Gut microbiome in IBD patients during diet intervention
409 stool samples (adults, elderly, and adolescents) from participants with inflammatory bowel disease, studied in a single-arm pre-post intervention trial assessing the IBD Anti-Inflammatory Diet's effect on the gut microbiome. machine-written summary
409 samples · 409 runs · US · Adult · 2021 · 0.25 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,442 sample values (age, sex, subject id, timepoint) |
| ✓ Abstract / description | 818 sample values (health condition, health condition detail) |
| ✓ Full text | 1,227 sample values (antibiotic exposure, collection date, country) · PMC10408196, PMC8942410 |
| ○ 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 |
intervention — arms not resolved
Controlled / prescribed diet or feeding regimen design single_arm_before_after · population ibd_unspecified · IBD Anti-Inflammatory Diet (IBD-AID), pre-post single-arm trial
“single-arm, pre-post intervention trial” — abstract:35311458 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
22 of 22 people sampled more than once (409 samples; median 18, up to 42 per person). Schedule stated by the source: “Bi-weekly stool samples collected throughout baseline period and an 8-week IBD-AID dietary intervention”.
Genera, mean relative abundance over 294 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 | 409 | 100% | ||||
| country | 409 | 100% | 409 | |||
| health_condition | 409 | 100% | 409 | |||
| subject_id | 409 | 100% | 409 | |||
| age_at_collection_days | 409 | 100% | 409 | |||
| antibiotic_exposure | 409 | 100% | 409 | |||
| collection_date | 409 | 100% | 409 | |||
| health_condition_detail | 409 | 100% | 409 | |||
| sex | 409 | 100% | 409 | |||
| timepoint_label | 215 | 53% | 215 |
- Dietary manipulation of the gut microbiome in inflammatory bowel disease patients: Pilot study. 2022 PMID 35311458 PMC8942410 own_data
- Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions. 2023 PMID 37553697 PMC10408196 unsure
Archive description
Inflammatory bowel diseases (IBD), such as Crohn's disease and ulcerative colitis, are chronic recurrent inflammatory disorders of the gastrointestinal tract affecting roughly 1 in 200 people in the US. There is an increasing interest in developing microbiome-centered therapies to treat IBD. Given that diet can rapidly shape the gut microbiome, dietary interventions may produce beneficial microbiome shifts. Participating subjects adopted the IBD Anti-inflammatory diet developed by the UMass Medical School Center for Applied Nutrition. The influence of diet on the microbiome and disease was assessed.
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.title · “Gut microbiome of subjects”
- body site study.description · “disorders of the gastrointestinal tract affecting roughly”
- 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 |
|---|---|---|---|---|---|---|
| SAMN15393362 | age_at_collection_days | 17872.0 | R1 | 0.85 | sample.attr.age | 49 |
| SAMN15393362 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | use of the antibiotic within 3 months at the time of recruitment |
| SAMN15393362 | collection_date | 2017-02/2019-01 | R3 | 0.60 | paper.fulltext.results | recruited for the study between February 2017 and January 2019 |
| SAMN15393362 | country | US | R3 | 0.70 | paper.fulltext.methods | approved by the IRB at UMASS |
| SAMN15393362 | health_condition | ibd_unspecified | R4 | 0.50 | study.title | subjects with inflammatory bowel disease |
| SAMN15393362 | health_condition_detail | All subjects had inflammatory bowel disease | R4 | 0.50 | study.title | subjects with inflammatory bowel disease |
| SAMN15393362 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN15393362 | subject_id | IBDAID_002 | R1 | 0.85 | biosample.attribute:isolate | isolate: IBDAID_002 |
| SAMN15393371 | timepoint_label | 10 | R1 | 0.70 | sample.name_rule:alias | IBDAID_002_10 |
Sequencing
409 runs over 409 samples · mean 0.51 Gbp per run (median 0.25 Gbp, total 207.05 Gbp; 409 runs with a base count) · layout PAIRED 409 · platform ILLUMINA 409 · models NextSeq 500 (409) · 72% of runs with a Sandpiper profile · first public 2021-12-10
Authors (20)
Olendzki B first · Bucci V · Cawley C · Maserati R · McManus M · Olednzki E · Madziar C · Chiang D · Ward DV · Pellish R · Foley C · Bhattarai S · McCormick BA · Maldonado-Contreras A last · Chen J first · Siliceo SL · Ni Y · Nielsen HB · Xu A · Panagiotou G last
Downloads
PRJNA642308.csv.gz (9.8 KB) · parquet (83.6 KB) — all 409 samples, every field with route and confidence · PRJNA642308_determinations.csv.gz (20.3 KB) — 3,487 evidence rows