Gut Microbiome of Infants in the Neonatal Intensive Care Unit
895 samples from a longitudinal cohort of infants/neonates (with some child and adult samples) who spent time in the NICU, studying gut microbiome and antimicrobial resistome development related to later atopy, infections, and antibiotic resistance. machine-written summary
Sequencing depth per sample · this project all projects
Sampling design and relatedness
longitudinalparent–child — not resolved
121 of 146 people sampled more than once (870 samples; median 7, up to 20 per person) · follow-up median 2.4 y (max 3.9 y) · median interval between samples 3 mo(time from age at collection).
Schedule stated by the source: “serial stool samples from infants during and after NICU stay; host_age given in days per sample (e.g. 7-28 days)” (time origin: birth).
Each row is one person (36 shown of 121); dots are samples at days since that person's first sample.
NICU infants and 18 parent stool samples (TITLE Parent/Child); family linkage not stated in the archive.
Bifidobacterium 12.9%Klebsiella 10.3%Enterococcus 6.5%Escherichia 6.4%Staphylococcus 4.8%Bacteroides 4.2%Blautia_A 3.3%Mediterraneibacter 3.3%Veillonella 3.1%Faecalibacterium 2.7%Streptococcus 2.6%Phocaeicola 2.4%not assigned to a genus 2.3%other genera 35.1%
Genera, mean relative abundance over 870 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Colibactin genes are highly prevalent in the developing infant gut microbiome. PMID 41405404PMC12716031curated
Details
Archive description
We are studying the longitudinal microbiome and antimicrobial resistome development of infants who have spent time in the NICU and after they leave the NICU in an attempt to better understand outcomes related to atopy (allergies, asthma, eczema), infections, and antibiotic resistance later in life. We plan on using metagenomic shotgun sequencing of serial stool samples from about 130 infants to achieve this.
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.
body sitestudy.title · “Gut Microbiome of Infants”
body sitestudy.description · “sequencing of serial stool samples from about”
life stageexternal_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
life stagestudy.title · “Gut Microbiome of Infants in the Neonatal”
life stagestudy.title · “Infants in the Neonatal Intensive Care Unit”
life stagestudy.description · “time in the NICU and after they”
Evidence examples (one per field × route)
sample
field
value
route
conf.
source
quote
SAMN49537762
age_at_collection_days
13514
R1
0.90
sample.attr.host_age
37 years
SAMN49537764
age_at_collection_days
7
R1
0.90
biosample_attr
7 days
SAMN49537762
collection_date
2016-03-17
R1
0.85
biosample.attribute:collection_date
2016-03-17
SAMN49537762
country
US
R1
0.90
biosample_attr
USA:Maryland
SAMN49537762
family_role
parent
R1
0.85
biosample.attribute:TITLE
TITLE: Parent stool metagenomic sample
SAMN49537762
gestational_age_weeks
38.0
R1
0.90
biosample_attr
38
SAMN49537764
health_condition
preterm_nicu
R1
0.85
biosample.attribute:title
Child stool metagenomic sample
SAMN49537764
health_condition_detail
Child stool metagenomic sample
R1
0.85
biosample.attribute:title
Child stool metagenomic sample
SAMN49537762
location_site
Inova Fairfax Neonatal Intensive Care Unit
R3
0.70
paper.fulltext.methods
Inova Fairfax Neonatal Intensive Care Unit (NICU) were enrolled
SAMN49537762
preterm_status
term
R1
0.85
biosample_attr
38
SAMN49537762
sex
female
R1
0.90
biosample_attr
female
SAMN49537762
subject_id
10000101
R1
0.85
biosample.attribute:source_material_id
10000101
Sequencing
895 runs over 895 samples · mean 10.62 Gbp per run (median 10.56 Gbp, total 9,502.63 Gbp; 895 runs with a base count) · layout PAIRED 895 · platform ILLUMINA 895 · models Illumina NovaSeq X (895) · 97% of runs with a Sandpiper profile · first public 2026-03-22