Preterm infant gut microbiome in NEC vs controls, UK
Longitudinal metagenomic analysis of the gut microbiome in preterm infants diagnosed with necrotising enterocolitis and matched controls
644 longitudinal stool samples from preterm infants in the United Kingdom (195 from infants with necrotising enterocolitis, 437 from matched healthy controls), analysed by metagenomic sequencing in a case-control design. machine-written summary
Sequencing depth per sample · this project all projects
Sampling design and relatedness
longitudinal
48 of 48 people sampled more than once (644 samples; median 13, up to 33 per person) · follow-up median 3 mo (max 16 mo) · median interval between samples 6 d(time from age at collection).
Schedule stated by the source: “Repeated stool sampling per infant (644 samples/48 subjects); 'day of life at sample collection' has 168 distinct values; published timepoint_label bins: 0 - 1 month; 1 - 6 months; 6 months - 1 yr; 1 ” (time origin: birth); stated follow-up 16 mo.
Each row is one person (36 shown of 48); dots are samples at days since that person's first sample.
Bifidobacterium 34.2%Enterococcus 13.1%Escherichia 11.4%Enterobacter 6.6%Klebsiella 6.6%Staphylococcus 6.6%Enterococcus_B 2.3%Streptococcus 1.7%Veillonella 1.6%Pantoea 1.2%Proteus 1.2%Lactobacillus 1.1%not assigned to a genus 3.0%other genera 9.4%
Genera, mean relative abundance over 588 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543PMC10269646curated
Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032PMC11019788curated
Human milk microbiota, oligosaccharide profiles, and infant gut microbiome in preterm infants diagnosed with necrotizing enterocolitis. PMID 39216480PMC11524953curated
Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373PMC11494892curated
The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset. PMID 41025564PMC12677589curated
Details
Archive description
Necrotising enterocolitis (NEC) is a severe intestinal disease affecting predominantly preterm infants. The mechanisms leading to disease onset are poorly understood. Gut rich in Proteobacteria has been associated with disease onset, even though no specific causative microorganism has been identified. Moreover, intestinal microbiome instability seems to precede NEC development. To date, preterm microbiome studies relied mostly on 16S rRNA gene sequencing which allows to retrieve information down to the genus level, while metagenomic sequencing allows to identify species and gene content harboured by a microbial community. In this study, we applied metagenomic sequencing on longitudinal stool samples from 14 infants affected from NEC and 34 matched controls. A total of 644 stool samples were analysed, with samples ranging from birth up to 500 days 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.
body sitestudy.title · “analysis of the gut microbiome in preterm”
body sitestudy.description · “is a severe intestinal disease affecting predominantly”
life stageexternal_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
life stagestudy.title · “microbiome in preterm infants diagnosed with necrotising”
life stagestudy.title · “gut microbiome in preterm infants diagnosed with”
life stagestudy.description · “disease affecting predominantly preterm infants. The mechanisms”
Evidence examples (one per field × route)
sample
field
value
route
conf.
source
quote
SAMEA7096762
age_at_collection_days
12
R1
0.90
biosample_attr
12
SAMEA7096762
antibiotic_exposure
no
R1
0.85
biosample_attr
Not_during
SAMEA7096762
birth_weight_grams
640
R1
0.90
biosample_attr
640
SAMEA7096762
collection_date
2014
R1
0.85
biosample.attribute:collection date
collection date: 2014
SAMEA7096762
country
GB
R1
0.90
biosample_attr
United Kingdom
SAMEA7096762
delivery_mode
vaginal
R1
0.90
biosample_attr
Vaginal
SAMEA7096762
feeding_mode
mixed
R2
0.75
paper.supp.table
Feeding pattern=combined
SAMEA7096762
gestational_age_weeks
24.0
R1
0.90
biosample_attr
24
SAMEA7096768
health_condition
preterm_nicu
R1
0.85
biosample.attribute:nec
nec: N
SAMEA7097228
health_condition
nec
R1
0.80
biosample.attribute:prenec
prenec: PostNEC
SAMEA7096762
health_condition
healthy_control
R2
0.70
paper.supp.table
PreNEC=noNEC
SAMEA7096762
health_condition_detail
NoNEC
R1
0.90
biosample.attribute:prenec
prenec: NoNEC
SAMEA7096762
nec_status
no
R1
0.85
biosample_attr
N
SAMEA7096762
preterm_status
preterm
R1
0.85
biosample_attr
24
SAMEA7096762
probiotic_exposure
yes
R1
0.85
biosample_attr
During
SAMEA7096762
sex
male
R1
0.90
biosample_attr
Male
SAMEA7096762
subject_id
367
R1
0.85
biosample_attr
367
SAMEA7096762
timepoint_label
0 - 1 month
R2
0.75
paper.supp.table
AGE GROUP G12=0 - 1 month
Sequencing
644 runs over 644 samples · mean 3.55 Gbp per run (median 3.33 Gbp, total 2,287.68 Gbp; 644 runs with a base count) · layout PAIRED 644 · platform ILLUMINA 644 · models HiSeq X Ten (644) · 91% of runs with a Sandpiper profile · first public 2020-11-23