Gut microbiota in kidney stone patients, Vancouver

Gut microbiota of Kidney Stone patients and live-in partners

Cross-sectional shotgun metagenomic study of 33 samples from adults in Vancouver, Canada, comparing gut microbiota between kidney stone patients and their healthy live-in partners. machine-written summary

33 samples · 33 runs · CA · Adult · 2021 · 1.26 Gbp / sample

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Sources

✓Sequence archive 231○Abstract / description–Full text–Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave

✓ Sequence archive	231 sample values (country, health condition, health condition detail, latitude, location locality, location region, longitude)
○ Abstract / description	read; no usable statement
– Full text	no open-access full text linked
– Supplementary tables	no supplementary tables available (or none open access)
– External resources	not covered by the external resources we ingest
– User contribution	nothing uploaded yet
– Human verified	not yet checked by a person · I checked this project — verify it

Samples at a glance

1 sampling locations · 1 country

Age

adult33

Condition

healthy_control17

kidney_disease16

Country

CA33

Body site

primary33

Sequencing depth per sample · this project all projects

Sampling design and relatedness

partners / couples — not resolved

17 kidney-stone patients and live-in partners as controls; no published pair key linking partners.

How longitudinal and relatedness information is derived

Community composition

Bacteroides 8.5%Phocaeicola 6.4%Blautia_A 5.1%Akkermansia 4.9%Roseburia 4.9%Faecalibacterium 4.1%Prevotella 3.6%Alistipes 2.9%Fimenecus 2.1%Vescimonas 2.1%Gemmiger 2.1%Lachnospira 1.6%not assigned to a genus 12.2%other genera 39.5%

Genera, mean relative abundance over 31 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage

field	samples	coverage	R1
age_category	33	100%
country	33	100%	33
health_condition	33	100%	33
subject_id	0	0%
detailed_location	33	100%
health_condition_detail	33	100%	33
latitude	33	100%	33
location_locality	33	100%	33
location_region	33	100%	33
longitude	33	100%	33

Papers (2)

Metagenomic and phylogenetic analyses reveal gene-level selection constrained by bacterial phylogeny, surrounding oxalate metabolism in the gut microbiota. 2025 PMID 40358144 PMC12188714 cites_accession
Deficient butyrate metabolism in the intestinal microbiome is a potential risk factor for recurrent kidney stone disease. 2024 PMID 38413462 own_data

Details

Archive description

Comparative shotgun metagenomic study of individuals with kidney stones and their live-in partners.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.

host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
body site study.title · “Gut microbiota of Kidney”
body site external_curation.infant_catalog · “body_site_call gut”
life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN19971472	country	CA	R1	0.90	sample.attr.geo_loc_name	Canada: Vancouver
SAMN19971472	health_condition	healthy_control	R1	0.85	biosample.attribute:DESCRIPTION	DESCRIPTION: Control
SAMN19971472	health_condition_detail	Control	R1	0.85	biosample.attribute:DESCRIPTION	DESCRIPTION: Control
SAMN19971472	latitude	49.2800	R1	0.90	biosample.attribute:lat_lon	49.28 N 123.12 W
SAMN19971472	location_locality	Vancouver	R1	0.85	biosample.attribute:geo_loc_name	Canada: Vancouver
SAMN19971472	location_region	British Columbia	R1	0.60	biosample.attribute:lat_lon	49.28 N 123.12 W
SAMN19971472	longitude	-123.1200	R1	0.90	biosample.attribute:lat_lon	49.28 N 123.12 W

Sequencing

33 runs over 33 samples · mean 1.38 Gbp per run (median 1.26 Gbp, total 45.45 Gbp; 33 runs with a base count) · layout PAIRED 33 · platform ILLUMINA 33 · models Illumina HiSeq 2500 (33) · 94% of runs with a Sandpiper profile · first public 2021-07-05

Authors (17)

Argentini C first · Lugli GA · Tarracchini C · Fontana F · Mancabelli L · Viappiani A · Anzalone R · Angelini L · Alessandri G · Longhi G · Bianchi MG · Taurino G · Bussolati O · Milani C · van Sinderen D · Turroni F · Ventura M last

Downloads

PRJNA742740.csv.gz (1.7 KB) · parquet (70.7 KB) — all 33 samples, every field with route and confidence · PRJNA742740_determinations.csv.gz (1.9 KB) — 231 evidence rows

Samples (33 · every field this project has values for · hover a cell for its source)

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