Pediatric IBD gut microbiome case-control cohort, Jerusalem
134 fecal samples from pediatric IBD patients and controls enrolled at Shaare Zedek Medical Center, Jerusalem, Israel, analyzed by shotgun metagenomics and methylation-based human DNA profiling in a case-control design. machine-written summary
134 samples · 134 runs · IL · Child · 2025 · 0.94 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 938 sample values (collection date, country, health condition, health condition detail, location locality, subject id, timepoint) |
| ✓ Abstract / description | 134 sample values (location site) |
| ○ Full text | read; no usable statement or table · PMC13045140 |
| ✓ Supplementary tables | 134 sample values (age) |
| – 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 |
longitudinal
25 of 101 people sampled more than once (58 samples; median 2, up to 3 per person) · follow-up median 12 mo (max 3.0 y) · median interval between samples 12 mo (time from age at collection).
Each row is one person (15 shown of 25); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 128 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 | 134 | 100% | ||||
| country | 134 | 100% | 134 | |||
| health_condition | 134 | 100% | 134 | |||
| subject_id | 134 | 100% | 134 | |||
| age_at_collection_days | 134 | 100% | 134 | |||
| collection_date | 134 | 100% | 134 | |||
| detailed_location | 134 | 100% | ||||
| health_condition_detail | 134 | 100% | 134 | |||
| location_locality | 134 | 100% | 134 | |||
| location_site | 134 | 100% | 134 | |||
| timepoint_label | 134 | 100% | 134 |
- Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum. 2026 PMID 41742321 PMC13045140 own_data
Archive description
This cohort of pediatric IBD patients was enrolled at Shaare Zedek Medical Center, Jerusalem, Israel. Majority of subjects were sampled once, few patients were sampled two or three times.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage reason_code age_unknown_no_evidence”
- body site study.title · “Gut microbiome in pediatric”
- life stage study.title · “Gut microbiome in pediatric IBD patients”
- life stage study.description · “This cohort of pediatric IBD patients was”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN48635712 | age_at_collection_days | 5479 | R2 | 0.85 | paper.supp.40168_2026_2344_MOESM2_ESM.xlsx[Supplementary Table 5 pediatric!age_visit] | 15 |
| SAMN48635712 | collection_date | 2022 | R1 | 0.90 | biosample.attribute:collection_date | 2022 |
| SAMN48635712 | country | IL | R1 | 0.90 | sample.attr.geo_loc_name | Israel: Jerusalem |
| SAMN48635712 | health_condition | crohns_disease | R1 | 0.70 | sample.name_rule:title | CD_366_1 |
| SAMN48635712 | health_condition_detail | CD | R1 | 0.70 | sample.name_rule:title | CD_366_1 |
| SAMN48635712 | location_locality | Jerusalem | R1 | 0.85 | biosample.attribute:geo_loc_name | Israel: Jerusalem |
| SAMN48635712 | location_site | Shaare Zedek Medical Center | R4 | 0.45 | ena.study_description | enrolled at Shaare Zedek Medical Center, Jerusalem, Israel |
| SAMN48635712 | subject_id | 366 | R1 | 0.70 | sample.name_rule:title | CD_366_1 |
| SAMN48635712 | timepoint_label | 1 | R1 | 0.70 | sample.name_rule:title | CD_366_1 |
Sequencing
134 runs over 134 samples · mean 0.98 Gbp per run (median 0.94 Gbp, total 131.40 Gbp; 134 runs with a base count) · layout SINGLE 134 · platform ILLUMINA 134 · models Illumina MiSeq (134) · 96% of runs with a Sandpiper profile · first public 2025-06-23
Authors (13)
Mazzoni C first · Ochana BL · Orlanski-Meyer E · Ben Ya'acov A · Focht G · Harpenas E · Shmorak S · Ledder O · Lev-Tzion R · Shemer R · Shteyer E · Dor Y · Yassour M last
Downloads
PRJNA1265906.csv.gz (4.9 KB) · parquet (76.3 KB) — all 134 samples, every field with route and confidence · PRJNA1265906_determinations.csv.gz (11.3 KB) — 1,206 evidence rows