IBD biologic therapy response, stool/blood, Boston, USA
114 samples from adults and elderly patients with Crohn's disease or ulcerative colitis in Boston, USA, profiling baseline stool and blood before starting anti-cytokine or anti-integrin drug therapy in a prospective intervention study. machine-written summary
114 samples · 114 runs · US · Adult · 2021 · 2.90 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,140 sample values (age, antibiotic exposure, bmi, country, health condition, health condition detail, intervention, location locality) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 228 sample values (location site, subject id) · PMC11239293, PMC12268991, PMC8366279 |
| ○ 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 observational_with_procedure · population ibd_unspecified · Anti-TNF, anti-IL12/23, or anti-integrin biologic therapy
“initiating anti-cytokine therapy (anti-TNF or -IL12/23) or anti-integrin therapy” — abstract:34297922 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 104 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 | 114 | 100% | ||||
| country | 114 | 100% | 114 | |||
| health_condition | 114 | 100% | 114 | |||
| subject_id | 114 | 100% | 114 | |||
| age_at_collection_days | 114 | 100% | 114 | |||
| antibiotic_exposure | 114 | 100% | 114 | |||
| bmi | 114 | 100% | 114 | |||
| detailed_location | 114 | 100% | ||||
| health_condition_detail | 114 | 100% | 114 | |||
| intervention | 114 | 100% | 114 | |||
| location_locality | 114 | 100% | 114 | |||
| location_site | 114 | 100% | 114 | |||
| sex | 114 | 100% | 114 | |||
| smoking_status | 114 | 100% | 114 |
- Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease. 2021 PMID 34297922 PMC8366279 own_data
- Discovery of disease-adapted bacterial lineages in inflammatory bowel diseases. 2024 PMID 38917808 PMC11239293 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
The intestinal microbiome is a key determinant of response to biologic therapy in inflammatory bowel disease. We conducted a prospective study, profiling baseline stool and blood samples, in patients with moderate-to-severe Crohn's disease or ulcerative colitis initiating anti-TNF, anti-IL12/23 (grouped as anti-cytokine therapy), or anti-intergrin therapy. Patients were assessed at 14 weeks for clinical remission and 52 weeks for clinical and endoscopic remission. Baseline microbial richness was a key feature indicating preferential response to anti-cytokine therapy. Increase diversity of baseline samples could be attributed to increased abundance of microbial specific competent in the 7-alpha/beta-dehydroxylation of primary to secondary bile acids. Paired serum metabolomic analysis reaffirmed the readouts of microbial-derived secondary bile acids. Serum signatures of immune-proteins reflective of microbial diversity identify a subset of patients who were more likely to achieve remission with anti-cytokine therapy. Twenty seven unique serum immune-proteins profiles associated with remission in this study were unique to specific therapeutic classes. The multi -omic profiles identified from this study could aid physicians to determine a. priori the therapeutic class most likely to benefit patients, as well as potentially serve as novel targets for newer therapies to treat IBD.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “profiling baseline stool and blood samples”
- life stage sample.attr.age · “31 (n=96/114)”
- life stage sample.attr.age · “62 (n=17/114)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17082932 | age_at_collection_days | 11305.8 | R1 | 0.85 | sample.attr.age | 31 |
| SAMN17082932 | antibiotic_exposure | yes | R1 | 0.90 | biosample_attr | Yes |
| SAMN17082932 | bmi | 25.93 | R1 | 0.90 | sample.attr.bmi | 25.92592593 |
| SAMN17082932 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: Boston |
| SAMN17082932 | health_condition | crohns_disease | R1 | 0.90 | biosample_attr | CD |
| SAMN17082932 | health_condition_detail | CD | R1 | 0.90 | sample.attr.ibd_subtype | CD |
| SAMN17082932 | intervention | drug_therapy | R1 | 0.85 | biosample.attribute:biologic | VEDO |
| SAMN17082932 | location_locality | Boston | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: Boston |
| SAMN17082932 | location_site | Massachusetts General Hospital Crohn's and Colitis Center | R3 | 0.70 | paper.fulltext.methods | seeking care at the MGH Crohn’s and Colitis center |
| SAMN17082932 | sex | male | R1 | 0.90 | sample.attr.sex | male |
| SAMN17082932 | smoking_status | never | R1 | 0.80 | biosample.attribute:smoking | No |
| SAMN17082932 | subject_id | SAMN17082932 | R3 | 0.75 | design.one_sample_per_subject:fulltext | Stool and blood samples were collected at baseline, and each stool sample was subjected to metagenomic sequencing |
Sequencing
114 runs over 114 samples · mean 3.02 Gbp per run (median 2.90 Gbp, total 343.90 Gbp; 114 runs with a base count) · layout PAIRED 114 · platform ILLUMINA 114 · models Illumina HiSeq 2500 (114) · 91% of runs with a Sandpiper profile · first public 2021-08-25
Authors (34)
Lee JWJ first · Plichta D · Hogstrom L · Borren NZ · Lau H · Gregory SM · Tan W · Khalili H · Clish C · Vlamakis H · Xavier RJ · Ananthakrishnan AN last · Kumbhari A first · Cheng TNH · Kochar B · Burke KE · Shannon K · Smillie CS last · Elmassry MM first · Sugihara K · Chankhamjon P · Kim Y · Camacho FR · Wang S · Sugimoto Y · Chatterjee S · Chen LA · Kamada N · Donia MS last · Schroer HW first · Beghini F · Raygoza Garay JA · Christakis NA · Bosch DE last
Downloads
PRJNA685168.csv.gz (5.1 KB) · parquet (77.6 KB) — all 114 samples, every field with route and confidence · PRJNA685168_determinations.csv.gz (11.2 KB) — 1,368 evidence rows