Gut microbiome in pouch, IBD, and healthy subjects, Israel
118 fecal metagenome samples from adults and elderly individuals in Tel-Aviv, Israel, mostly with unspecified IBD plus some colorectal adenoma, studying microbial dysbiosis in pouchitis versus other conditions in a case-control design. machine-written summary
118 samples · 118 runs · IL · Adult · 2021 · 1.18 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,155 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 · PMC8546988 |
| ✓ Supplementary tables | 168 sample values (antibiotic exposure, subject id) |
| – 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 |
health condition: two sequence archives disagree for 38 samples (e.g. ibd_unspecified vs healthy_control) — withheld.
The sources disagree on 38 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (38)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN15103517 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103522 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103526 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103530 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103531 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103534 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103546 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103547 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103548 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103549 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103550 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103551 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103553 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103554 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103555 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103556 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103557 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103558 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103559 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103560 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103561 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103562 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103564 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103565 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103566 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103567 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103568 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103571 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103572 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103574 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103575 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103576 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103579 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103603 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103606 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103607 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103608 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
| SAMN15103609 | health condition | ibd_unspecified (sequence archive) | healthy_control (sequence archive) | withheld: neither value published |
longitudinal
21 of 53 people sampled more than once (72 samples; median 3, up to 6 per person) · follow-up median 2.0 y (max 4.2 y) · median interval between samples 8 mo (time from age at collection).
Each row is one person (21 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 88 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 | 117 | 99% | ||||
| country | 118 | 100% | 118 | |||
| health_condition | 80 | 68% | 80 | |||
| subject_id | 104 | 88% | 20 | 84 | ||
| detailed_location | 118 | 100% | ||||
| health_condition_detail | 118 | 100% | 118 | |||
| latitude | 118 | 100% | 118 | |||
| location_locality | 118 | 100% | 118 | |||
| location_region | 118 | 100% | 118 | |||
| longitude | 118 | 100% | 118 | |||
| age_at_collection_days | 117 | 99% | 117 | |||
| sex | 117 | 99% | 117 | |||
| collection_date | 113 | 96% | 113 | |||
| antibiotic_exposure | 84 | 71% | 84 |
- 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
Pouchitis develops in former patients with UC after total proctocolectomy and ileal pouch anal anastomosis ("pouch surgery"), and is characterized by inflammation of the previously normal small intestine comprising the pouch. The extent to which microbial dysbiosis in pouchitis resembles that of CD or UC has not been investigated in depth and the pathogenesis of pouchitis largely remains unknown.</p><p>Here we analyzed the shotgun metagenomes of patients with a pouch, IBD and healthy subjects with the following aims: 1) To identify microbial signatures (species and functional genes) that might be common to disease phenotypes and thus to place patients with a pouch in the context of "primary" IBD. 2) To examine several key bacterial functions that may underlie the pathogenesis of pouchitis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of adult and elderly by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- body site run.scientific_name · “feces metagenome”
- life stage sample.attr.host_age · “37 (n=96/118)”
- life stage sample.attr.host_age · “68.75 (n=15/118)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN15103515 | age_at_collection_days | 11919.0 | R1 | 0.85 | sample.attr.host_age | 32.6666666666667 |
| SAMN15103515 | antibiotic_exposure | no | R2 | 0.75 | paper.supp.msystems.00984-20-sd001.xlsx[Data Set S1-sheet1 - Metadata for Pouch patients cohort (discovery)!Time_elapsed_since_last_antibiotic_treatment] | L10: Time_elapsed_since_last_antibiotic_treatment=over_6_months |
| SAMN15103515 | collection_date | 2013-10-28 | R1 | 0.90 | biosample.attribute:collection_date | 2013-10-28 |
| SAMN15103515 | country | IL | R1 | 0.90 | sample.attr.geo_loc_name | Israel: Tel-Aviv |
| SAMN15103515 | health_condition | ibd_unspecified | R1 | 0.85 | biosample_attr | Pouchitis |
| SAMN15103515 | health_condition_detail | Chronic | R1 | 0.90 | sample.attr.host_phenotype | Chronic |
| SAMN15103515 | latitude | 32.0806 | R1 | 0.90 | biosample.attribute:lat_lon | 32.0806 N 34.7898 E |
| SAMN15103515 | location_locality | Tel Aviv | R1 | 0.75 | biosample.attribute:geo_loc_name | Israel: Tel-Aviv |
| SAMN15103515 | location_region | Tel Aviv | R1 | 0.60 | biosample.attribute:lat_lon | 32.0806 N 34.7898 E |
| SAMN15103515 | longitude | 34.7898 | R1 | 0.90 | biosample.attribute:lat_lon | 32.0806 N 34.7898 E |
| SAMN15103515 | sex | male | R1 | 0.90 | sample.attr.host_sex | male |
| SAMN18024157 | subject_id | np3 | R1 | 0.85 | sample.attr.host_subject_id | np3 |
| SAMN15103515 | subject_id | po18 | R2 | 0.75 | paper.supp.msystems.00984-20-sd001.xlsx[Data Set S1-sheet1 - Metadata for Pouch patients cohort (discovery)!Patient_ID] | L10: Patient_ID=po18 |
Sequencing
118 runs over 118 samples · mean 1.66 Gbp per run (median 1.18 Gbp, total 196.38 Gbp; 118 runs with a base count) · layout PAIRED 118 · platform ILLUMINA 118 · models NextSeq 500 (118) · 75% of runs with a Sandpiper profile · first public 2021-02-01 – 2021-03-01
Authors (9)
Dubinsky V first · Reshef L · Rabinowitz K · Yadgar K · Godny L · Zonensain K · Wasserberg N · Dotan I · Gophna U last
Downloads
PRJNA637365.csv.gz (5.5 KB) · parquet (77.7 KB) — all 118 samples, every field with route and confidence · PRJNA637365_determinations.csv.gz (12.1 KB) — 1,323 evidence rows