Colonic mucosal virome-bacteriome in IBD adolescents, Ottawa
9 samples from adolescents with inflammatory bowel disease in Ottawa, Canada, studied using a case-control design combining metagenomics, metaviromics, and metatranscriptomics of the colonic mucosal-luminal interface. machine-written summary
9 samples · 18 runs · CA · Adolescent · 2023 · 69.09 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 45 sample values (age, country, location locality, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 18 sample values (health condition, health condition detail) · PMC9980608 |
| ○ 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 |
Genera, mean relative abundance over 3 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 | 9 | 100% | ||||
| country | 9 | 100% | 9 | |||
| health_condition | 9 | 100% | 9 | |||
| subject_id | 9 | 100% | 9 | |||
| age_at_collection_days | 9 | 100% | 9 | |||
| detailed_location | 9 | 100% | ||||
| health_condition_detail | 9 | 100% | 9 | |||
| location_locality | 9 | 100% | 9 | |||
| sex | 9 | 100% | 9 |
- Multiomic spatial analysis reveals a distinct mucosa-associated virome. 2023 PMID 36823020 PMC9980608 own_data
Archive description
The human gut virome has been increasingly explored in recent years, revealing the presence of individualized, temporally stable viral communities. However, nearly all virome sequencing efforts rely solely on fecal sampling and few studies leverage multiomic approaches to study phage-host relationships at the community level. Here, we combine metagenomics, metaviromics, and meta-transcriptomics to study virome-bacteriome interactions at the colonic mucosal-luminal interface. Systems biology approaches such as those presented in this report will enhance our understanding of the human gut virome and its interactions with our microbiome and our health, especially as continue to uncover viral communities across our complex host biogeography
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids mixed assays of adolescent by sonnet_x2 with confidence 0.70. Assay mixed.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
- body site sample.attr.isolation_source · “mli aspirate (n=6/9)”
- life stage sample.attr.age · “14.5 (n=9/9)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN26851544 | age_at_collection_days | 6320.0 | R1 | 0.85 | sample.attr.age | 17.3 |
| SAMN26851544 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada: Ottawa |
| SAMN26851544 | health_condition | ibd_unspecified | R3 | 0.70 | paper.fulltext.abstract | cohort of three individuals with inflammatory bowel disease |
| SAMN26851544 | health_condition_detail | cohort of three individuals with inflammatory bowel disease | R3 | 0.70 | paper.fulltext.abstract | cohort of three individuals with inflammatory bowel disease |
| SAMN26851544 | location_locality | Ottawa | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada: Ottawa |
| SAMN26851544 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN26851544 | subject_id | F | R1 | 0.70 | sample.name_rule:alias | subjectF_pc |
Sequencing
18 runs over 9 samples · mean 39.53 Gbp per run (median 44.54 Gbp, total 711.61 Gbp; 18 runs with a base count) · layout PAIRED 18 · platform ILLUMINA 18 · models Illumina NovaSeq 6000 (18) · 94% of runs with a Sandpiper profile · first public 2023-02-27
Downloads
PRJNA818303.csv.gz (1.2 KB) · parquet (70.1 KB) — all 9 samples, every field with route and confidence · PRJNA818303_determinations.csv.gz (1.1 KB) — 63 evidence rows