Exploring Fecal Microbiome in the CHILD COVID-19 sub-project
4,102 stool samples from children and adults in CHILD Cohort households, mostly in Canada, collected longitudinally to study gut microbiome links with COVID-19 infection, vaccination, pandemic-related health and household members' microbiomes. machine-written summary
4,102 samples · 4,348 runs · CA, US · Child · 2026 · 2.49 Gbp / sample
Sequencing depth per sample · this project all projects
Sampling design and relatedness
longitudinalfamilieshouseholds
1,153 of 2,949 people sampled more than once (2,306 samples; median 2, up to 2 per person) · follow-up median 6 mo (max 9 mo) · median interval between samples 6 mo(time from collection dates).
Schedule stated by the source: “Biweekly surveys, quarterly questionnaires, and stool sample collection over the pandemic period; repeat stool samples per subject in catalog (784/1184 subjects with >=2 samples)”.
Each row is one person (36 shown of 1,153); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).
1,462 households (5,378 participants) enrolled; catalog shows 821 distinct family_subject_id groups, up to 19 samples/household · 763 families with 2,528 sampled people.
267 × unknown×3
213 × unknown×4
188 × unknown×2
79 × unknown×5
13 × unknown×6
1 × unknown×9
1 × unknown×10
1 × unknown×7
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: 24 of 763 families (one per family structure, then more). 2,949 people in the project overall.
Faecalibacterium 14.2%Alistipes 13.1%Bacteroides 6.8%Prevotella 3.9%Roseburia 3.1%Phocaeicola 2.7%Gemmiger 2.7%Bifidobacterium 2.6%Akkermansia 1.5%Vescimonas 1.3%Acetatifactor 1.2%Sutterella 1.2%not assigned to a genus 9.4%other genera 36.3%
Genera, mean relative abundance over 2,577 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
study aims to: (1) determine SARS-CoV-2 infection prevalence and transmission (2) identify infection predictors and severity factors and (3) assess health and psychosocial impacts. Building upon the CHILD Cohort Study, we engage 1,462 households (5,378 participants) in biweekly surveys, quarterly questionnaires, and biological sampling. This project expands our dataset to explore the gut microbiome's associations with COVID-19 infections and vaccinations, pandemic-related health statuses, and household members' microbiomes.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and adult by deterministic_rule with confidence 0.90. Assay shotgun_dna.
hostrun.host_tax_id · “host_tax_id 9606”
body sitestudy.title · “Exploring Fecal Microbiome in the”
body sitestudy.description · “to explore the gut microbiome's associations with”
life stagestudy.title · “Microbiome in the CHILD COVID-19 sub-project”
life stagestudy.description · “Building upon the CHILD Cohort Study, we”
life stagesample.attr.host_life_stage · “adult (n=2054/4102)”
mixed_case_control: COVID-19 infected vs uninfected, vaccinated vs unvaccinated, pandemic health impacts
R4
0.40
study.description
COVID-19 infections and vaccinations, pandemic-related health statuses
SAMEA121606568
latitude
43.2609
R1
0.90
biosample.attribute:latitude+longitude
43.2609 -79.9192
SAMEA121606568
location_region
Ontario
R1
0.60
biosample.attribute:latitude+longitude
43.2609 -79.9192
SAMEA121606568
longitude
-79.9192
R1
0.90
biosample.attribute:latitude+longitude
43.2609 -79.9192
SAMEA121606568
sex
female
R1
0.90
sample.attr.host_sex
female
SAMEA121606568
subject_id
1E1V6CM
R1
0.85
biosample.attribute:host_subject_id
host_subject_id = 1E1V6CM
SAMEA121606611
subject_id
6C8L5
R1
0.85
sample.attr.family_subject_id
6C8L5
Sequencing
4,348 runs over 4,102 samples · mean 2.25 Gbp per run (median 2.41 Gbp, total 9,778.99 Gbp; 4,348 runs with a base count) · layout PAIRED 4,348 · platform ILLUMINA 4,348 · models Illumina NovaSeq X (4,348) · 59% of runs with a Sandpiper profile · first public 2026-02-19 – 2026-03-05