Longitudinal gut microbiome in IBD and controls, USA
2041 fecal metagenome samples from adult and pediatric IBD patients (Crohn's disease, ulcerative colitis) and non-IBD controls in the USA, collected biweekly over up to a year in a longitudinal cohort design. machine-written summary
2,041 samples · 2,041 runs · US · Infant / toddler · 2017 · 1.46 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 14,639 sample values (age, collection date, country, health condition, health condition detail, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10769871, PMC13288982, PMC9403272 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 3,448 sample values (age, antibiotic exposure, health condition, health condition detail) · from GMrepo v3, HMP / iHMP data portal |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
age: sequence archive and hmp_ihmp disagree for 254 samples (e.g. 9131.2 vs 13612.2) — withheld.
The sources disagree on 254 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (40 of 254)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN07509536 | age | 9131.2 (sequence archive) | 13612.2 (hmp_ihmp) | withheld: neither value published |
| SAMN07509538 | age | 4748.2 (sequence archive) | 9594.5 (hmp_ihmp) | withheld: neither value published |
| SAMN07509546 | age | 4748.2 (sequence archive) | 9510.5 (hmp_ihmp) | withheld: neither value published |
| SAMN07509552 | age | 10592.2 (sequence archive) | 15768.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509554 | age | 10227.0 (sequence archive) | 15845.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509555 | age | 8766.0 (sequence archive) | 11751.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509562 | age | 12053.2 (sequence archive) | 17257.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509565 | age | 21184.5 (sequence archive) | 27843.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509567 | age | 10957.5 (sequence archive) | 18641.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509572 | age | 17166.8 (sequence archive) | 27871.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509573 | age | 16071.0 (sequence archive) | 20496.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509574 | age | 12053.2 (sequence archive) | 17264.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509582 | age | 8766.0 (sequence archive) | 19414.2 (hmp_ihmp) | withheld: neither value published |
| SAMN07509588 | age | 10592.2 (sequence archive) | 15817.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509590 | age | 12053.2 (sequence archive) | 17278.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509591 | age | 16071.0 (sequence archive) | 20510.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509598 | age | 21184.5 (sequence archive) | 27864.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509603 | age | 12053.2 (sequence archive) | 17292.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509605 | age | 8766.0 (sequence archive) | 11793.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509615 | age | 12053.2 (sequence archive) | 17306.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509616 | age | 10227.0 (sequence archive) | 15901.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509622 | age | 10957.5 (sequence archive) | 18690.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509633 | age | 4383.0 (sequence archive) | 11702.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509634 | age | 12053.2 (sequence archive) | 17320.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509640 | age | 13514.2 (sequence archive) | 18283.5 (hmp_ihmp) | withheld: neither value published |
| SAMN07509641 | age | 8766.0 (sequence archive) | 19470.2 (hmp_ihmp) | withheld: neither value published |
| SAMN07509646 | age | 16071.0 (sequence archive) | 20566.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509647 | age | 13514.2 (sequence archive) | 18290.5 (hmp_ihmp) | withheld: neither value published |
| SAMN07509648 | age | 17166.8 (sequence archive) | 27941.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509653 | age | 12053.2 (sequence archive) | 17334.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509654 | age | 4383.0 (sequence archive) | 11716.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509664 | age | 10592.2 (sequence archive) | 15887.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509671 | age | 4383.0 (sequence archive) | 11730.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509672 | age | 12053.2 (sequence archive) | 17348.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509676 | age | 21184.5 (sequence archive) | 27934.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509678 | age | 10957.5 (sequence archive) | 18739.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509685 | age | 12053.2 (sequence archive) | 17362.8 (hmp_ihmp) | withheld: neither value published |
| SAMN07509686 | age | 8766.0 (sequence archive) | 11863.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509689 | age | 21184.5 (sequence archive) | 27948.0 (hmp_ihmp) | withheld: neither value published |
| SAMN07509699 | age | 17166.8 (sequence archive) | 27983.0 (hmp_ihmp) | withheld: neither value published |
longitudinal
106 of 106 people sampled more than once (2,041 samples; median 18, up to 43 per person) · follow-up median 9 mo (max 3.0 y) · median interval between samples 15 d (time from collection dates). Schedule stated by the source: “biweekly over up to a year” (time origin: enrolment); stated follow-up 12 mo.
