Gut virome in IBD patients on biological therapy
432 longitudinal fecal samples from 181 IBD patients (Crohn's disease and ulcerative colitis) collected before and after starting one of four biological therapies, examining gut virome composition and association with treatment response. machine-written summary
432 samples · 432 runs · Adult · 2022 · 3.48 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,888 sample values (age, health condition, health condition detail, intervention, intervention detail, medication, medication detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10588789 |
| ✓ Supplementary tables | 1,678 sample values (bmi, collection date, smoking status, timepoint) |
| – 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 resolved
Non-antibiotic pharmaceutical given as the study intervention (metformin design single_arm_before_after · population ibd_unspecified · Biological therapy (one of four agents) for IBD, pre/post samples
“treated with one out of four biological therapies” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
181 of 181 people sampled more than once (432 samples; median 2, up to 6 per person) · follow-up median 6 mo (max 8.1 y) · median interval between samples 4 mo (time from age at collection). Schedule stated by the source: “Baseline (pre-intervention) and follow-up/primary endpoint sample per patient; 50 CD patients also have an additional week 14 sample.”.
Each row is one person (36 shown of 181); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 369 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 | 432 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 432 | 100% | 432 | |||
| subject_id | 432 | 100% | 432 | |||
| age_at_collection_days | 432 | 100% | 432 | |||
| health_condition_detail | 432 | 100% | 432 | |||
| intervention | 432 | 100% | 432 | |||
| intervention_detail | 432 | 100% | 432 | |||
| medication | 432 | 100% | 432 | |||
| medication_detail | 432 | 100% | 432 | |||
| sex | 432 | 100% | 432 | |||
| collection_date | 423 | 98% | 423 | |||
| smoking_status | 423 | 98% | 423 | |||
| timepoint_label | 423 | 98% | 423 | |||
| bmi | 409 | 95% | 409 |
- Community Types of the Human Gut Virome are Associated with Endoscopic Outcome in Ulcerative Colitis. 2023 PMID 37052201 PMC10588789 own_data
Archive description
The gut microbiota is a complex ecosystem that consists of viruses, fungi, bacteria, archaea, and protozoa. They can exert beneficial functions such as protection against pathogen invasion or production of essential vitamins. Occasionally, this ecosystem gets out of balance, resulting in gut dysbiosis. Gut dysbiosis is associated with several diseases, one of which is inflammatory bowel disease (IBD). Thus far, little is known about the role of the viral component in IBD aetiology and activity. To elucidate it further, we investigated the gut virome in a large prospective cohort of active patients initiating biological therapy. Fecal samples were collected from a total of 181 IBD patients. All patients had active disease at baseline and were treated with one out of four biological therapies. Pre-intervention and post-intervention samples were collected from every patient. We hypothesized and showed associations between the patients gut virota and therapy response.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by opus_adjudicated with confidence 0.75. Assay shotgun_dna.
- host study.description · “a total of 181 IBD patients”
- body site study.description · “Fecal samples were collected”
- life stage sample.attr.age · “21 years (n=359/432)”
- life stage sample.attr.age · “66.8 years (n=44/432)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN25740319 | age_at_collection_days | 12711.0 | R1 | 0.90 | sample.attr.age | 34.8 years |
| SAMN25740328 | bmi | 19.13 | R2 | 0.80 | paper.supp.jjad061_suppl_supplementary_table.xlsx[Supplementary Table 1!BMI] | B10 | BMI: 19.13 |
| SAMN25740328 | collection_date | 2011-03-08 | R2 | 0.80 | paper.supp.jjad061_suppl_supplementary_table.xlsx[Supplementary Table 1!Sample date] | B10 | Sample date: 2011-03-08 00:00:00 |
| SAMN25740319 | health_condition | crohns_disease | R1 | 0.90 | biosample_attr | CD |
| SAMN25740319 | health_condition_detail | inflammed | R1 | 0.90 | sample.attr.health_state | inflammed |
| SAMN25740319 | intervention | drug_therapy | R1 | 0.80 | biosample.attribute:treatment | treatment: ADA |
| SAMN25740319 | intervention_detail | adalimumab biologic therapy | R1 | 0.80 | biosample.attribute:treatment | treatment: ADA |
| SAMN25740319 | medication | immunosuppressant_or_biologic | R1 | 0.90 | biosample.attribute:treatment | ADA |
| SAMN25740319 | medication_detail | ADA | R1 | 0.90 | biosample.attribute:treatment | ADA |
| SAMN25740319 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN25740328 | smoking_status | never | R2 | 0.80 | paper.supp.jjad061_suppl_supplementary_table.xlsx[Supplementary Table 1!Smoking 2] | B10 | Smoking 2: Non |
| SAMN25740319 | subject_id | 8089 | R1 | 0.85 | biosample.attribute:isolate | 8089 |
| SAMN25740328 | timepoint_label | 0 | R2 | 0.80 | paper.supp.jjad061_suppl_supplementary_table.xlsx[Supplementary Table 1!Week] | B10 | Week: 0 |
Sequencing
432 runs over 432 samples · mean 3.53 Gbp per run (median 3.48 Gbp, total 1,526.01 Gbp; 432 runs with a base count) · layout PAIRED 432 · platform ILLUMINA 432 · models Illumina NovaSeq 6000 (432) · 89% of runs with a Sandpiper profile · first public 2022-10-15
Authors (10)
Jansen D first · Falony G · Vieira-Silva S · Simsek C · Marcelis T · Caenepeel C · Machiels K · Raes J · Vermeire S · Matthijnssens J last
Downloads
PRJNA804384.csv.gz (19.5 KB) · parquet (94.7 KB) — all 432 samples, every field with route and confidence · PRJNA804384_determinations.csv.gz (51.6 KB) — 5,566 evidence rows