Longitudinal gut multi-omics in IBS, USA
532 longitudinal samples from USA participants (364 IBS, 168 healthy controls), studying gut microbiome, metabolome, epigenome, and transcriptome links to irritable bowel syndrome. machine-written summary
532 samples · 532 runs · US · Age unknown · 2020 · 0.16 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,184 sample values (collection date, country, latitude, longitude, subject id, timepoint) |
| ✓ Abstract / description | 28 sample values (health condition, health condition detail) |
| ○ Full text | read; no usable statement or table · PMC11538712, PMC11645270, PMC8109273, PMC9159953, PMC9649010 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| ✓ External resources | 1,036 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
76 of 80 people sampled more than once (524 samples; median 7, up to 11 per person). Schedule stated by the source: “Multiple stool samples per participant over time, numbered sequentially (e.g. Sample 1, Sample 2, ... up to Sample 8)” (time origin: enrolment).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 0 | 0% | ||||
| country | 532 | 100% | 532 | |||
| health_condition | 532 | 100% | 518 | 14 | ||
| subject_id | 528 | 99% | 528 | |||
| collection_date | 532 | 100% | 532 | |||
| health_condition_detail | 532 | 100% | 518 | 14 | ||
| latitude | 532 | 100% | 532 | |||
| longitude | 532 | 100% | 532 | |||
| timepoint_label | 528 | 99% | 528 |
- Longitudinal Multi-omics Reveals Subset-Specific Mechanisms Underlying Irritable Bowel Syndrome. 2020 PMID 32916129 PMC8109273 own_data
- Identification of shared and disease-specific host gene-microbiome associations across human diseases using multi-omic integration. 2022 PMID 35577971 PMC9159953 own_data
- Faecal microbiome-based machine learning for multi-class disease diagnosis. 2022 PMID 36357393 PMC9649010 unsure
- Cross-Cohort Gut Microbiome Signatures of Irritable Bowel Syndrome Presentation and Treatment. 2024 PMID 39243395 PMC11538712 unsure
- Noninvasive, microbiome-based diagnosis of inflammatory bowel disease. 2024 PMID 39367251 PMC11645270 unsure
Archive description
The gut microbiome has been implicated in multiple human chronic gastrointestinal (GI) disorders but it has been difficult to determine its mechanistic role in disease pathogenesis due to the apparent disconnect between animal and human studies and a lack of integrated multi-omics approach in relation to disease specific physiologic changes. To uncover such mechanisms, we integrated longitudinal multi-omics data from the gut microbiome, metabolome, host epigenome and transcriptome in the context of irritable bowel syndrome (IBS) host physiology. We identified IBS subtype-specific and symptom-related changes in microbial composition and functions. A subset of these changes corresponds to host physiological changes in IBS. Using integration of multiple data layers, we identified purine metabolism as a novel host-microbial metabolic pathway in IBS with potential effects on gastrointestinal barrier function. This study highlights the importance of integrating longitudinal complementary multi-omics data to identify functional mechanisms that can serve as therapeutic targets in a comprehensive treatment strategy for chronic GI diseases.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.scientific_name · “human metagenome”
- body site study.description · “gut microbiome has been implicated in multiple human chronic”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA7501053 | collection_date | 2016 | R1 | 0.90 | biosample.attribute:collection_date | 2016 |
| SAMEA7501053 | country | US | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | USA |
| SAMEA7501057 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMEA7501053 | health_condition | ibs | R4 | 0.50 | study.title | irritable bowel syndrome |
| SAMEA7501057 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMEA7501053 | health_condition_detail | irritable bowel syndrome (IBS) | R4 | 0.50 | study.title | irritable bowel syndrome |
| SAMEA7501053 | latitude | 44.9000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 44.9 N 93.2 W |
| SAMEA7501053 | longitude | -93.2000 | R1 | 0.90 | biosample.attribute:geographic_location_latitude+geographic_location_longitude | 44.9 N 93.2 W |
| SAMEA7501057 | subject_id | 1 | R1 | 0.70 | sample.name_rule:title | Participant 1 Sample 0 |
| SAMEA7501057 | timepoint_label | 0 | R1 | 0.70 | sample.name_rule:title | Participant 1 Sample 0 |
Sequencing
532 runs over 532 samples · mean 0.15 Gbp per run (median 0.16 Gbp, total 81.88 Gbp; 532 runs with a base count) · layout SINGLE 532 · platform ILLUMINA 532 · models Illumina HiSeq 4000 (532) · 0% of runs with a Sandpiper profile · first public 2020-10-30
Authors (68)
Mars RAT first · Yang Y · Ward T · Houtti M · Priya S · Lekatz HR · Tang X · Sun Z · Kalari KR · Korem T · Bhattarai Y · Zheng T · Bar N · Frost G · Johnson AJ · van Treuren W · Han S · Ordog T · Grover M · Sonnenburg J · D'Amato M · Camilleri M · Elinav E · Segal E · Blekhman R · Farrugia G · Swann JR · Knights D · Kashyap PC last · Burns MB · Adamowicz B · Lock EF · 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 · Li J first · Ghosh TS · Arendt E · Shanahan F · O'Toole PW 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
Downloads
PRJEB37924.csv.gz (11.9 KB) · parquet (87.2 KB) — all 532 samples, every field with route and confidence · PRJEB37924_determinations.csv.gz (29.6 KB) — 4,248 evidence rows