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PRJNA838575 SRP377293

Canadian infant gut metagenomes, longitudinal cohort

CHILD Infant Stool Raw sequence reads

Shotgun metagenomic sequencing of 2934 infant stool samples from Canada, collected at 3-month and 1-year visits as part of a longitudinal cohort study (CHILD). machine-written summary

2,934 samples · 2,934 runs · CA · Infant / toddler · 2022 · 1.63 Gbp / sample

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Sources
✓Sequence archive 11,736○Abstract / description○Full text○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 archive11,736 sample values (age, collection date, country, timepoint)
○ Abstract / descriptionread; no usable statement
○ Full textread; no usable statement or table · PMC10465508, PMC12280908, PMC13130633, PMC13291349
○ Supplementary tablesfiles read; no table could be matched to the samples
– External resourcesnot covered by the external resources we ingest
– User contributionnothing uploaded yet · share metadata
– Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 country
Age
infant2,934
Country
CA2,934
Body site
primary2,934
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 8 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 13 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 14 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 183 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 2,650 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 66 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)all projects, 30–100 Gbp: 3,024 samples (1 %)all projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 1.63 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinal — not resolved

Schedule stated by the source: “Two visits per infant: 3-month and 1-year stool collections (CHILD birth cohort)” (time origin: birth).

How longitudinal and relatedness information is derived

Community composition
Bifidobacterium 45.4%Blautia_A 6.8%Mediterraneibacter 5.1%Streptococcus 3.8%Escherichia 3.7%Bacteroides 3.1%Collinsella 1.9%Klebsiella 1.7%Phocaeicola 1.6%Faecalibacterium 1.6%Anaerostipes 1.4%Fusicatenibacter 1.0%not assigned to a genus 6.2%other genera 16.6%

Genera, mean relative abundance over 2,665 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category2,934 100%
country2,934 100%2,934
health_condition0 0%
subject_id0 0%
age_at_collection_days2,934 100%2,934
collection_date2,934 100%2,934
timepoint_label2,934 100%2,934
Papers (4)
  • Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease. PMID 37644001 PMC10465508 curated
  • Human milk IgA promotes normal immune development by limiting Th17-inducing Erysipelatoclostridium ramosum in the infant gut. PMID 40623174 PMC12280908 curated
  • Breastfeeding may lessen socioeconomic disparities in child health through differences in the infant gut microbiome. PMID 41980780 PMC13130633 curated
  • Saccharomycetes and Malassezia fungi associate with early-life gut maturation and allergic disease risk in childhood. PMID 42337243 PMC13291349 curated
Details
Archive description

Shotgun metagenomic sequence of CHILD Infant stool collected at 3 month and 1 year visit.

How this project entered the registry

Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.

  • host external_curation.infant_catalog · “infant triage verdict include”
  • body site study.title · “CHILD Infant Stool Raw sequence reads”
  • body site study.description · “of CHILD Infant stool collected at 3”
  • life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
  • life stage study.title · “CHILD Infant Stool Raw sequence”
  • life stage study.title · “CHILD Infant Stool Raw”
  • life stage study.description · “metagenomic sequence of CHILD Infant stool collected”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMN28495809age_at_collection_days365R10.90biosample_attr1 year
SAMN28495809collection_date2012R10.85biosample.attribute:collection_datecollection_date: 2012
SAMN28495809countryCAR10.90biosample_attrCanada
SAMN28495809timepoint_label1 yearR10.85biosample.attribute:host_agehost_age: 1 year
Sequencing

2,934 runs over 2,934 samples · mean 1.69 Gbp per run (median 1.63 Gbp, total 4,954.98 Gbp; 2,934 runs with a base count) · layout SINGLE 2,934 · platform ILLUMINA 2,934 · models NextSeq 500 (2,934) · 91% of runs with a Sandpiper profile · first public 2022-12-07 – 2022-12-08

Authors (34)

Hoskinson C first · Dai DLY · Del Bel KL · Becker AB · Moraes TJ · Mandhane PJ · Finlay BB · Simons E · Kozyrskyj AL · Azad MB · Subbarao P · Petersen C · Turvey SE last · Donald K first · Serapio-Palacios A · Bozorgmehr T · Ma M · Garcia MAI · Mandhane P · Turvey S · Manus MB · Jiang J · Sbihi H · Miliku K · Campisi SC · Korczak DJ · Duan Q · Lishman H · Patrick DM · Chawes B · Bønnelykke K · Sørensen SJ · Thorsen J · Stokholm J

Help complete this project

2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata

Downloads

PRJNA838575.csv.gz (71.1 KB) · parquet (192.6 KB) — all 2,934 samples, every field with route and confidence · PRJNA838575_determinations.csv.gz (51.6 KB) — 11,736 evidence rows

Samples (2,934 · every field this project has values for · hover a cell for its source)
Loading the sample table…