IBD microbiomes during vedolizumab therapy, Boston
Metagenomes from 174 samples of inflammatory bowel disease patients (86 ulcerative colitis, 42 Crohn's disease) receiving vedolizumab treatment in Boston, USA. Intervention study examining microbiome changes during drug therapy. machine-written summary
174 samples · 174 runs · US · Adult · 2019 · 2.66 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,169 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC12268991, PMC6759048, PMC7216530 |
| ○ 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
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population ibd_unspecified · Vedolizumab therapy in IBD patients, sampled over treatment
“patient receiving vedolizamub therapy” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
53 of 84 people sampled more than once (143 samples; median 3, up to 4 per person). Schedule stated by the source: “stool at week 0 (baseline), week 14, week 30 and week 52 of vedolizumab therapy” (time origin: intervention_start); stated follow-up 12 mo.
Genera, mean relative abundance over 151 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 | 174 | 100% | ||||
| country | 174 | 100% | 174 | |||
| health_condition | 174 | 100% | 174 | |||
| subject_id | 174 | 100% | 174 | |||
| age_at_collection_days | 174 | 100% | 174 | |||
| collection_date | 174 | 100% | 174 | |||
| detailed_location | 174 | 100% | ||||
| health_condition_detail | 174 | 100% | 174 | |||
| latitude | 174 | 100% | 174 | |||
| location_locality | 174 | 100% | 174 | |||
| location_region | 174 | 100% | 174 | |||
| longitude | 174 | 100% | 174 | |||
| sex | 174 | 100% | 174 | |||
| timepoint_label | 174 | 100% | 174 | |||
| medication | 81 | 47% | 81 |
- Microbial genes and pathways in inflammatory bowel disease. 2019 PMID 31249397 PMC6759048 unsure
- Host DNA contents in fecal metagenomics as a biomarker for intestinal diseases and effective treatment. 2020 PMID 32393180 PMC7216530 unsure
- A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules. 2025 PMID 39947133 PMC12268991 unsure
Archive description
Studies of metagenomes of inflammatory bowel disease patient receiving vedolizamub therapy
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.62. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- life stage study.title · “inflammatory bowel disease patient”
- life stage sample.attr.age · “62 (n=25/174)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN06831080 | age_at_collection_days | 9496.5 | R1 | 0.85 | sample.attr.age | 26 |
| SAMN06831080 | collection_date | 2015 | R1 | 0.90 | biosample.attribute:collection_date | 2015 |
| SAMN06831080 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Boston MA |
| SAMN06831080 | health_condition | ulcerative_colitis | R1 | 0.90 | biosample_attr | UC000001 |
| SAMN06831083 | health_condition | crohns_disease | R1 | 0.70 | sample.name_rule:host_disease | CD000004 |
| SAMN06831080 | health_condition_detail | UC000001 | R1 | 0.90 | sample.attr.host_disease | UC000001 |
| SAMN06831080 | latitude | 42.3620 | R1 | 0.90 | biosample.attribute:lat_lon | 42.361959 N 71.065882 W |
| SAMN06831080 | location_locality | Boston | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Boston MA |
| SAMN06831080 | location_region | Massachusetts | R1 | 0.75 | biosample.attribute:geo_loc_name | USA: Boston MA |
| SAMN06831080 | longitude | -71.0659 | R1 | 0.90 | biosample.attribute:lat_lon | 42.361959 N 71.065882 W |
| SAMN06831083 | medication | corticosteroid | R1 | 0.90 | biosample.attribute:current_steroids | 1 |
| SAMN06831080 | sex | female | R1 | 0.85 | biosample.attribute:female | 1 |
| SAMN06831080 | subject_id | P9092 | R1 | 0.85 | biosample.attribute:prism_id | P9092 |
| SAMN06831080 | timepoint_label | 1 | R1 | 0.85 | biosample.attribute:week_14 | 1 |
| SAMN06831081 | timepoint_label | 1 | R1 | 0.85 | biosample.attribute:week_0 | 1 |
| SAMN06831082 | timepoint_label | 1 | R1 | 0.85 | biosample.attribute:week_52 | 1 |
| SAMN06831093 | timepoint_label | 1 | R1 | 0.85 | biosample.attribute:week_30 | 1 |
Sequencing
174 runs over 174 samples · mean 2.83 Gbp per run (median 2.66 Gbp, total 492.59 Gbp; 174 runs with a base count) · layout SINGLE 174 · platform ILLUMINA 174 · models NextSeq 500 (174) · 87% of runs with a Sandpiper profile · first public 2019-04-28
Authors (20)
Schirmer M first · Garner A · Vlamakis H · Xavier RJ last · Jiang P first · Lai S · Wu S · Zhao XM · Chen WH · Elmassry MM first · Sugihara K · Chankhamjon P · Kim Y · Camacho FR · Wang S · Sugimoto Y · Chatterjee S · Chen LA · Kamada N · Donia MS last
Downloads
PRJNA384246.csv.gz (6.7 KB) · parquet (79.4 KB) — all 174 samples, every field with route and confidence · PRJNA384246_determinations.csv.gz (19.3 KB) — 2,169 evidence rows