Premature infant gut metagenome from Chicago NICU

Gut metagenome from two premature infants

2 fecal metagenome samples from premature infants in a Chicago, IL intensive care unit, collected every three days; case series paired with room-based 16S rRNA surveys to track microbial reservoirs. machine-written summary

2 samples · 2 runs · US · Infant / toddler · 2014 · 16.04 Gbp / sample

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Sources

✓Sequence archive 14○Abstract / description✓Full text 12○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	14 sample values (age, collection date, country, health condition, health condition detail, preterm status, subject id)
○ Abstract / description	read; no usable statement
✓ Full text	12 sample values (antibiotic exposure, birth weight grams, delivery mode, feeding mode, gestational age weeks, location site) · PMC10269646, PMC10769871, PMC4392516
○ 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

Samples at a glance

1 country

Age

neonate2

Condition

preterm_nicu2

Country

US2

Body site

primary2

Sequencing depth per sample · this project all projects

Sampling design and relatedness

hospital ward — not resolved

2 premature infants in one NICU room; room surfaces surveyed to trace ICU reservoirs into the infant gut.

How longitudinal and relatedness information is derived

Community composition

Enterococcus 32.0%Bacteroides 28.1%Escherichia 14.6%Staphylococcus 8.0%Klebsiella 4.1%Veillonella 2.8%Finegoldia 2.2%Pseudomonas 1.4%Pauljensenia 1.2%Dermabacter 1.2%ECMA0423 1.0%Anaerococcus 0.8%not assigned to a genus 1.6%other genera 1.1%

Genera, mean relative abundance over 2 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
age_category	2	100%
country	2	100%	2
health_condition	2	100%	2
subject_id	2	100%	2
age_at_collection_days	2	100%	2
antibiotic_exposure	2	100%		2
birth_weight_grams	2	100%		2
collection_date	2	100%	2
delivery_mode	2	100%		2
detailed_location	2	100%
feeding_mode	2	100%		2
gestational_age_weeks	2	100%		2
health_condition_detail	2	100%	2
location_site	2	100%		2
preterm_status	2	100%	2

Papers (3)

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants. PMID 24468033 PMC4392516 curated
Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646 curated
BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871 curated

Details

Archive description

We have developed a high-throughput culture-independent approach that integrates room surveys based on full-length 16S rRNA gene sequences with metagenomic analysis of fecal samples collected from infants in the room. The approach enabled identification of discrete ICU reservoirs of microbes that also colonized the infant gut and provided evidence for the presence of certain organisms in the room prior to their detection in the gut. Gut metagenomes from two premature infants based on fresh fecal samples were collected every three days in a hospital intensive care unit.

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 · “Gut metagenome from two”
body site study.description · “metagenomic analysis of fecal samples collected from”
life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
life stage study.title · “from two premature infants”
life stage study.title · “metagenome from two premature infants”
life stage study.description · “metagenomes from two premature infants based on”

Evidence examples (one per field × route)

sample	field	value	route	conf.	source	quote
SAMN02364490	age_at_collection_days	0	R1	0.90	biosample_attr	newborn (premature)
SAMN02364490	antibiotic_exposure	yes	R3	0.80	paper.fulltext.methods	DOL 1 to 7 antibiotics Ampicillin, gentamycin
SAMN02364490	birth_weight_grams	951	R3	0.60	paper.fulltext.methods	Weight 951 g
SAMN02364490	collection_date	2012-01	R1	0.85	biosample.attribute:collection_date	2012-01
SAMN02364490	country	US	R1	0.90	biosample_attr	USA: Chicago, IL
SAMN02364490	delivery_mode	vaginal	R3	0.80	paper.fulltext.methods	Delivery mode Vaginal Vaginal
SAMN02364490	feeding_mode	exclusive_breast	R3	0.40	paper.fulltext.methods	Feeding initiated DOL 3, maternal milk
SAMN02364490	gestational_age_weeks	26.43	R3	0.60	paper.fulltext.methods	Gestational age 26 3/7 weeks
SAMN02364490	health_condition	preterm_nicu	R1	0.85	biosample.attribute:age	newborn (premature)
SAMN02364490	health_condition_detail	newborn (premature)	R1	0.85	biosample.attribute:age	newborn (premature)
SAMN02364490	location_site	Magee-Womens Hospital NICU, University of Pittsburgh Medical Center	R3	0.70	paper.fulltext.methods	private-style NICU at Magee-Womens Hospital of the University of Pittsburgh
SAMN02364490	preterm_status	preterm	R1	0.85	biosample_attr	newborn (premature)
SAMN02364490	subject_id	1	R1	0.70	sample.title	General Sample for Brooks et al. 2012 gut metagenome of premature infant

Sequencing

2 runs over 2 samples · mean 16.04 Gbp per run (median 16.04 Gbp, total 32.08 Gbp; 2 runs with a base count) · layout PAIRED 2 · platform ILLUMINA 2 · models Illumina HiSeq 2000 (2) · 100% of runs with a Sandpiper profile · first public 2014-02-05

Authors (36)

Brooks B first · Firek BA · Miller CS · Sharon I · Thomas BC · Baker R · Morowitz MJ · Banfield JF 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 · Hall B first · Levy S · Dufault-Thompson K · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Jiang X last

Downloads

PRJNA221723.csv.gz (1.0 KB) · parquet (70.7 KB) — all 2 samples, every field with route and confidence · PRJNA221723_determinations.csv.gz (1.3 KB) — 26 evidence rows

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

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