Faecal plasmidome in IBD vs healthy controls, Cork, Ireland
87 faecal samples from adults in Cork, Ireland, comparing healthy controls (48) with ulcerative colitis (20) and Crohn's disease (19) patients in a case-control design, with FMT as an intervention of interest. machine-written summary
87 samples · 87 runs · IE · Adult · 2022 · 1.86 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,017 sample values (age, bmi, collection date, country, health condition, health condition detail, latitude, location region) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 design observational_with_procedure · population ibd_unspecified · Faecal microbiota transplant cohorts compared for plasmidome diversity restoration
“faecal microbiota transplants can restore plasmidome diversity” — abstract:35654877 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 81 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 | 87 | 100% | ||||
| country | 87 | 100% | 87 | |||
| health_condition | 87 | 100% | 87 | |||
| subject_id | 87 | 100% | 87 | |||
| collection_date | 87 | 100% | 87 | |||
| detailed_location | 87 | 100% | ||||
| health_condition_detail | 87 | 100% | 87 | |||
| latitude | 87 | 100% | 87 | |||
| location_region | 87 | 100% | 87 | |||
| longitude | 87 | 100% | 87 | |||
| timepoint_label | 86 | 99% | 86 | |||
| sex | 80 | 92% | 80 | |||
| age_at_collection_days | 79 | 91% | 79 | |||
| bmi | 76 | 87% | 76 |
- Metagenomic assembled plasmids of the human microbiome vary across disease cohorts. 2022 PMID 35654877 PMC9163076 unsure
Archive description
Plasmids in the human microbiome are overlooked and should be integrated into investigations regarding their role in promoting health or disease. In order to investigate the human gut plasmidome, a database of human-associated metagenome assembled plasmid (MAP) database was constructed using whole genome sequencing data.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site study.title · “faecal microbiomes from healthy controls and patients”
- life stage sample.attr.host_age · “23 (n=72/87)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN26521050 | age_at_collection_days | 15696.8 | R1 | 0.85 | sample.attr.host_age | 43 |
| SAMN26521050 | bmi | 33.13 | R1 | 0.90 | sample.attr.host_body_mass_index | 33.13134 |
| SAMN26521050 | collection_date | 2019-10-16 | R1 | 0.90 | biosample.attribute:collection_date | 2019-10-16 |
| SAMN26521050 | country | IE | R1 | 0.90 | sample.attr.geo_loc_name | Ireland: Cork |
| SAMN26521050 | health_condition | ulcerative_colitis | R1 | 0.85 | biosample.attribute:gastrointest_disord | gastrointest_disord: UC |
| SAMN26521050 | health_condition_detail | UC | R1 | 0.90 | sample.attr.gastrointest_disord | UC |
| SAMN26521050 | latitude | 51.8985 | R1 | 0.90 | biosample.attribute:lat_lon | 51.8985 N 8.4756 W |
| SAMN26521050 | location_region | Cork | R1 | 0.85 | biosample.attribute:geo_loc_name | Ireland: Cork |
| SAMN26521050 | longitude | -8.4756 | R1 | 0.90 | biosample.attribute:lat_lon | 51.8985 N 8.4756 W |
| SAMN26521050 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN26521050 | subject_id | Subject_320 | R1 | 0.85 | biosample.attribute:env_local_scale | env_local_scale: Subject_320 |
| SAMN26521050 | timepoint_label | T1 | R1 | 0.70 | sample.name_rule:library_names | X320_T1 |
Sequencing
87 runs over 87 samples · mean 1.71 Gbp per run (median 1.86 Gbp, total 148.35 Gbp; 87 runs with a base count) · layout PAIRED 87 · platform ILLUMINA 87 · models Illumina HiSeq 2500 (87) · 93% of runs with a Sandpiper profile · first public 2022-10-24
Authors (14)
Stockdale SR first · Harrington RS · Shkoporov AN · Khokhlova EV · Daly KM · McDonnell SA · O'Reagan O · Nolan JA · Sheehan D · Lavelle A · Draper LA · Shanahan F · Ross RP · Hill C last
Downloads
PRJNA813736.csv.gz (3.8 KB) · parquet (75.8 KB) — all 87 samples, every field with route and confidence · PRJNA813736_determinations.csv.gz (9.6 KB) — 1,017 evidence rows