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PRJNA649273 SRP276112

Gut metagenomes in kidney stone patients vs controls, Canada

KiSMi Kidney stone patients - gut samples

61 gut samples from a case-control study in London, Canada, comparing kidney stone formers (36) to healthy controls (25) using metagenomic sequencing. machine-written summary

61 samples · 61 runs · CA · Age unknown · 2020 · 6.64 Gbp / sample

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Sources

✓Sequence archive 549○Abstract / description✓Full text 61✓Supplementary tables 180–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	549 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude)
○ Abstract / description	read; no usable statement
✓ Full text	61 sample values (antibiotic exposure) · PMC10675928
✓ Supplementary tables	180 sample values (age, bmi, sex, smoking status)
– 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

adult44

elderly15

unknown2

Condition

kidney_disease36

healthy_control25

Sex

male38

female23

Country

CA61

Body site

primary61

Sequencing depth per sample · this project all projects

Community composition

Bacteroides 12.1%Phocaeicola 7.2%Alistipes 6.5%Faecalibacterium 5.0%Roseburia 4.3%Escherichia 3.6%Prevotella 3.6%Blautia_A 2.1%Ruminococcoides 1.8%Vescimonas 1.6%Mediterraneibacter 1.4%Gemmiger 1.4%not assigned to a genus 4.4%other genera 44.9%

Genera, mean relative abundance over 55 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	R2	R3
age_category	59	97%
country	61	100%	61
health_condition	61	100%	61
subject_id	61	100%	61
antibiotic_exposure	61	100%			61
collection_date	61	100%	61
detailed_location	61	100%
health_condition_detail	61	100%	61
latitude	61	100%	61
location_locality	61	100%	61
location_region	61	100%	61
longitude	61	100%	61
sex	61	100%		61
age_at_collection_days	59	97%		59
bmi	58	95%		58
smoking_status	2	3%		2

Papers (1)

Multi-site microbiota alteration is a hallmark of kidney stone formation. 2023 PMID 38007438 PMC10675928 own_data

Details

Archive description

Metagenomic sequencing of the gut from kidney stone patients and healthy controls

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.57. Assay shotgun_dna.

host run.host_tax_id · “9606”
host study.description · “Metagenomic sequencing of the gut from kidney stone patients”
body site study.title · “KiSMi Kidney stone patients - gut samples”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN15661738	age_at_collection_days	18993.0	R2	0.85	paper.supp.40168_2023_1703_MOESM1_ESM.xlsx[1A!Age]	Age: 52
SAMN15661738	antibiotic_exposure	no	R3	0.60	paper.fulltext.results	no participants had antibiotic exposure for at least 90 days
SAMN15661738	bmi	42.2	R2	0.85	paper.supp.40168_2023_1703_MOESM1_ESM.xlsx[1A!BMI]	BMI: 42.2
SAMN15661738	collection_date	2015-08-20/2019-03-30	R1	0.90	biosample.attribute:collection_date	2015-08-20/2019-03-30
SAMN15661738	country	CA	R1	0.90	sample.attr.geo_loc_name	Canada: London
SAMN15661738	health_condition	kidney_disease	R1	0.60	biosample_attr	stone former
SAMN15661738	health_condition_detail	stone former	R1	0.85	biosample.attribute:cohort	stone former
SAMN15661738	latitude	42.9800	R1	0.90	biosample.attribute:lat_lon	42.98 N 81.24 W
SAMN15661738	location_locality	London	R1	0.85	biosample.attribute:geo_loc_name	Canada: London
SAMN15661738	location_region	Ontario	R1	0.60	biosample.attribute:lat_lon	42.98 N 81.24 W
SAMN15661738	longitude	-81.2400	R1	0.90	biosample.attribute:lat_lon	42.98 N 81.24 W
SAMN15661738	sex	male	R2	0.85	paper.supp.40168_2023_1703_MOESM1_ESM.xlsx[1A!Sex]	Sex: male
SAMN15661750	smoking_status	current	R2	0.85	paper.supp.40168_2023_1703_MOESM1_ESM.xlsx[1A!CurrentSmoker]	CurrentSmoker: yes
SAMN15661738	subject_id	participant 101	R1	0.85	sample.attr.participant	participant 101

Sequencing

61 runs over 61 samples · mean 7.08 Gbp per run (median 6.64 Gbp, total 432.15 Gbp; 61 runs with a base count) · layout PAIRED 61 · platform ILLUMINA 61 · models Illumina NovaSeq 6000 (61) · 90% of runs with a Sandpiper profile · first public 2020-08-07

Authors (10)

Al KF first · Joris BR · Daisley BA · Chmiel JA · Bjazevic J · Reid G · Gloor GB · Denstedt JD · Razvi H · Burton JP last

Downloads

PRJNA649273.csv.gz (3.1 KB) · parquet (74.0 KB) — all 61 samples, every field with route and confidence · PRJNA649273_determinations.csv.gz (6.7 KB) — 790 evidence rows

Samples (61 · every field this project has values for · hover a cell for its source)

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