Fecal metagenomes in Crohn's disease vs healthy adults, NY
46 fecal samples from adults in New York, NY, including Crohn's disease patients with active ileal disease and age-matched healthy controls, in a case-control study of adherent-invasive E. coli and intestinal inflammation. machine-written summary
46 samples · 46 runs · US · Adult · 2021 · 1.64 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 455 sample values (age, collection date, country, health condition, health condition detail, latitude, location locality, location region) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10352622, PMC8049981 |
| ○ 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 43 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 | 46 | 100% | ||||
| country | 46 | 100% | 46 | |||
| health_condition | 22 | 48% | 22 | |||
| subject_id | 46 | 100% | 46 | |||
| age_at_collection_days | 46 | 100% | 46 | |||
| detailed_location | 46 | 100% | ||||
| latitude | 46 | 100% | 46 | |||
| location_locality | 46 | 100% | 46 | |||
| location_region | 46 | 100% | 46 | |||
| longitude | 46 | 100% | 46 | |||
| sex | 46 | 100% | 46 | |||
| collection_date | 43 | 93% | 43 | |||
| health_condition_detail | 22 | 48% | 22 |
- Adherent-invasive E. coli metabolism of propanediol in Crohn's disease regulates phagocytes to drive intestinal inflammation. 2021 PMID 33539767 PMC8049981 own_data
- SnakeWRAP: a Snakemake workflow to facilitate automated processing of metagenomic data through the metaWRAP pipeline. 2022 PMID 37469625 PMC10352622 unsure
Archive description
Fecal samples were collected from 22 healthy and 24 Crohn's disease patients for metagenomic shotgun sequencing. Inclusion criteria for Crohn's disease included active endoscopic ileal disease consistent with a clinical diagnosis of ileal or ileo-colonic Crohn's disease and a Harvery-Bradshaw score of >4 indicative of active disease. Healthy controls were age-matched controls without evidence of intestinal inflammation or a history of CD.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_adult_only”
- body site study.title · “and Crohn's disease fecal samples”
- body site study.description · “Fecal samples were collected”
- life stage external_curation.infant_catalog · “infant triage reason_code age_adult_only”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN17149459 | age_at_collection_days | 10234.0 | R1 | 0.85 | sample.attr.host_age | 28 |
| SAMN17149459 | collection_date | 2015-09-14 | R1 | 0.90 | biosample.attribute:collection_date | 2015-09-14 |
| SAMN17149459 | country | US | R1 | 0.90 | sample.attr.geo_loc_name | USA: New York, NY |
| SAMN17149459 | health_condition | crohns_disease | R1 | 0.90 | biosample_attr | Crohn's |
| SAMN17149459 | health_condition_detail | Crohn's | R1 | 0.90 | sample.attr.gastrointest_disord | Crohn's |
| SAMN17149459 | latitude | 40.7100 | R1 | 0.90 | biosample.attribute:lat_lon | 40.71 N 74.0 W |
| SAMN17149459 | location_locality | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: New York, NY |
| SAMN17149459 | location_region | New York | R1 | 0.85 | biosample.attribute:geo_loc_name | USA: New York, NY |
| SAMN17149459 | longitude | -74.0000 | R1 | 0.90 | biosample.attribute:lat_lon | 40.71 N 74.0 W |
| SAMN17149459 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN17149459 | subject_id | RI068 | R1 | 0.85 | sample.attr.host_subject_id | RI068 |
Sequencing
46 runs over 46 samples · mean 1.60 Gbp per run (median 1.64 Gbp, total 73.76 Gbp; 46 runs with a base count) · layout PAIRED 46 · platform ILLUMINA 46 · models Illumina HiSeq 2500 (46) · 93% of runs with a Sandpiper profile · first public 2021-01-30
Authors (31)
Viladomiu M first · Metz ML · Lima SF · Jin WB · Chou L · JRI Live Cell Bank · Guo CJ · Diehl GE · Simpson KW · Scherl EJ · Longman RS last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C last · Krapohl J first · Pickett BE last · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · van Sinderen D
Downloads
PRJNA687536.csv.gz (2.5 KB) · parquet (72.8 KB) — all 46 samples, every field with route and confidence · PRJNA687536_determinations.csv.gz (4.1 KB) — 455 evidence rows