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PRJNA630999 SRP307844

Preterm infant gut microbiome, probiotic cohort, USA

Premature infant microbiome Metagenome

293 gut metagenome samples from preterm infants (190 infant, 103 neonate age category; 19 with NEC) in Anaheim and Irvine, USA, from a longitudinal cohort study of probiotic (B. infantis) intervention. machine-written summary

293 samples · 293 runs · US · Infant / toddler · 2021 · 10.00 Gbp / sample

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Sources

✓Sequence archive 1,462○Abstract / description✓Full text 568✓Supplementary tables 941–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	1,462 sample values (collection date, country, shared setting id, shared setting type, subject id)
○ Abstract / description	read; no usable statement
✓ Full text	568 sample values (collection date, feeding mode, preterm status) · PMC10269646, PMC11497992, PMC12677589, PMC7921802
✓ Supplementary tables	941 sample values (age, birth weight grams, delivery mode, gestational age weeks, health condition, intervention, preterm status, probiotic exposure)
– 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 resolved

non-randomised arms

Probiotic (live microorganisms; single strain or mixture) design non_randomized_controlled · population preterm_nicu · B. infantis EVC001 8x10^9 CFU daily vs unfed cohort, preterm infants

“fed activated Bifidobacterium longum subsp. infantis” — abstract:33665175 (study level; per-sample arms are in the intervention column below)

Samples at a glance

1 country

Age

neonate164

infant129

Condition

nec19

Sex

male30

female19

Country

US293

Body site

primary293

Sequencing depth per sample · this project all projects

Sampling design and relatedness

longitudinalhospital ward

56 of 77 people sampled more than once (272 samples; median 4, up to 13 per person) · follow-up median 14 d (max 3 mo) · median interval between samples 5 d (time from age at collection). Schedule stated by the source: “Longitudinal follow-up of preterm infants with host_age given as corrected gestational age in weeks; multiple collection_dates per subject, exact intervals not stated”.

Each row is one person (36 shown of 56); dots are samples at days since that person's first sample.

Preterm infants in two NICUs (Anaheim, Irvine) per geo_loc_name; 4 infants sampled in both units; no family links2 shared settings.

member · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 2 shared settings. 77 people in the project overall.

How longitudinal and relatedness information is derived

Community composition

Bifidobacterium 40.0%Klebsiella 18.2%Escherichia 14.8%Staphylococcus 4.5%Enterococcus 4.2%Enterobacter 3.2%Veillonella 2.4%Streptococcus 1.3%Cutibacterium 1.2%Serratia 1.1%Phocaeicola 0.8%Citrobacter_B 0.7%not assigned to a genus 2.0%other genera 5.5%

Genera, mean relative abundance over 269 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	R3
age_category	293	100%
country	293	100%	293
health_condition	19	6%		19
subject_id	293	100%	293
collection_date	293	100%	292		1
feeding_mode	293	100%			293
preterm_status	293	100%		19	274
age_at_collection_days	292	100%		292
intervention	292	100%		292
shared_setting_id	292	100%	292
shared_setting_type	292	100%	292
probiotic_exposure	174	59%		174
sex	49	17%		49
birth_weight_grams	39	13%		39
delivery_mode	38	13%		38
gestational_age_weeks	19	6%		19

Papers (4)

Impact of Probiotic B. infantis EVC001 Feeding in Premature Infants on the Gut Microbiome, Nosocomially Acquired Antibiotic Resistance, and Enteric Inflammation. PMID 33665175 PMC7921802 curated
Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646 curated
Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy. PMID 39428758 PMC11497992 curated
The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset. PMID 41025564 PMC12677589 curated

Details

Archive description

Preterm infants are colonized with nosocomially acquired gut microbes, including pathogens, and experience enteric inflammation, which has been related to adverse clinical outcomes. There have been limited probiotic interventions that show meaningful improvement of quantifiable health indicators. Here we prospectively and longitudinally followed a cohort of preterm infants in two neonatal intensive care units. Our results demonstrate that feeding Bifidobacterium longum subsp. infantis (B. infantis) EVC001, resulted in significant beneficial impacts on the infants enteric inflammatory profile, human milk utilization, and that human milk feeding facilitates colonization by B. infantis. Further, these infants required fewer antibiotic exposures, had a significant reduction in antibiotic resistant genes (ARG) abundance, and significantly fewer incidences of diaper rash. These data show feeding B. infantis EVC001 to premature infants provides a meaningful strategy to reduce gut dysbiosis and antibiotic resistant gene abundance, as well as decrease enteric inflammation and may reduce the risk of morbidity and mortality in hospitalized infants.

