, Canada.
Jeremy P BurtonCentre for Human Microbiome and Probiotic Research, Lawson Health Research Institute, London, ON, Canada. Jeremy.burton@lawsonresearch.com.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundInquiry 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.

resultsAmplicon 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.

conclusionsWe 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.

Indexed as

Kidney CalculiMicrobiotaBacteriaHumansMetagenomeOxalatesOxalatesGut microbiotaKidney stonesMicrobiotaShotgun metagenomic sequencingUrinary microbiotaUrology

Identifiers

PMID38007438
PMCPMC10675928

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.