Preterm infant gut microbiome and cholestasis, Houston, USA
114 stool samples from preterm infants in Houston, USA, studied in a case-control design examining the liver-gut-microbiome axis and cholestasis in extreme prematurity. machine-written summary
114 samples · 114 runs · US · Infant / toddler · 2023 · 5.09 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 228 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 684 sample values (gestational age weeks, location locality, location site, maternal antibiotics, nec status, preterm status) · PMC9980517 |
| – 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 |
longitudinal — not resolved
Schedule stated by the source: “Stool samples collected longitudinally from preterm infants; no specific schedule/intervals stated.”.
Genera, mean relative abundance over 95 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 | 114 | 100% | ||||
| country | 114 | 100% | 114 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 114 | 100% | 114 | |||
| detailed_location | 114 | 100% | ||||
| gestational_age_weeks | 114 | 100% | 114 | |||
| location_locality | 114 | 100% | 114 | |||
| location_site | 114 | 100% | 114 | |||
| maternal_antibiotics | 114 | 100% | 114 | |||
| nec_status | 114 | 100% | 114 | |||
| preterm_status | 114 | 100% | 114 |
- Cholestasis impairs gut microbiota development and bile salt hydrolase activity in preterm neonates. PMID 36843227 PMC9980517 curated
Archive description
To gain insight into how the liver-gut-microbiome axis develops in extreme prematurity and how cholestasis alters this maturation, we collected 124 stool samples longitudinally from 24 preterm infants born at mean 27.2 weeks gestation and 946 grams, half of whom developed cholestasis. Samples were analyzed by whole metagenomic sequencing.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids 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.description · “how the liver- gut -microbiome axis develops”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.description · “into how the liver -gut-microbiome axis develops”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “metagenomic of preterm infants with cholestasis”
- life stage study.title · “Longitudinal metagenomic of preterm infants with cholestasis”
- life stage study.description · “develops in extreme prematurity and how cholestasis”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN30380029 | collection_date | 2019-04-27 | R1 | 0.85 | biosample.attribute:collection_date | 2019-04-27 |
| SAMN30380029 | country | US | R1 | 0.90 | biosample_attr | USA: Houston |
| SAMN30380029 | gestational_age_weeks | 27.2 | R3 | 0.40 | paper.fulltext.results | mean GA for all infants was 27.2 ± 1.8 weeks |
| SAMN30380029 | location_locality | Houston | R3 | 0.70 | paper.fulltext.methods | Texas Children's Hospital-Pavilion for Women (Houston, TX, United States of America) |
| SAMN30380029 | location_site | Texas Children's Hospital-Pavilion for Women | R3 | 0.70 | paper.fulltext.methods | Texas Children's Hospital-Pavilion for Women (Houston, TX, United States of America) |
| SAMN30380029 | maternal_antibiotics | yes | R3 | 0.40 | paper.fulltext.results | Maternal antibiotic use, n (%) 12 (100) 12 (100) |
| SAMN30380029 | nec_status | no | R3 | 0.65 | paper.fulltext.methods | excluded for ... Bell's Stage 2 or greater NEC |
| SAMN30380029 | preterm_status | preterm | R3 | 0.80 | paper.fulltext.abstract | 24 preterm infants born at mean 27.2 weeks gestation |
Sequencing
114 runs over 114 samples · mean 7.74 Gbp per run (median 5.09 Gbp, total 882.56 Gbp; 114 runs with a base count) · layout PAIRED 114 · platform ILLUMINA 114 · models Illumina NovaSeq 6000 (114) · 83% of runs with a Sandpiper profile · first public 2023-01-02 – 2025-01-25
Authors (8)
Lynch LE first · Hair AB · Soni KG · Yang H · Gollins LA · Narvaez-Rivas M · Setchell KDR · Preidis GA last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA870588.csv.gz (4.4 KB) · parquet (75.6 KB) — all 114 samples, every field with route and confidence · PRJNA870588_determinations.csv.gz (5.9 KB) — 912 evidence rows