Fiber intervention in IBD gut microbiome, Edmonton
52 gut metagenome samples from an intervention study in Edmonton, Canada, examining prebiotic/fiber supplementation in relation to inflammatory bowel disease and fiber-fermenting microbiota. machine-written summary
52 samples · 52 runs · CA · Age unknown · 2021 · 13.74 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 415 sample values (country, health condition, health condition detail, latitude, location locality, location region, longitude, subject id) |
| ○ 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
Prebiotic / dietary fibre supplement design randomized_controlled_trial · population ibd_unspecified · β-fructan (oligofructose) fiber supplementation in IBD RCT
“adult IBD randomized controlled trial examining β-fructan supplementation” — abstract:36183751 (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
6 of 45 people sampled more than once (12 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 48 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 | 0 | 0% | ||||
| country | 52 | 100% | 52 | |||
| health_condition | 52 | 100% | 52 | |||
| subject_id | 51 | 98% | 51 | |||
| detailed_location | 52 | 100% | ||||
| health_condition_detail | 52 | 100% | 52 | |||
| latitude | 52 | 100% | 52 | |||
| location_locality | 52 | 100% | 52 | |||
| location_region | 52 | 100% | 52 | |||
| longitude | 52 | 100% | 52 |
- Unfermented ß-fructan Fibers Fuel Inflammation in Select Inflammatory Bowel Disease Patients. 2023 PMID 36183751 own_data
Archive description
The putative loss of fiber fermenting-microbes populating the IBD gut could lead to dietary fibers not being efficiently broken down into their beneficial biproducts (e.g., short chain fatty acids SCFA), resulting in binding of intact fibers to pro-inflammatory host cell receptors.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of age unknown by sonnet_x2 with confidence 0.70. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “human gut metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17258198 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada:Edmonton |
| SAMN17258198 | health_condition | healthy_control | R1 | 0.85 | biosample.attribute:description | nonIBD_sample |
| SAMN17258198 | health_condition_detail | nonIBD_sample | R1 | 0.85 | biosample.attribute:description | nonIBD_sample |
| SAMN17258198 | latitude | 53.5461 | R1 | 0.90 | biosample.attribute:lat_lon | 53.5461 N 113.4938 W |
| SAMN17258198 | location_locality | Edmonton | R1 | 0.85 | biosample.attribute:geo_loc_name | Canada:Edmonton |
| SAMN17258198 | location_region | Alberta | R1 | 0.60 | biosample.attribute:lat_lon | 53.5461 N 113.4938 W |
| SAMN17258198 | longitude | -113.4938 | R1 | 0.90 | biosample.attribute:lat_lon | 53.5461 N 113.4938 W |
| SAMN17258198 | subject_id | 51 | R1 | 0.70 | sample.name_rule:library_names | pnt51 |
Sequencing
52 runs over 52 samples · mean 13.72 Gbp per run (median 13.74 Gbp, total 713.59 Gbp; 52 runs with a base count) · layout PAIRED 52 · platform ILLUMINA 52 · models Illumina NovaSeq 6000 (52) · 92% of runs with a Sandpiper profile · first public 2021-12-24
Authors (33)
Armstrong HK first · Bording-Jorgensen M · Santer DM · Zhang Z · Valcheva R · Rieger AM · Sung-Ho Kim J · Dijk SI · Mahmood R · Ogungbola O · Jovel J · Moreau F · Gorman H · Dickner R · Jerasi J · Mander IK · Lafleur D · Cheng C · Petrova A · Jeanson TL · Mason A · Sergi CM · Levine A · Chadee K · Armstrong D · Rauscher S · Bernstein CN · Carroll MW · Huynh HQ · Walter J · Madsen KL · Dieleman LA · Wine E last
Downloads
PRJNA690735.csv.gz (2.3 KB) · parquet (71.7 KB) — all 52 samples, every field with route and confidence · PRJNA690735_determinations.csv.gz (3.6 KB) — 415 evidence rows