Gut metagenomes in IBD case-control study, China
81 fecal samples from China, including Crohn's disease, ulcerative colitis, and healthy control subjects, analyzed in a case-control study of gut microbiota for non-invasive IBD diagnosis. machine-written summary
81 samples · 81 runs · CN · Age unknown · 2018 · 9.15 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 405 sample values (collection date, country, latitude, 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 | 162 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 71 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 | 0 | 0% | ||||
| country | 81 | 100% | 81 | |||
| health_condition | 81 | 100% | 81 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 81 | 100% | 81 | |||
| detailed_location | 81 | 100% | ||||
| health_condition_detail | 81 | 100% | 81 | |||
| latitude | 81 | 100% | 81 | |||
| location_region | 81 | 100% | 81 | |||
| longitude | 81 | 100% | 81 |
- Human gut bacterial metabolism drives Th17 activation and colitis. 2022 PMID 34822777 PMC8785648 unsure
- Faecal microbiome-based machine learning for multi-class disease diagnosis. 2022 PMID 36357393 PMC9649010 unsure
- Gut bacterial type III secretion systems aggravate colitis in mice and serve as biomarkers of Crohn's disease. 2024 PMID 39216231 PMC11402190 unsure
- Noninvasive, microbiome-based diagnosis of inflammatory bowel disease. 2024 PMID 39367251 PMC11645270 unsure
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991 unsure
5 more
- Balance between bile acid conjugation and hydrolysis activity can alter outcomes of gut inflammation. 2025 PMID 40210868 PMC11985902
- Constructing inflammatory bowel disease diagnostic models based on k-mer and machine learning. 2025 PMID 40636504 PMC12239758
- Megasphaera Elesdenii Dysregulates Colon Epithelial Homeostasis, Aggravates Colitis-Associated Tumorigenesis. 2025 PMID 40801433 PMC12591162
- Human intestinal fungus Clavispora lusitaniae attenuates colitis through Pyruvate decarboxylase-derived Indole-3-ethanol. 2025 PMID 41233306 PMC12615640
- A microbiota-IPA axis facilitates intestinal stem cell-mediated regeneration in colitis through a Hopx-associated program. 2026 PMID 41741429 PMC13057028
Archive description
Diet-microbiota-metabolite interaction networks reveal key players in inflammatory bowel disease
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08382793 | collection_date | 2015-02 | R1 | 0.90 | biosample.attribute:collection_date | 2015-02 |
| SAMN08382793 | country | CN | R1 | 0.90 | sample.attr.geo_loc_name | China |
| SAMN08382793 | health_condition | crohns_disease | R2 | 0.75 | external.gmrepo source | phenotype: Crohn Disease |
| SAMN08382793 | health_condition_detail | Crohn Disease | R2 | 0.75 | external.gmrepo source | phenotype: Crohn Disease |
| SAMN08382793 | latitude | 23.0800 | R1 | 0.90 | biosample.attribute:lat_lon | 23.08 N 113.14 E |
| SAMN08382793 | location_region | Guangdong | R1 | 0.60 | biosample.attribute:lat_lon | 23.08 N 113.14 E |
| SAMN08382793 | longitude | 113.1400 | R1 | 0.90 | biosample.attribute:lat_lon | 23.08 N 113.14 E |
Sequencing
81 runs over 81 samples · mean 11.17 Gbp per run (median 9.15 Gbp, total 905.13 Gbp; 81 runs with a base count) · layout PAIRED 81 · platform ILLUMINA 81 · models HiSeq X Ten (81) · 88% of runs with a Sandpiper profile · first public 2018-01-27
Authors (61)
Su Q first · Liu Q · Lau RI · Zhang J · Xu Z · Yeoh YK · Leung TWH · Tang W · Zhang L · Liang JQY · Yau YK · Zheng J · Liu C · Zhang M · Cheung CP · Ching JYL · Tun HM · Yu J · Chan FKL · Ng SC last · Xu J first · Li P · Li Z · Liu S · Guo H · Lesser CF · Ke J · Zhao W · Mou X last · Sun Q · Lu W · Ching J · Hamilton AL · Wilson O'Brien AL · Wei SC · Bernstein CN · Rubin DT · Chang EB · Morrison M · Kamm MA · Li L first · Liu Z · Qin J · Xiong G · Yang C · Cai F · Huang J last · Wu F first · Wang Y · Mai Z · Li S · Li Y · Yin R · Li J · Yu Z · Wu Y · Tian X · Feng X · Huo X · Wang C · Ma X last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJNA429990.csv.gz (2.8 KB) · parquet (73.1 KB) — all 81 samples, every field with route and confidence · PRJNA429990_determinations.csv.gz (4.1 KB) — 567 evidence rows