Each row is one person (36 shown of 106); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 1,220 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 | 1,768 | 87% | ||||
| country | 2,041 | 100% | 2,041 | |||
| health_condition | 2,041 | 100% | 1,496 | 545 | ||
| subject_id | 2,041 | 100% | 2,041 | |||
| antibiotic_exposure | 2,041 | 100% | 2,041 | |||
| collection_date | 2,041 | 100% | 2,041 | |||
| health_condition_detail | 2,041 | 100% | 1,496 | 545 | ||
| sex | 2,041 | 100% | 2,041 | |||
| timepoint_label | 2,020 | 99% | 2,020 | |||
| age_at_collection_days | 1,780 | 87% | 1,463 | 317 |
- Genomic reconstruction of short-chain fatty acid production by the human gut microbiota. PMID 36032669 PMC9403272 curated
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871 curated
- Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis. PMID 42171373 PMC13288982 curated
- Metagenomic estimation of dietary intake from human stool curated
Archive description
The main Inflammatory Bowel Disease (IBD) Multi'omics Database (IBDMDB) study includes multi’omics measurements from over 100 subjects, sampled biweekly over up to a year in both adult and pediatric patients with IBD (Crohn’s disease and ulcerative colitis), along with non-IBD controls. Data types include fecal metagenomes, metatranscriptomes, metabolomes, and proteomes, as well as host genetics, intestinal biopsy transcriptomes, epigenetics, and 16S amplicon profiles. Subjects’ medical histories and demographics are collected at baseline and medication, diet, and disease activity profiled longitudinally.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of infant / toddler and child and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “Data types include fecal metagenomes, metatranscriptomes, metabolomes,”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.description · “host genetics, intestinal biopsy transcriptomes, epigenetics, and”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “both adult and pediatric patients with IBD”
- life stage study.description · “year in both adult and pediatric patients”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07509534 | age_at_collection_days | 5844.0 | R1 | 0.85 | biosample.attribute:host_age | 16 |
| SAMN07509535 | age_at_collection_days | 4916.2 | R2 | 0.75 | external.hmp_ihmp source | consent_age: 13; week_num: 24 |
| SAMN07521881 | age_at_collection_days | 6574.5 | R2 | 0.75 | external.gmrepo source | host_age: 18.0 |
| SAMN07509534 | antibiotic_exposure | no | R2 | 0.75 | external.hmp_ihmp source | Antibiotics: No |
| SAMN07509534 | collection_date | 2014-12-09 | R1 | 0.85 | biosample.attribute:collection_date | 2014-12-09 |
| SAMN07509534 | country | US | R1 | 0.90 | biosample_attr | USA |
| SAMN07509534 | health_condition | ibd_or_gi_disease | R1 | 0.90 | sample.attr.host_disease | host_disease=Crohn's disease |
| SAMN07509535 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07793600 | health_condition | healthy_control | R2 | 0.75 | external.hmp_ihmp source | diagnosis: nonIBD |
| SAMN07509534 | health_condition_detail | Crohn's disease | R1 | 0.90 | biosample.attribute:host_disease | host_disease: Crohn's disease |
| SAMN07509535 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN07793600 | health_condition_detail | nonIBD (non-IBD control, IBDMDB) | R2 | 0.75 | external.hmp_ihmp source | diagnosis: nonIBD |
| SAMN07509534 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN07509534 | subject_id | 6009 | R1 | 0.85 | biosample_attr | 6009 |
| SAMN07509534 | timepoint_label | visit 3 | R1 | 0.70 | sample.name_rule:TITLE | Stool sample P6009C3 |
| SAMN07532641 | timepoint_label | 5 | R1 | 0.80 | biosample_attr | 5 |
Sequencing
2,041 runs over 2,041 samples · mean 1.41 Gbp per run (median 1.46 Gbp, total 2,869.23 Gbp; 2,041 runs with a base count) · layout PAIRED 2,041 · platform ILLUMINA 2,041 · models Illumina HiSeq 2000 (2,041) · 60% of runs with a Sandpiper profile · first public 2017-10-18 – 2018-02-03
Authors (47)
Zhang Y first · Bhosle A · Bae S · McIver LJ · Pishchany G · Accorsi EK · Thompson KN · Arze C · Wang Y · Subramanian A · Kearney SM · Pawluk A · Plichta DR · Rahnavard A · Shafquat A · Xavier RJ · Vlamakis H · Garrett WS · Krueger A · Huttenhower C · Franzosa EA last · Frolova MS first · Suvorova IA · Iablokov SN · Petrov SN · Rodionov DA last · Hall B first · Levy S · Dufault-Thompson K · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Jiang X last · Schroer HW first · Beghini F · Raygoza Garay JA · Christakis NA · Bosch DE last
Downloads
PRJNA398089.csv.gz (69.0 KB) · parquet (158.0 KB) — all 2,041 samples, every field with route and confidence · PRJNA398089_determinations.csv.gz (177.9 KB) — 18,087 evidence rows