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PRJNA799247 SRP356369

Longitudinal metagenomics, preterm infants, NEC

Metagenomics of preterm infant stool

2171 stool samples from preterm infants in St. Louis, Oklahoma City, and Louisville (USA), comparing necrotizing enterocolitis (624 samples) to healthy controls (1479 samples), in a longitudinal cohort design. machine-written summary

2,171 samples · 2,171 runs · US · Infant / toddler · 2023 · 1.11 Gbp / sample

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Sources

✓Sequence archive 4,342✓Abstract / description 2,171○Full text✓Supplementary tables 15,373–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	4,342 sample values (collection date, country)
✓ Abstract / description	2,171 sample values (preterm status)
○ Full text	read; no usable statement or table · PMC12677589, PMC13402684
✓ Supplementary tables	15,373 sample values (age, birth weight grams, gestational age weeks, health condition, nec status, sex, subject id, timepoint)
– 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

Samples at a glance

1 country

Age

neonate1,313

infant858

Condition

healthy_control1,479

nec624

Sex

male1,104

female999

Country

US2,171

Body site

primary2,103

excluded68

Collected 2009–2013

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinal

142 of 146 people sampled more than once (2,099 samples; median 12, up to 54 per person) · follow-up median 17 d (max 2 mo) · median interval between samples 1 d (time from age at collection). Schedule stated by the source: “Repeated stool sampling of the same preterm infants over the first four months of life; multiple samples per subject_id (e.g., same numeric id, different library_name suffix) seen in sample table.” (time origin: birth); stated follow-up 4 mo.

Each row is one person (36 shown of 142); dots are samples at days since that person's first sample.

How longitudinal and relatedness information is derived

Community composition

Staphylococcus 21.0%Enterococcus 17.4%Klebsiella 11.8%Enterobacter 9.4%Escherichia 9.3%Sarcina 3.9%Streptococcus 3.3%Veillonella 2.6%Bifidobacterium 2.0%Citrobacter 1.7%Enterococcus_B 1.7%Serratia 1.6%not assigned to a genus 3.0%other genera 11.2%

Genera, mean relative abundance over 1,891 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	R2	R4
age_category	2,171	100%
country	2,171	100%	2,171
health_condition	2,103	97%		2,103
subject_id	2,103	97%		2,103
collection_date	2,171	100%	2,171
preterm_status	2,171	100%			2,171
age_at_collection_days	2,103	97%		2,103
birth_weight_grams	2,103	97%		2,103
gestational_age_weeks	2,103	97%		2,103
nec_status	2,103	97%		2,103
sex	2,103	97%		2,103
timepoint_label	652	30%		652

Papers (2)

The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset. PMID 41025564 PMC12677589 curated
An ubiquitous antibacterial toxin from human gut bacteria engenders neonatal colonization advantage. PMID 42259839 PMC13402684 curated

Details

Archive description

Shotgun metagenomics and metatranscriptomics of stool samples collected from preterm infants in the first four months 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 · “of preterm infant stool”
body site study.description · “and metatranscriptomics of stool samples collected from”
life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
life stage study.title · “Metagenomics of preterm infant stool”
life stage study.title · “Metagenomics of preterm infant stool”
life stage study.description · “samples collected from preterm infants in the”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN25162242	age_at_collection_days	19	R2	0.85	paper.supp.table	Day of life=19
SAMN25162242	birth_weight_grams	740	R2	0.85	paper.supp.table	Birth weight (gram)=740
SAMN25162242	collection_date	2011	R1	0.85	biosample.attribute:collection_date	collection_date: 2011
SAMN25162242	country	US	R1	0.90	biosample_attr	USA: Louisville
SAMN25162242	gestational_age_weeks	26.0	R2	0.85	paper.supp.table	Gestational age (weeks)=26
SAMN25162242	health_condition	nec	R2	0.80	paper.supp.table	PreNEC=preNEC
SAMN25162242	nec_status	no	R2	0.85	paper.supp.table	PreNEC=preNEC
SAMN25162242	preterm_status	preterm	R4	0.50	study.description	stool samples collected from preterm infants
SAMN25162242	sex	male	R2	0.85	paper.supp.table	Sex=male
SAMN25162242	subject_id	1003.01	R2	0.85	paper.supp.table	Subject_ID=1003.01
SAMN25162248	timepoint_label	Window 41	R2	0.85	paper.supp.ADVS-12-e05154-s014.xlsx[Sheet1!Window]	41

Sequencing

2,171 runs over 2,171 samples · mean 1.20 Gbp per run (median 1.11 Gbp, total 2,611.06 Gbp; 2,171 runs with a base count) · layout PAIRED 2,171 · platform ILLUMINA 2,171 · models NextSeq 500 (2,171) · 89% of runs with a Sandpiper profile · first public 2023-07-25 – 2024-10-16

Authors (30)

Zeng S first · Wang H · Zhang L · Li S · Yuan Y · Tian M · Qu Y · Ying J · Zhou M · Hu Y · Huang J · Zou R · Zhao F · Su X · Liu Q · He Y · Feng J · Huang W · Luo Y · Zhou Z · Shen W · Mu D · Wang S last · Valguarnera E first · Tung J · Pak JJ · Russell SK · Hecht DW · Schwartz DJ · Wardenburg JB last

Downloads

PRJNA799247.csv.gz (66.2 KB) · parquet (159.6 KB) — all 2,171 samples, every field with route and confidence · PRJNA799247_determinations.csv.gz (155.5 KB) — 21,886 evidence rows

Samples (2,171 · every field this project has values for · hover a cell for its source)

Loading the sample table…