Bile acids and inflammation in UC ileal pouches vs FAP
16 stool samples from colectomy patients with ileal pouches, comparing ulcerative colitis to familial adenomatous polyposis controls; case-control design examining secondary bile acid-producing bacteria and intestinal inflammation. machine-written summary
16 samples · 16 runs · Adult · 2020 · 2.80 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 48 sample values (age, sex, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8172352 |
| – 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
Surgical procedure studied before/after (bariatric surgery design observational_with_procedure · population ulcerative_colitis · Stool sampling after colectomy/ileal pouch surgery in UC vs FAP
“colectomy-treated patients with ulcerative colitis” — abstract:32101703 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 14 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 | 16 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 16 | 100% | 16 | |||
| age_at_collection_days | 16 | 100% | 16 | |||
| sex | 16 | 100% | 16 |
- Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation. 2020 PMID 32101703 PMC8172352 unsure
- Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease. 2021 PMID 33653942 PMC8546988 unsure
Archive description
to investigate the abundance of bacteria associated with primary bile acid conversion in Ulcerative colitis pouch
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host run.scientific_name · “human gut metagenome”
- body site run.scientific_name · “human gut metagenome”
- life stage sample.attr.age · “20 (n=13/16)”
- life stage sample.attr.age · “70 (n=3/16)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN13810505 | age_at_collection_days | 25567.5 | R1 | 0.70 | sample.attr.age | 70 |
| SAMN13810505 | sex | female | R1 | 0.90 | sample.attr.sex | female |
| SAMN13810505 | subject_id | Subject9 | R1 | 0.70 | sample.name_rule:alias | Subject9.control |
Sequencing
16 runs over 16 samples · mean 2.68 Gbp per run (median 2.80 Gbp, total 42.90 Gbp; 16 runs with a base count) · layout PAIRED 16 · platform ILLUMINA 16 · models Illumina HiSeq 2500 (16) · 88% of runs with a Sandpiper profile · first public 2020-01-11
Authors (24)
Sinha SR first · Haileselassie Y · Nguyen LP · Tropini C · Wang M · Becker LS · Sim D · Jarr K · Spear ET · Singh G · Namkoong H · Bittinger K · Fischbach MA · Sonnenburg JL · Habtezion A last · Dubinsky V first · Reshef L · Rabinowitz K · Yadgar K · Godny L · Zonensain K · Wasserberg N · Dotan I · Gophna U last
Downloads
PRJNA600269.csv.gz (1.4 KB) · parquet (69.5 KB) — all 16 samples, every field with route and confidence · PRJNA600269_determinations.csv.gz (1018 B) — 48 evidence rows