Long. Infant Gut Metagenomes in Israel, Healthy Cohort
80 stool metagenome samples from healthy infants and neonates in Israel, collected as part of a longitudinal cohort study on Bifidobacterium variability relative to maternal milk HMO composition. machine-written summary
80 samples · 80 runs · IL · Infant / toddler · 2023 · 0.69 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 320 sample values (age, collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10827747 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| ✓ External resources | 160 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
20 of 21 people sampled more than once (79 samples; median 3, up to 8 per person) · follow-up median 2 mo (max 9 mo) · median interval between samples 29 d (time from age at collection). Schedule stated by the source: “Matched breast milk and infant stool samples collected at multiple time points during the first year of life” (time origin: birth); stated follow-up 12 mo.
Each row is one person (20 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 10 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 | 80 | 100% | ||||
| country | 80 | 100% | 80 | |||
| health_condition | 80 | 100% | 80 | |||
| subject_id | 80 | 100% | 80 | |||
| age_at_collection_days | 80 | 100% | 80 | |||
| collection_date | 80 | 100% | 80 | |||
| health_condition_detail | 80 | 100% | 80 |
- Longitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition. PMID 38291346 PMC10827747 curated
- Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly. PMID 39242817 PMC11445081 curated
- Longitudinal Variability of Bifidobacterium Species in the Infant Gut is Independent of Maternal Milk HMO Composition curated
Archive description
Metagenomic shotgun sequencing from infant stool samples after filtered for host reads.
How this project entered the registry
Classified as human gut / stool / human milk shotgun DNA metagenome of infant / toddler and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “in the Infant Gut is Independent of”
- body site study.description · “sequencing from infant stool samples after filtered”
- body site study.title · “Independent of Maternal Milk HMO Composition”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Species in the Infant Gut is Independent”
- life stage study.title · “is Independent of Maternal Milk HMO Composition”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN36427021 | age_at_collection_days | 73 | R1 | 0.90 | biosample_attr | 10.4285714285714 |
| SAMN36427021 | collection_date | 2021 | R1 | 0.85 | biosample.attribute:collection_date | 2021 |
| SAMN36427021 | country | IL | R1 | 0.90 | biosample_attr | Israel |
| SAMN36427021 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN36427021 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN36427021 | subject_id | inf01 | R1 | 0.85 | biosample.attribute:Infant | inf01 |
Sequencing
80 runs over 80 samples · mean 0.71 Gbp per run (median 0.69 Gbp, total 56.53 Gbp; 80 runs with a base count) · layout SINGLE 80 · platform ILLUMINA 80 · models NextSeq 500 (80) · 12% of runs with a Sandpiper profile · first public 2023-07-17
Authors (18)
Ennis D first · Shmorak S · Jantscher-Krenn E · Yassour M last · Shao Y first · Garcia-Mauriño C · Clare S · Dawson NJR · Mu A · Adoum A · Harcourt K · Liu J · Browne HP · Stares MD · Rodger A · Brocklehurst P · Field N · Lawley TD last
Downloads
PRJNA994433.csv.gz (3.3 KB) · parquet (73.9 KB) — all 80 samples, every field with route and confidence · PRJNA994433_determinations.csv.gz (4.3 KB) — 480 evidence rows