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PRJEB49383 ERP133886

VLBW preterm infant stool metagenomes, Newcastle UK

Preterm Neonatal Stool Metagenomes

2351 stool metagenome samples from very low birth weight preterm infants at RVI Newcastle upon Tyne, UK, studied in a longitudinal cohort design with probiotic intervention. machine-written summary

2,351 samples · 2,352 runs · GB · Infant / toddler · 2022 · 3.21 Gbp / sample

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Sources

✓Sequence archive 7,041✓Abstract / description 2,351✓Full text 7,051○Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave

✓ Sequence archive	7,041 sample values (collection date, country, health condition, health condition detail)
✓ Abstract / description	2,351 sample values (preterm status)
✓ Full text	7,051 sample values (collection date, location locality, location site) · PMC12015168, PMC9519454
○ 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

Interventions

intervention — arms not resolved

Probiotic (live microorganisms; single strain or mixture) design observational_with_procedure · population preterm_nicu · Probiotic (Infloran or Labinic) given to preterm infant cohorts

“Infloran (Bifidobacterium bifidum and Lactobacillus acidophilus) or Labinic” — abstract:36163498 (study level; per-sample arms are in the intervention column below)

Samples at a glance

1 country

Age

infant2,351

Condition

preterm_nicu2,344

Country

GB2,351

Body site

primary2,346

unknown5

Collected 2011–2019

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal — not resolved

How longitudinal and relatedness information is derived

Community composition

Bifidobacterium 27.3%Escherichia 13.0%Enterococcus 12.5%Klebsiella 10.1%Staphylococcus 9.4%Enterobacter 6.9%Enterococcus_B 2.1%Streptococcus 1.3%Lactobacillus 1.3%Veillonella 1.0%Citrobacter 0.9%Serratia 0.8%not assigned to a genus 3.5%other genera 9.9%

Genera, mean relative abundance over 1,994 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage

field	samples	coverage	R1	R3	R4
age_category	2,351	100%
country	2,351	100%	2,351
health_condition	2,344	100%	2,344
subject_id	0	0%
collection_date	2,351	100%	2	2,349
detailed_location	2,351	100%
location_locality	2,351	100%		2,351
location_site	2,351	100%		2,351
preterm_status	2,351	100%			2,351
health_condition_detail	2,344	100%	2,344

Papers (2)

Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants. PMID 36163498 PMC9519454 curated
Impact of probiotics on gut microbiome of extremely preterm or extremely low birthweight infants. PMID 39183307 PMC12015168 curated

Details

Archive description

Collection of Metagenomics sequencing runs from VLBW preterm infant stool samples collected from RVI Newcastle upon Tyne, UK. (Paired with submission PRJEB110894) Data utilised in several studies.

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 · “Preterm Neonatal Stool Metagenomes”
body site study.description · “VLBW preterm infant stool samples collected from”
life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
life stage study.description · “from VLBW preterm infant stool samples collected”
life stage study.title · “Preterm Neonatal Stool Metagenomes”
life stage study.description · “runs from VLBW preterm infant stool samples”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMEA9973262	collection_date	2019	R1	0.85	biosample.attribute:collection_date	2019
SAMEA11122569	collection_date	2011/2021	R3	0.60	paper.fulltext.results	admitted over a 10-year period, covering a period before probiotic
SAMEA11122569	country	GB	R1	0.90	biosample_attr	United Kingdom
SAMEA11122577	health_condition	preterm_nicu	R1	0.85	biosample.attribute:environment_biome	Severely preterm infant
SAMEA11122577	health_condition_detail	Severely preterm infant	R1	0.85	biosample.attribute:environment_biome	Severely preterm infant
SAMEA11122569	location_locality	Newcastle upon Tyne	R3	0.70	paper.fulltext.methods	were cared for in the NICU of the Royal Victoria Infirmary, Newcastle
SAMEA11122569	location_site	Royal Victoria Infirmary NICU	R3	0.70	paper.fulltext.methods	cared for in the NICU of the Royal Victoria Infirmary, Newcastle
SAMEA11122569	preterm_status	preterm	R4	0.50	study.title	Preterm Neonatal Stool Metagenomes

Sequencing

2,352 runs over 2,351 samples · mean 3.75 Gbp per run (median 3.21 Gbp, total 8,809.81 Gbp; 2,352 runs with a base count) · layout PAIRED 2,352 · platform ILLUMINA 2,352 · models NextSeq 500 (2,295), Illumina HiSeq 2000 (57) · 85% of runs with a Sandpiper profile · first public 2022-10-01 – 2026-04-08

Authors (12)

Beck LC first · Masi AC · Young GR · Vatanen T · Lamb CA · Smith R · Coxhead J · Butler A · Marsland BJ · Embleton ND · Berrington JE · Stewart CJ last

Downloads

PRJEB49383.csv.gz (60.7 KB) · parquet (171.3 KB) — all 2,351 samples, every field with route and confidence · PRJEB49383_determinations.csv.gz (68.6 KB) — 16,443 evidence rows

Samples (2,351 · every field this project has values for · hover a cell for its source)

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