Stool metagenomics in preterm infants with LOS, Germany
614 stool samples from preterm infants (some with late-onset sepsis, some probiotic-supplemented) in Germany, collected longitudinally within the first month after birth. machine-written summary
614 samples · 614 runs · DE · Infant / toddler · 2022 · 0.57 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,842 sample values (country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
intervention — arms not resolved
Probiotic (live microorganisms; single strain or mixture) design observational_with_procedure · population preterm_nicu · Probiotic supplementation in preterm infants
“38 infants with probiotic supplementation” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
207 of 235 people sampled more than once (586 samples; median 3, up to 4 per person). Schedule stated by the source: “Stool samples collected longitudinally within the first month after birth across multiple timepoints (TP labels, e.g. TP01-TP23+).” (time origin: birth); stated follow-up 30 d.
Genera, mean relative abundance over 458 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 | 614 | 100% | 614 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 614 | 100% | 614 | |||
| timepoint_label | 614 | 100% | 614 |
Archive description
We studied stool samples from 70 preterm infants with LOS (38 infants with probiotic supplementation) and 164 unaffected controls (70 with probiotic supplementation). Administration of probiotics led to an early colonization of the probiotic bacteria in the preterm infant gut in line with an increase of fecal concentrations of most metabolites, which were found to increase with higher gestational age and days of life.
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 · “Longitudinal stool metagenomics from preterm”
- body site study.description · “We studied stool samples from 70”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “metagenomics from preterm infants within the first”
- life stage study.title · “stool metagenomics from preterm infants within the”
- life stage study.description · “samples from 70 preterm infants with LOS”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA110138387 | country | DE | R1 | 0.90 | biosample_attr | Germany |
| SAMEA110138387 | subject_id | LOS001 | R1 | 0.70 | sample.name_rule:title | LOS001_TP08 |
| SAMEA110138387 | timepoint_label | TP08 | R1 | 0.70 | sample.title | LOS001_TP08 |
Sequencing
614 runs over 614 samples · mean 1.80 Gbp per run (median 0.57 Gbp, total 1,107.72 Gbp; 614 runs with a base count) · layout PAIRED 614 · platform ILLUMINA 614 · models Illumina NovaSeq 6000 (614) · 75% of runs with a Sandpiper profile · first public 2022-06-22 – 2022-06-24
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJEB52938.csv.gz (17.0 KB) · parquet (94.4 KB) — all 614 samples, every field with route and confidence · PRJEB52938_determinations.csv.gz (15.3 KB) — 1,842 evidence rows