VLP transfer and DSS-colitis in HMA mice, Montreal
72 virus-like-particle shotgun metagenome samples from Montreal, Canada, studying fecal VLP transfer (FMT/phage therapy) from ulcerative colitis and healthy donors into human microbiota-associated mice with DSS-induced colitis; an intervention study. machine-written summary
9 samples · 72 runs · CA · Age unknown · 2021 · 90.9 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 50 sample values (collection date, country, health condition, latitude, location locality, longitude) |
| ✓ Abstract / description | 9 sample values (health condition detail) |
| ✓ Full text | 9 sample values (antibiotic exposure) · PMC9264660 |
| ○ 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
Faecal microbiota transplantation Bacteriophage therapy design non_randomized_controlled · population ulcerative_colitis · Fecal VLP (phage) transplant from UC patients or healthy controls into HMA mice, +/- DSS colitis
“fecal virus-like particles (VLPs) isolated from UC patients and healthy controls” — abstract:35799219 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
Schedule stated by the source: “Repeated fecal sampling of mice over VLP gavage, DSS colitis, and washout periods (multiple dates per mouse cage/animal ID)”.
Genera, mean relative abundance over 4 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 | 5 | 56% | 5 | |||
| subject_id | 0 | 0% | ||||
| antibiotic_exposure | 9 | 100% | 9 | |||
| collection_date | 9 | 100% | 9 | |||
| detailed_location | 9 | 100% | ||||
| health_condition_detail | 9 | 100% | 9 | |||
| latitude | 9 | 100% | 9 | |||
| location_locality | 9 | 100% | 9 | |||
| longitude | 9 | 100% | 9 |
- Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis. 2022 PMID 35799219 PMC9264660 own_data
Archive description
The impact of bacteriophages on DSS-colitis and microbiota composition - VLP shotgun
How this project entered the registry
Classified as human and non-human (mixed) gut / stool shotgun DNA metagenome of age unknown by opus_adjudicated with confidence 0.50. Assay shotgun_dna.
- host run.scientific_name · “mouse gut metagenome”
- host run.scientific_name · “human gut metagenome”
- body site sample.attr.env_medium · “Fecal sample (n=72/72)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN19340483 | antibiotic_exposure | no | R3 | 0.70 | paper.fulltext.methods | had not taken antibiotics in the 3 months prior |
| SAMN19340483 | collection_date | 2019 | R1 | 0.90 | biosample.attribute:collection_date | 2019 |
| SAMN19340483 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada: Montreal |
| SAMN19340487 | health_condition | ulcerative_colitis | R1 | 0.90 | biosample_attr | UC stock |
| SAMN19340483 | health_condition_detail | mixed_case_control: VLPs isolated from ulcerative colitis patients vs healthy controls | R4 | 0.50 | paper.abstract | UC patients and healthy controls |
| SAMN19340483 | latitude | 45.5000 | R1 | 0.90 | biosample.attribute:lat_lon | 45.5 N 73.58 W |
| SAMN19340483 | location_locality | Montreal | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada: Montreal |
| SAMN19340483 | longitude | -73.5800 | R1 | 0.90 | biosample.attribute:lat_lon | 45.5 N 73.58 W |
Sequencing
72 runs over 9 samples · mean 0.15 Gbp per run (median 90.9 Mbp, total 10.87 Gbp; 72 runs with a base count) · layout PAIRED 72 · platform ILLUMINA 72 · models Illumina MiSeq (72) · 17% of runs with a Sandpiper profile · first public 2021-07-22
Authors (7)
Sinha A first · Li Y · Mirzaei MK · Shamash M · Samadfam R · King IL · Maurice CF last
Downloads
PRJNA732769.csv.gz (1.1 KB) · parquet (70.4 KB) — all 9 samples, every field with route and confidence · PRJNA732769_determinations.csv.gz (1.3 KB) — 68 evidence rows