Longitudinal Stool Microbiome in IBD and Controls, USA
262 stool samples from patients with IBD (unspecified type) and healthy controls in Boston and Atlanta, USA, collected as part of a longitudinal study combining the PRISM and STINKI cohorts. machine-written summary
262 samples · 262 runs · US · Age unknown · 2017 · 2.97 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,619 sample values (collection date, country, health condition, health condition detail, latitude, location locality, location region, longitude) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10191612, PMC10439275, PMC12210856, PMC12520552, PMC5704459 |
| ○ 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 |
health condition: sequence archive and curatedMetagenomicData disagree for 1 sample (e.g. ibd_unspecified vs healthy_control) — withheld.
The sources disagree on 1 sample. 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 (1)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN07200322 | health condition | ibd_unspecified (sequence archive) | healthy_control (curatedMetagenomicData) | withheld: neither value published |
longitudinal
32 of 32 people sampled more than once (262 samples; median 8, up to 12 per person) · follow-up median 7 mo (max 11 mo) · median interval between samples 30 d (time from timepoint labels).
Each row is one person (32 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 232 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 | 262 | 100% | 262 | |||
| health_condition | 261 | 100% | 261 | |||
| subject_id | 262 | 100% | 262 | |||
| collection_date | 262 | 100% | 262 | |||
| detailed_location | 262 | 100% | ||||
| health_condition_detail | 262 | 100% | 262 | |||
| latitude | 262 | 100% | 262 | |||
| location_locality | 262 | 100% | 262 | |||
| location_region | 262 | 100% | 262 | |||
| longitude | 262 | 100% | 262 | |||
| timepoint_label | 262 | 100% | 262 |
- A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. 2017 PMID 29183332 PMC5704459 own_data
- Deciphering associations between gut microbiota and clinical factors using microbial modules. 2023 PMID 37084255 PMC10191612 own_data
- Commensal bacteria promote azathioprine therapy failure in inflammatory bowel disease via decreasing 6-mercaptopurine bioavailability. 2023 PMID 37586320 PMC10439275 own_data
- Synergistic gut microbiome-mediated degradation of <i>Astragalus membranaceus</i> polysaccharides and <i>Codonopsis pilosula</i> polysaccharides into butyric acid: a metatranscriptomic analysis. 2025 PMID 40422281 PMC12210856 own_data
- Akkermansia muciniphila-Derived N-Acetylspermidine Modulates the Localization of Intestinal α1,2-Fucosylated Proteins to Maintain Gut Homeostasis. 2025 PMID 40776401 PMC12520552 own_data
18 more
- Microbial genes and pathways in inflammatory bowel disease. 2019 PMID 31249397 PMC6759048
- Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease. 2019 PMID 31370880 PMC6670193
- Gut Microbiota and Metabolic Specificity in Ulcerative Colitis and Crohn's Disease. 2020 PMID 33330572 PMC7729129
- The taxonomic distribution of histamine-secreting bacteria in the human gut microbiome. 2021 PMID 34563136 PMC8465708
- Microbial genes outperform species and SNVs as diagnostic markers for Crohn's disease on multicohort fecal metagenomes empowered by artificial intelligence. 2023 PMID 37278203 PMC10246480
- Bacterial indole-3-lactic acid affects epithelium-macrophage crosstalk to regulate intestinal homeostasis. 2023 PMID 37903267 PMC10636326
- Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts. 2023 PMID 37932270 PMC10628233
- Enhancing insights into diseases through horizontal gene transfer event detection from gut microbiome. 2024 PMID 38884260 PMC11317153
- Enhanced microbiota profiling in patients with quiescent Crohn's disease through comparison with paired healthy first-degree relatives. 2024 PMID 38942021 PMC11293350
- Noninvasive, microbiome-based diagnosis of inflammatory bowel disease. 2024 PMID 39367251 PMC11645270
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991
- Megasphaera Elesdenii Dysregulates Colon Epithelial Homeostasis, Aggravates Colitis-Associated Tumorigenesis. 2025 PMID 40801433 PMC12591162
- Gut Microbes Secretions May Trigger Mononuclear Cell Migration and Offer Comorbidity Mechanism Between Inflammatory Bowel Disease and Diabetic Retinopathy. 2025 PMID 41333916 PMC12668851
- Deciphering the personalized functional redundancy hierarchy in the gut microbiome. 2025 PMID 41345980 PMC12781464
- <i>Parasutterella excrementihominis</i> exacerbates experimental colitis and colitis-associated colorectal cancer via pathogenic NETosis activation. 2026 PMID 41448880 PMC13151518
- A microbiota-IPA axis facilitates intestinal stem cell-mediated regeneration in colitis through a Hopx-associated program. 2026 PMID 41741429 PMC13057028
- Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals. 2026 PMID 42312244 PMC13269251
- Global gut microbiome atlas identifies epidemiologic-stage-specific signatures in inflammatory bowel disease. 2026 PMID 42575094 PMC13589510
Archive description
Longitudinal Stool Study of patients with IBD and controls. This project combines data from PRISM and STINKI cohorts to characterize the gut microbiome of individuals with IBD and controls over time.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.72. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site study.title · “Longitudinal Stool Study”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07199828 | collection_date | 2013 | R1 | 0.90 | biosample.attribute:collection_date | 2013 |
| SAMN07199828 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA:Boston |
| SAMN07199828 | health_condition | ibd_unspecified | R1 | 0.85 | biosample.attribute:DESCRIPTION | IBD |
| SAMN07199828 | health_condition_detail | IBD | R1 | 0.85 | biosample.attribute:DESCRIPTION | IBD |
| SAMN07199828 | latitude | 42.3632 | R1 | 0.90 | biosample.attribute:lat_lon | 42.3632 N 71.0688 W |
| SAMN07199828 | location_locality | Boston | R1 | 0.85 | biosample.attribute:geo_loc_name | USA:Boston |
| SAMN07199828 | location_region | Massachusetts | R1 | 0.60 | biosample.attribute:lat_lon | 42.3632 N 71.0688 W |
| SAMN07199828 | longitude | -71.0688 | R1 | 0.90 | biosample.attribute:lat_lon | 42.3632 N 71.0688 W |
| SAMN07199828 | subject_id | p8582 | R1 | 0.85 | sample.attr.subject | p8582 |
| SAMN07199828 | timepoint_label | month 1 | R1 | 0.85 | biosample.attribute:month | 1 |
Sequencing
262 runs over 262 samples · mean 3.38 Gbp per run (median 2.97 Gbp, total 886.38 Gbp; 262 runs with a base count) · layout PAIRED 262 · platform ILLUMINA 262 · models Illumina HiSeq 2000 (262) · 90% of runs with a Sandpiper profile · first public 2017-12-14
Authors (42)
Rong X first · Zhu L · Shu Q last · Yao Y first · Pei Z · Dai Y · Chen Y · Chang Z · Wang H · Zhao J · Zhang H · Zhai Q · Lu W · Chen W last · Xu B first · Wu S · Huang J · Lin M · Liu Q · Li X · Fu M · Xia Z · Yi G last · Tan H first · Huang L · Wang J · Huang H · Lin Z · Yang S · Shi Y · Li J · Zhou Y · Huang C last · Zhai J first · Li Y · Liu J · Su X · Cui R · Zheng D · Sun Y · Yu J · Dai C last
Downloads
PRJNA385949.csv.gz (7.8 KB) · parquet (79.4 KB) — all 262 samples, every field with route and confidence · PRJNA385949_determinations.csv.gz (16.4 KB) — 2,619 evidence rows