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PRJNA1056458 SRP479915

Gut metagenomes in Israeli Crohn disease case-control study

Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort

38 fecal metagenome samples from treatment-naive Israeli Crohn disease patients and healthy controls, part of the SOURCE study on diet, exposures, and microbiome in Crohn disease; case-control design. machine-written summary

38 samples · 38 runs · IL · Adult · 2024 · 0.67 Gbp / sample

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Sources

✓Sequence archive 338○Abstract / description○Full text✓Supplementary tables 38–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	338 sample values (age, bmi, country, health condition, health condition detail, latitude, location region, longitude)
○ Abstract / description	read; no usable statement
○ Full text	read; no usable statement or table · PMC11069498
✓ Supplementary tables	38 sample values (subject id)
– 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

Interventions

intervention — arms not resolved

design observational_with_procedure

Samples at a glance

1 sampling locations · 1 country

Age

adult37

elderly1

Condition

healthy_control21

crohns_disease17

Sex

male21

female17

Country

IL38

Body site

primary38

Sequencing depth per sample · this project all projects

Community composition

Bacteroides 19.5%Phocaeicola 19.1%Prevotella 16.9%Roseburia 2.7%Alistipes 2.6%Parabacteroides 2.2%Lachnospira 1.4%Faecalibacterium 1.3%Acetatifactor 1.2%Escherichia 1.1%Ruminococcoides 1.0%Akkermansia 0.8%not assigned to a genus 15.5%other genera 14.7%

Genera, mean relative abundance over 37 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
age_category	38	100%
country	38	100%	38
health_condition	38	100%	38
subject_id	38	100%		38
age_at_collection_days	38	100%	38
detailed_location	38	100%
health_condition_detail	38	100%	38
latitude	38	100%	38
location_region	38	100%	38
longitude	38	100%	38
sex	38	100%	38
bmi	34	89%	34

Papers (1)

Diet-omics in the Study of Urban and Rural Crohn disease Evolution (SOURCE) cohort. 2024 PMID 38704361 PMC11069498 unsure

Details

Archive description

The Study Of Urban and Rural Crohn disease Evolution (SOURCE) characterized exposures, diet, and microbial factors in newly diagnosed Crohn Disease (CD) patients and controls in rural and urban China, and in treatment-naive Israeli CD patients and controls. Time spent by rural residents in urban environments, diet, and exposures were linked with gut microbial composition.</p><p>Here are deposited 38 Israeli fecal metagenomics samples from this study.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.82. Assay shotgun_dna.

host run.scientific_name · “human gut metagenome”
body site study.description · “Israeli fecal metagenomics samples”
life stage sample.attr.age · “24 (n=37/38)”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN39099283	age_at_collection_days	10227.0	R1	0.70	sample.attr.age	28
SAMN39099283	bmi	27.5	R1	0.90	sample.attr.bmi	27.5
SAMN39099283	country	IL	R1	0.90	sample.attr.geo_loc_name	Israel
SAMN39099283	health_condition	healthy_control	R1	0.80	biosample_attr	Israel control
SAMN39099283	health_condition_detail	Israel control	R1	0.90	sample.attr.patient_group	Israel control
SAMN39099283	latitude	31.0460	R1	0.90	biosample.attribute:lat_lon	31.046 N 34.8516 E
SAMN39099283	location_region	Southern District	R1	0.60	biosample.attribute:lat_lon	31.046 N 34.8516 E
SAMN39099283	longitude	34.8516	R1	0.90	biosample.attribute:lat_lon	31.046 N 34.8516 E
SAMN39099283	sex	female	R1	0.90	sample.attr.gender	female
SAMN39099283	subject_id	A002	R2	0.75	paper.supp.41467_2024_48106_MOESM4_ESM.xlsx[Samples_Datasets!pn_ID]	pn_ID: A002

Sequencing

38 runs over 38 samples · mean 0.64 Gbp per run (median 0.67 Gbp, total 24.23 Gbp; 38 runs with a base count) · layout SINGLE 38 · platform ILLUMINA 38 · models NextSeq 500 (38) · 97% of runs with a Sandpiper profile · first public 2024-02-25

Authors (26)

Braun T first · Feng R · Amir A · Levhar N · Shacham H · Mao R · Hadar R · Toren I · Algavi Y · Abu-Saad K · Zhuo S · Efroni G · Malik A · Picard O · Yavzori M · Agranovich B · Liu TC · Stappenbeck TS · Denson L · Kalter-Leibovici O · Gottlieb E · Borenstein E · Elinav E · Chen M · Ben-Horin S · Haberman Y last

Downloads

PRJNA1056458.csv.gz (2.2 KB) · parquet (72.2 KB) — all 38 samples, every field with route and confidence · PRJNA1056458_determinations.csv.gz (3.4 KB) — 376 evidence rows

Samples (38 · every field this project has values for · hover a cell for its source)

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