Infant gut mycobiome development in Philadelphia-area cohort
Gut Mycobiome Maturation and Its Determinants during Infancy: A Comparison of Shotgun Metagenomic and ITS2 Amplicon-Based Sequencing Approaches
1033 fecal samples from infants and neonates in the Philadelphia, Pennsylvania metro area, collected longitudinally from birth to 24 months, comparing shotgun metagenomic and ITS2 amplicon sequencing in antibiotic-exposed and control groups. machine-written summary
Sequencing depth per sample · this project all projects
Sampling design and relatedness
longitudinal
161 of 187 people sampled more than once (1,007 samples; median 5, up to 23 per person) · follow-up median 11 mo (max 22 mo) · median interval between samples 42 d(time from age at collection).
Schedule stated by the source: “Collected within a few days of birth and then every three months until 24 months of age” (time origin: birth); stated follow-up 2.0 y.
Each row is one person (36 shown of 161); dots are samples at days since that person's first sample.
Bifidobacterium 16.4%Bacteroides 10.8%Escherichia 9.6%Faecalibacterium 8.4%Phocaeicola 7.2%Klebsiella 6.2%Veillonella 3.3%Clostridium 1.9%Prevotella 1.8%Enterocloster 1.8%Parabacteroides 1.4%Streptococcus 1.3%not assigned to a genus 6.1%other genera 23.5%
Genera, mean relative abundance over 890 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Gut mycobiome maturation and its determinants during early childhood: a comparison of ITS2 amplicon and shotgun metagenomic sequencing approaches. PMID 40469735PMC12133761curated
Details
Archive description
Samples from subjects recruited as part of the "Microbiome, Antibiotic and Growth Infant Cohort" (MAGIC) study. Fecal samples from enrolled children born at Pennsylvania Hospitals were collected within a few days of birth and then every three months until the infant reached 24 months of age. Demographic information, including antibiotic usage and exposure, was collected at every time point for each subject. DNA was extracted and sequenced using two methods: shotgun metagenomics and ITS2 amplicon sequencing. This dataset can be used to compare and contrast sequencing methods in the context of the developing infant gut mycobiome in both antibiotics-exposed and control infant populations.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of neonate and infant / toddler by sonnet_x2 with confidence 0.78. Assay shotgun_dna.
hostrun.host_tax_id · “9606”
body sitestudy.description · “Fecal samples from enrolled children”
life stagestudy.description · “collected within a few days of birth”
life stagestudy.description · “every three months until the infant reached 24 months”
Evidence examples (one per field × route)
sample
field
value
route
conf.
source
quote
SAMN31820954
age_at_collection_days
7
R1
0.90
biosample_attr
1 weeks
SAMN31820954
collection_date
2016-12-22
R1
0.85
biosample.attribute:collection_date
2016-12-22
SAMN31820954
country
US
R1
0.90
biosample_attr
USA: Pennsylvania, Philadelphia metro area
SAMN31820954
location_locality
Philadelphia
R3
0.70
paper.fulltext.methods
children born at Pennsylvania Hospital (Philadelphia, PA)
SAMN31820954
location_site
Pennsylvania Hospital
R3
0.70
paper.fulltext.methods
children born at Pennsylvania Hospital (Philadelphia, PA)
SAMN31820954
sex
female
R1
0.90
biosample_attr
female
SAMN31820954
subject_id
106
R1
0.85
biosample_attr
106
Sequencing
1,033 runs over 1,033 samples · mean 3.19 Gbp per run (median 3.10 Gbp, total 3,293.91 Gbp; 1,033 runs with a base count) · layout PAIRED 1,033 · platform ILLUMINA 1,033 · models Illumina NovaSeq 6000 (1,033) · 86% of runs with a Sandpiper profile · first public 2023-11-02