How this project entered the registry

Classified as human gut / stool / human milk 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 · “with nosocomially acquired gut microbes, including pathogens,”
body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
body site study.description · “enteric inflammatory profile, human milk utilization, and that”
life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
life stage study.title · “Premature infant microbiome Metagenome”
life stage study.title · “Premature infant microbiome Metagenome”
life stage study.description · “Preterm infants are colonized”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN18040230	age_at_collection_days	5	R2	0.85	paper.supp.table	Day Of Life=5
SAMN18040262	birth_weight_grams	500	R2	0.75	paper.supp.table	Birth weight (gram)=500
SAMN18040230	collection_date	2019-06-11	R1	0.85	biosample.attribute:collection_date	collection_date: 2019-06-11
SAMN18040459	collection_date	2019-05/2019-10	R3	0.70	paper.fulltext.methods	enrolled during the period of May 2019 to October 2019
SAMN18040230	country	US	R1	0.90	biosample_attr	USA:Anaheim
SAMN18040262	delivery_mode	vaginal	R2	0.75	paper.supp.table	Delivery mode=vaginal
SAMN18040230	feeding_mode	mixed	R3	0.40	paper.fulltext.results	predominantly human milk diet via maternal, donor, and/or commercial human milk
SAMN18040230	gestational_age_weeks	27.14	R2	0.75	paper.supp.table	Gestational_age=27.1428571428571
SAMN18040230	health_condition	nec	R2	0.80	paper.supp.table	PreNEC=preNEC
SAMN18040230	intervention	no_intervention	R2	0.80	paper.supp.Table_2.XLSX[Shannon.csv][Probiotic]	Probiotic: no
SAMN18040230	preterm_status	preterm	R2	0.75	paper.supp.table	PreNEC=preNEC
SAMN18040235	preterm_status	preterm	R3	0.80	paper.fulltext.results	Seventy-seven [77] preterm infants were enrolled
SAMN18040230	probiotic_exposure	no	R2	0.85	paper.supp.table	Probiotic=no
SAMN18040230	sex	female	R2	0.75	paper.supp.table	Gender=female
SAMN18040230	shared_setting_id	Anaheim NICU	R1	0.60	biosample.attribute:geo_loc_name	geo_loc_name: USA:Anaheim
SAMN18040230	shared_setting_type	hospital_ward	R1	0.60	biosample.attribute:geo_loc_name	geo_loc_name: USA:Anaheim
SAMN18040230	subject_id	17	R1	0.85	biosample_attr	17

Sequencing

293 runs over 293 samples · mean 9.89 Gbp per run (median 10.00 Gbp, total 2,896.80 Gbp; 293 runs with a base count) · layout PAIRED 293 · platform ILLUMINA 293 · models Illumina NovaSeq 6000 (293) · 92% of runs with a Sandpiper profile · first public 2021-03-01 – 2023-01-01

Authors (62)

Nguyen M first · Holdbrooks H · Mishra P · Abrantes MA · Eskew S · Garma M · Oca CG · McGuckin C · Hein CB · Mitchell RD · Kazi S · Chew S · Casaburi G · Brown HK · Frese SA · Henrick BM last · Rizzo SM first · Alessandri G · Lugli GA · Fontana F · Tarracchini C · Mancabelli L · Viappiani A · Bianchi MG · Bussolati O · van Sinderen D · Ventura M · Turroni F last · Minot SS first · Mayer-Blackwell K · Fiore-Gartland A · Johnson A · Self S · Bhatti P · Yao L · Liu L · Sun X · Jinfa Y · Kublin J last · 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

Downloads

PRJNA630999.csv.gz (11.3 KB) · parquet (85.0 KB) — all 293 samples, every field with route and confidence · PRJNA630999_determinations.csv.gz (25.6 KB) — 2,971 evidence rows

Samples (293 · every field this project has values for · hover a cell for its source)

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