Longitudinal gut virome in IBD and healthy adults, Cork
233 unamplified faecal virome samples from adults in Cork, Ireland, comprising healthy controls and IBD patients, collected longitudinally over three time points to characterise the human gut virome without amplification bias. machine-written summary
233 samples · 233 runs · IE · Adult · 2022 · 0.59 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,773 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location region) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC9968284 |
| ✓ Supplementary tables | 562 sample values (antibiotic exposure, medication, smoking status) |
| – 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 |
longitudinal
79 of 79 people sampled more than once (233 samples; median 3, up to 3 per person) · follow-up median 6 mo (max 13 mo) · median interval between samples 3 mo (time from collection dates). Schedule stated by the source: “100-day intervals (T2: mean 93.2, SD 28.8; T3: mean 192.3, SD 71.7)” (time origin: enrolment).
Each row is one person (36 shown of 79); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 187 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 | 233 | 100% | ||||
| country | 233 | 100% | 233 | |||
| health_condition | 233 | 100% | 233 | |||
| subject_id | 233 | 100% | 233 | |||
| age_at_collection_days | 233 | 100% | 233 | |||
| detailed_location | 233 | 100% | ||||
| health_condition_detail | 233 | 100% | 233 | |||
| latitude | 233 | 100% | 233 | |||
| location_region | 233 | 100% | 233 | |||
| longitude | 233 | 100% | 233 | |||
| sex | 233 | 100% | 233 | |||
| timepoint_label | 233 | 100% | 233 | |||
| antibiotic_exposure | 228 | 98% | 228 | |||
| bmi | 224 | 96% | 224 | |||
| collection_date | 219 | 94% | 219 | |||
| smoking_status | 196 | 84% | 196 | |||
| medication | 138 | 59% | 138 |
- Interpersonal variability of the human gut virome confounds disease signal detection in IBD. 2023 PMID 36841913 PMC9968284 own_data
Archive description
Viruses are increasingly recognised as important components of the human microbiome, fulfilling numerous ecological roles including bacterial predation, immune stimulation, genetic diversification, horizontal gene transfer, microbial interactions, and augmentation of metabolic functions. However, our current view of the human gut virome is tainted by previous sequencing requirements that necessitated the amplification of starting nucleic acids. In this study, we performed an original longitudinal analysis of 40 healthy control, 19 Crohns disease, and 20 ulcerative colitis viromes over three time points without an amplification bias.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.68. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.description · “human gut virome”
- life stage sample.attr.host_age · “23 (n=214/233)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN27654482 | age_at_collection_days | 15696.8 | R1 | 0.85 | sample.attr.host_age | 43 |
| SAMN27654482 | antibiotic_exposure | no | R2 | 0.85 | paper.supp.metadata_vlp_V2.csv[!Recent_anticiotic_use] | NG-17954_320_T1_lib298604: Recent_anticiotic_use=No |
| SAMN27654482 | bmi | 33.13 | R1 | 0.90 | sample.attr.host_body_mass_index | 33.13134 |
| SAMN27654482 | collection_date | 2014-12-15 | R1 | 0.90 | biosample.attribute:collection_date | 2014-12-15 |
| SAMN27654482 | country | IE | R1 | 0.90 | sample.attr.geo_loc_name | Ireland: Cork |
| SAMN27654482 | health_condition | ibd_unspecified | R1 | 0.85 | biosample_attr | IBD |
| SAMN27654482 | health_condition_detail | UC | R1 | 0.90 | sample.attr.gastrointest_disord | UC |
| SAMN27654482 | latitude | 51.8834 | R1 | 0.90 | biosample.attribute:lat_lon | 51.88338182 N 8.51011814 W |
| SAMN27654482 | location_region | Cork | R1 | 0.85 | biosample.attribute:geo_loc_name | Ireland: Cork |
| SAMN27654482 | longitude | -8.5101 | R1 | 0.90 | biosample.attribute:lat_lon | 51.88338182 N 8.51011814 W |
| SAMN27654482 | medication | other_medication | R2 | 0.85 | paper.supp.metadata_vlp_V2.csv[!X5_ASA] | NG-17954_320_T1_lib298604: X5_ASA=Asacolon |
| SAMN27654482 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN27654482 | smoking_status | former | R2 | 0.85 | paper.supp.metadata_vlp_V2.csv[!Smoking_Status] | NG-17954_320_T1_lib298604: Smoking_Status=Ex_smoker |
| SAMN27654482 | subject_id | 320 | R1 | 0.70 | sample.name_rule:title | X320_T1 |
| SAMN27654482 | timepoint_label | T1 | R1 | 0.70 | sample.name_rule:title | X320_T1 |
Sequencing
233 runs over 233 samples · mean 0.71 Gbp per run (median 0.59 Gbp, total 165.43 Gbp; 233 runs with a base count) · layout PAIRED 233 · platform ILLUMINA 233 · models Illumina HiSeq 2500 (233) · 81% of runs with a Sandpiper profile · first public 2022-04-21
Authors (16)
Stockdale SR first · Shkoporov AN · Khokhlova EV · Daly KM · McDonnell SA · O' Regan O · Nolan JA · Sutton TDS · Clooney AG · Ryan FJ · Sheehan D · Lavelle A · Draper LA · Shanahan F · Ross RP · Hill C last
Downloads
PRJNA828396.csv.gz (9.0 KB) · parquet (83.2 KB) — all 233 samples, every field with route and confidence · PRJNA828396_determinations.csv.gz (31.5 KB) — 3,335 evidence rows