Bacterial translocation in Crohn's disease mesenteric fat
Metagenomic analysis of 354 samples from diseased and healthy controls in the USA, examining bacterial communities in mesenteric fat tissue associated with Crohn's disease using case-control design. machine-written summary
354 samples · 1,335 runs · US · Adult · 2025 · 17.9 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,052 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 354 sample values (location site) · PMC12635244 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 |
longitudinal — not resolved
32 of 139 people sampled more than once (64 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 9 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 354 | 100% | ||||
| country | 354 | 100% | 354 | |||
| health_condition | 287 | 81% | 287 | |||
| subject_id | 354 | 100% | 354 | |||
| collection_date | 354 | 100% | 354 | |||
| detailed_location | 354 | 100% | ||||
| latitude | 354 | 100% | 354 | |||
| location_locality | 354 | 100% | 354 | |||
| location_region | 354 | 100% | 354 | |||
| location_site | 354 | 100% | 354 | |||
| longitude | 354 | 100% | 354 | |||
| health_condition_detail | 287 | 81% | 287 |
- Calculating fast differential genome coverages among metagenomic sources using micov. 2025 PMID 41266796 PMC12635244 own_data
Archive description
A study of bacterial translocation into mesenteric fat in Crohn's disease.
How this project entered the registry
Classified as human blood / tissue / internal fluids / gut / stool / skin shotgun DNA metagenome of adult by opus_adjudicated with confidence 0.55. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “bacterial translocation into mesenteric fat”
- body site sample.attr.host_body_product · “intestinal mucosa (n=104/354)”
- body site sample.attr.host_body_product · “UBERON:skin of abdomen (n=43/354)”
- life stage sample.attr.host_life_stage · “adult (n=287/354)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA120246872 | collection_date | 2022 | R1 | 0.90 | biosample.attribute:collection_date | 2022 |
| SAMEA120246872 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA120246872 | health_condition | other_disease | R1 | 0.50 | biosample_attr | disease |
| SAMEA120246872 | health_condition_detail | disease | R1 | 0.85 | biosample.attribute:status | disease |
| SAMEA120246872 | latitude | 34.0500 | R1 | 0.90 | biosample.attribute:latitude+longitude | 34.05 -118.25 |
| SAMEA120246872 | location_locality | Los Angeles | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:CA:Los Angeles |
| SAMEA120246872 | location_region | California | R1 | 0.75 | biosample.attribute:geo_loc_name | USA:CA:Los Angeles |
| SAMEA120246872 | location_site | Cedars-Sinai Medical Center | R3 | 0.70 | paper.fulltext.methods | approved by the Cedars-Sinai Medical Center Institutional Review Board |
| SAMEA120246872 | longitude | -118.2500 | R1 | 0.90 | biosample.attribute:latitude+longitude | 34.05 -118.25 |
| SAMEA120246872 | subject_id | A05 | R1 | 0.85 | sample.attr.host_subject_id | A05 |
Sequencing
1,335 runs over 354 samples · mean 0.17 Gbp per run (median 2.1 Mbp, total 224.25 Gbp; 1,335 runs with a base count) · layout PAIRED 1,335 · platform ILLUMINA 1,335 · models Illumina NovaSeq X (1,335) · 1% of runs with a Sandpiper profile · first public 2025-10-02 – 2025-10-04
Authors (30)
Weng Y first · Guccione C · McDonald D · Oles R · Devkota S · Kopylova E · Sepich-Poore GD · Salido RA · Din MO · Song SJ · Curtius K · Chu H · Bartko A · Hasty J · Knight R last · So Y first · Pichler MJ · Kappel SS · Jin C · Eriksen C · Chatzigiannidou I · Andersen MHB · Tsiamis V · Lukassen MV · Skytthe LE · Teneberg S · Kristiansen K · Brix S · Aunsholt L · Abou Hachem M last
Downloads
PRJEB98012.csv.gz (10.0 KB) · parquet (84.4 KB) — all 354 samples, every field with route and confidence · PRJEB98012_determinations.csv.gz (24.0 KB) — 3,406 evidence rows