Gut microbiome in Crohn's disease vs healthy controls
130 gut samples (41 Crohn's disease, 89 healthy controls) from adults, analyzed in a case-control design to characterize microbial community diversity. machine-written summary
130 samples · 130 runs · CN · Adult · 2022 · 8.74 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 520 sample values (age, health condition, health condition detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 130 sample values (location site) · PMC10173549, PMC11328384, PMC11510655 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 130 sample values (country) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 119 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 | 130 | 100% | ||||
| country | 130 | 100% | 130 | |||
| health_condition | 130 | 100% | 130 | |||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 130 | 100% | 130 | |||
| detailed_location | 130 | 100% | ||||
| health_condition_detail | 130 | 100% | 130 | |||
| location_site | 130 | 100% | 130 | |||
| sex | 130 | 100% | 130 |
- Oxidative stress gene expression, DNA methylation, and gut microbiota interaction trigger Crohn's disease: a multi-omics Mendelian randomization study. 2023 PMID 37170220 PMC10173549 own_data
- Microbial assimilatory sulfate reduction-mediated H<sub>2</sub>S: an overlooked role in Crohn's disease development. 2024 PMID 39152482 PMC11328384 unsure
- Oral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis. 2024 PMID 39458395 PMC11510655 unsure
Archive description
The microbial community diversities of gut from patients with Crohn's Disease and healthy controls
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.scientific_name · “Homo sapiens”
- body site study.description · “microbial community diversities of gut”
- life stage sample.attr.age · “21 (n=128/130)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN24583735 | age_at_collection_days | 8034.0 | R1 | 0.85 | sample.attr.age | 22 |
| SAMN24583735 | country | CN | R2 | 0.75 | external.gmrepo source | country: China |
| SAMN24583735 | health_condition | crohns_disease | R1 | 0.90 | biosample_attr | Crohn's disease |
| SAMN24583735 | health_condition_detail | NO | R1 | 0.90 | sample.attr.health_state | NO |
| SAMN24583735 | location_site | First Affiliated Hospital of Sun Yat-sen University | R3 | 0.70 | paper.fulltext.methods | First Affiliated Hospital of Sun Yat-sen University (FAH-SYS) IBD multi-omics cohort |
| SAMN24583735 | sex | male | R1 | 0.90 | sample.attr.sex | male |
Sequencing
130 runs over 130 samples · mean 8.84 Gbp per run (median 8.74 Gbp, total 1,149.07 Gbp; 130 runs with a base count) · layout PAIRED 130 · platform ILLUMINA 130 · models Illumina NovaSeq 6000 (130) · 92% of runs with a Sandpiper profile · first public 2022-06-20
Authors (27)
Xu S first · Li X · Zhang S · Qi C · Zhang Z · Ma R · Xiang L · Chen L · Zhu Y · Tang C · Bourgonje AR · Li M · He Y · Zeng Z · Hu S · Feng R · Chen M last · Luo W first · Zhao M · Dwidar M · Gao Y · Wu X · Medema MH · Schäfer H · Wang L first · Wang Q · Zhou Y last
Downloads
PRJNA793776.csv.gz (4.4 KB) · parquet (75.3 KB) — all 130 samples, every field with route and confidence · PRJNA793776_determinations.csv.gz (5.0 KB) — 780 evidence rows