IBD multi-omic cross-sectional cohort, San Diego, USA
210 stool samples from San Diego, USA adults (mostly), with Crohn's disease, ulcerative colitis, or healthy controls, studied cross-sectionally using metaproteomics, shotgun metagenomics, 16S sequencing, metabolomics, and host genetics. machine-written summary
210 samples · 210 runs · US · Adult · 2023 · 0.25 Gbp / sample · cohort Multi-omics analyses of the ulcerative colitis gut
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,013 sample values (age, antibiotic exposure, country, health condition, health condition detail, location locality, location region, medication) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8852248, PMC9400277 |
| ○ 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 |
antibiotic exposure: two sequence archives disagree for 2 samples (e.g. yes vs no) — withheld; sex differs between samples of the same subject id (1 subjects, 2 samples) — sex withheld; subject ids shared by samples of both sexes (1 ids, 2 samples) — ids withheld.
The sources disagree on 4 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 (6)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA7731530 | antibiotic exposure | yes (sequence archive) | no (sequence archive) | withheld: neither value published |
| SAMEA7731609 | antibiotic exposure | yes (sequence archive) | no (sequence archive) | withheld: neither value published |
| SAMEA7731429 | sex | male (sequence archive) | subject 133: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA7731558 | sex | female (sequence archive) | subject 133: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMEA7731429 | subject id | 133 | male (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMEA7731558 | subject id | 133 | female (sequence archive) | subject id withheld (samples of both sexes share it) |
longitudinal
33 of 166 people sampled more than once (75 samples; median 2, up to 4 per person) · follow-up median 19.0 y (max 34.0 y) · median interval between samples 19.0 y (time from age at collection).
Each row is one person (2 shown of 33); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 210 | 100% | ||||
| country | 210 | 100% | 210 | |||
| health_condition | 210 | 100% | 210 | |||
| subject_id | 208 | 99% | 208 | |||
| detailed_location | 210 | 100% | ||||
| health_condition_detail | 210 | 100% | 210 | |||
| location_locality | 210 | 100% | 210 | |||
| location_region | 210 | 100% | 210 | |||
| age_at_collection_days | 192 | 91% | 192 | |||
| sex | 188 | 90% | 188 | |||
| smoking_status | 185 | 88% | 185 | |||
| timepoint_label | 57 | 27% | 57 | |||
| medication | 50 | 24% | 50 | |||
| medication_detail | 50 | 24% | 50 | |||
| antibiotic_exposure | 33 | 16% | 33 |
- Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity. 2022 PMID 35087228 PMC8852248 own_data
- Location-specific signatures of Crohn's disease at a multi-omics scale. 2022 PMID 35999575 PMC9400277 own_data
- Pangenomic analysis identifies correlations between <i>Akkermansia</i> species and subspecies and human health outcomes. 2024 PMID 39421249 PMC11480726 unsure
- Phylo-Spec: a phylogeny-fusion deep learning model advances microbiome status identification. 2025 PMID 41283667 PMC12710343 unsure
Archive description
Inflammatory Bowel Disease (IBD) remains a difficult disease to treat and diagnose and is of growing global prevalence. With an increasing number of studies linking the gut microbiome to IBD, we set out to further characterize the molecular landscape of IBD through the collection of multiple meta -omic data layers on 200 patient samples. The data types collected feature a multiplexed metaproteomic analysis through the use of tandem mass tag MS3 based technology, with integrated shotgun metagenomics, 16S sequencing and metabolomics. With this data we hope to identify further clues about IBD etiology and potential biomarkers for the disease.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.description · “studies linking the gut microbiome to IBD,”
- body site external_curation.infant_catalog · “body_site_call gut”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7731429 | age_at_collection_days | 12053.2 | R1 | 0.90 | sample.attr.host_age | 33 |
| SAMEA7731433 | antibiotic_exposure | yes | R1 | 0.80 | sample.attr.antibiotics | Flagyl PO 05/2018 |
| SAMEA7731556 | antibiotic_exposure | yes | R1 | 0.85 | biosample_attr | Flagyl unk dose (1995-unk) |
| SAMEA7731409 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:CA:San Diego |
| SAMEA7731409 | health_condition | healthy_control | R1 | 0.90 | biosample_attr | Healthy_control |
| SAMEA7731409 | health_condition_detail | Healthy_control | R1 | 0.90 | sample.attr.diagnosis | Healthy_control |
| SAMEA7731409 | location_locality | San Diego | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:CA:San Diego |
| SAMEA7731409 | location_region | California | R1 | 0.75 | biosample.attribute:geo_loc_name | USA:CA:San Diego |
| SAMEA7731500 | medication | immunosuppressant_or_biologic | R1 | 0.85 | biosample.attribute:biologic_therapy | ADA 160 mg (unk) |
| SAMEA7731512 | medication | corticosteroid | R1 | 0.75 | biosample.attribute:steroids | Cortafoam unk (1990-pres) |
| SAMEA7731513 | medication | corticosteroid | R1 | 0.85 | biosample.attribute:other_nonbiologic_therapy | Budesonide unk |
| SAMEA7731500 | medication_detail | ADA 160 mg (unk) | R1 | 0.85 | biosample.attribute:biologic_therapy | ADA 160 mg (unk) |
| SAMEA7731512 | medication_detail | Cortafoam unk (1990-pres) | R1 | 0.75 | biosample.attribute:steroids | Cortafoam unk (1990-pres) |
| SAMEA7731513 | medication_detail | Budesonide unk | R1 | 0.85 | biosample.attribute:other_nonbiologic_therapy | Budesonide unk |
| SAMEA7731431 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMEA7731429 | smoking_status | never | R1 | 0.80 | biosample.attribute:smoking | N |
| SAMEA7731409 | subject_id | HC1 | R1 | 0.85 | sample.attr.patient_number | HC1 |
| SAMEA7731409 | timepoint_label | Healthy_control | R1 | 0.85 | sample.attr.visit_number | Healthy_control |
Sequencing
210 runs over 210 samples · mean 0.27 Gbp per run (median 0.25 Gbp, total 55.96 Gbp; 210 runs with a base count) · layout PAIRED 210 · platform ILLUMINA 210 · models Illumina NovaSeq 6000 (210) · 0% of runs with a Sandpiper profile · first public 2023-05-15
Authors (37)
Mills RH first · Dulai PS · Vázquez-Baeza Y · Sauceda C · Daniel N · Gerner RR · Batachari LE · Malfavon M · Zhu Q · Weldon K · Humphrey G · Carrillo-Terrazas M · Goldasich LD · Bryant M · Raffatellu M · Quinn RA · Gewirtz AT · Chassaing B · Chu H · Sandborn WJ · Dorrestein PC · Knight R · Gonzalez DJ last · Gonzalez CG first · Mueller KD first · Panzetta ME · Davey L · McCann JR · Rawls JF · Flores GE · Valdivia RH last · Zhang J first · Meng F · Sun Y · Xu W · Wu S · Su X last
Downloads
PRJEB42155.csv.gz (7.8 KB) · parquet (81.5 KB) — all 210 samples, every field with route and confidence · PRJEB42155_determinations.csv.gz (17.3 KB) — 2,013 evidence rows