Preterm infant gut and gastric microbiome, Jerusalem, Israel
272 stool and gastric residual samples from premature infants in Jerusalem, Israel, collected as part of a longitudinal cohort study. machine-written summary
272 samples · 272 runs · IL · Infant / toddler · 2025 · 0.67 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,080 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 812 sample values (location locality, location site, probiotic exposure) · PMC12594796 |
| ○ 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 · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
39 of 39 people sampled more than once (268 samples; median 5, up to 33 per person).
Genera, mean relative abundance over 42 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 | 272 | 100% | 272 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 268 | 99% | 268 | |||
| collection_date | 272 | 100% | 272 | |||
| detailed_location | 272 | 100% | ||||
| location_locality | 272 | 100% | 272 | |||
| location_site | 272 | 100% | 272 | |||
| probiotic_exposure | 268 | 99% | 268 | |||
| timepoint_label | 268 | 99% | 268 |
- Development of the preterm infant gut and gastric residuals microbiome. PMID 41203618 PMC12594796 curated
Archive description
Sequencing data of stool and gastric residuals from 39 premature infants
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and neonate by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “the preterm infant gut and gastric residuals”
- body site study.description · “Sequencing data of stool and gastric residuals”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “of the preterm infant gut and gastric”
- life stage study.title · “Development of the preterm infant gut and”
- life stage study.description · “residuals from 39 premature infants”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN50854044 | collection_date | 2020 | R1 | 0.85 | biosample.attribute:collection_date | 2020 |
| SAMN50854044 | country | IL | R1 | 0.90 | biosample_attr | Israel: Jerusalem |
| SAMN50854044 | location_locality | Jerusalem | R3 | 0.70 | paper.fulltext.methods | hospitalized in Hadassah Ein Karem Medical Center, Jerusalem |
| SAMN50854044 | location_site | Hadassah Ein Karem Medical Center | R3 | 0.70 | paper.fulltext.methods | hospitalized in Hadassah Ein Karem Medical Center, Jerusalem |
| SAMN50854044 | probiotic_exposure | no | R3 | 0.40 | paper.fulltext.results | probiotics are not administered in this NICU |
| SAMN50854044 | subject_id | 002 | R1 | 0.70 | sample.name_rule:source_material_id | Res_002_228_noHost.clipped.fastq.gz |
| SAMN50854044 | timepoint_label | 228 | R1 | 0.70 | sample.name_rule:source_material_id | Res_002_228_noHost.clipped.fastq.gz |
Sequencing
272 runs over 272 samples · mean 0.65 Gbp per run (median 0.67 Gbp, total 177.09 Gbp; 272 runs with a base count) · layout SINGLE 272 · platform ILLUMINA 272 · models NextSeq 500 (272) · 15% of runs with a Sandpiper profile · first public 2025-10-23
Authors (8)
Moriel N first · Jones L · Harpenas E · Rakow N · Shmorak S · Eventov Friedman S · Ofek Shlomai N · Yassour M last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA1312123.csv.gz (8.6 KB) · parquet (81.4 KB) — all 272 samples, every field with route and confidence · PRJNA1312123_determinations.csv.gz (13.1 KB) — 1,892 evidence rows