Gut microbiomes in premature neonates with bacteremia, Nashville
404 stool samples from premature neonates at VUMC, Nashville, TN, comparing cases with bacteremia to matched controls; case-control design. machine-written summary
404 samples · 404 runs · US · Infant / toddler · 2025 · 5.49 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,210 sample values (country, subject id, timepoint) |
| ✓ Abstract / description | 1,212 sample values (health condition, health condition detail, preterm status) |
| ○ Full text | read; no usable statement or table · PMC12316594 |
| ○ 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
78 of 80 people sampled more than once (401 samples; median 5, up to 9 per person). Schedule stated by the source: “weekly stool samples from birth until discharge or transfer; 5-8 samples per subject analyzed” (time origin: birth).
Genera, mean relative abundance over 389 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 | 404 | 100% | ||||
| country | 404 | 100% | 404 | |||
| health_condition | 404 | 100% | 404 | |||
| subject_id | 403 | 100% | 403 | |||
| health_condition_detail | 404 | 100% | 404 | |||
| preterm_status | 404 | 100% | 404 | |||
| timepoint_label | 403 | 100% | 403 |
- Associations between antibiotic exposure intensity, intestinal microbiome perturbations, and outcomes in premature neonates with bacteremia. 2025 PMID 40490486 PMC12316594 own_data
Archive description
There is growing evidence that microbiome dysbiosis among neonates is associated with serious complications, including necrotizing enterocolitis and sepsis. This study characterizes the intestinal microbiomes of premature neonates with bacteremia by performing whole metagenome sequencing and analysis on weekly stool samples collected from 40 cases and 39 matched controls.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of neonate and infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Intestinal microbiomes of premature”
- body site study.description · “study characterizes the intestinal microbiomes of premature”
- life stage study.title · “Intestinal microbiomes of premature neonates with bacteremia”
- life stage study.description · “microbiome dysbiosis among neonates is associated with”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40379555 | country | US | R1 | 0.90 | biosample_attr | USA: VUMC, Nashville, TN |
| SAMN40379555 | health_condition | preterm_nicu | R4 | 0.50 | paper.abstract | hospitalized preterm infants with birthweight ≤2000 g and postnatal age (PNA) ≤2 months |
| SAMN40379555 | health_condition_detail | hospitalized preterm infants with birthweight ≤2000 g and postnatal age (PNA) ≤2 months | R4 | 0.50 | paper.abstract | hospitalized preterm infants with birthweight ≤2000 g and postnatal age (PNA) ≤2 months |
| SAMN40379555 | preterm_status | preterm | R4 | 0.45 | study.title | premature neonates with bacteremia |
| SAMN40379555 | subject_id | 3 | R1 | 0.70 | sample.name_rule:source_material_id | 3_NICU_F003 |
| SAMN40379555 | timepoint_label | F | R1 | 0.70 | sample.name_rule:source_material_id | 3_NICU_F003 |
Sequencing
404 runs over 404 samples · mean 5.47 Gbp per run (median 5.49 Gbp, total 2,208.79 Gbp; 404 runs with a base count) · layout PAIRED 404 · platform ILLUMINA 404 · models Illumina NovaSeq 6000 (404) · 97% of runs with a Sandpiper profile · first public 2025-09-01
Authors (0)
No author record.
Downloads
PRJNA1086532.csv.gz (12.0 KB) · parquet (85.9 KB) — all 404 samples, every field with route and confidence · PRJNA1086532_determinations.csv.gz (17.0 KB) — 2,422 evidence rows