Infant gut microbiome before/after antibiotics, Canada
94 infant/neonate fecal samples from Canada, shallow shotgun sequenced before and after antibiotic treatment, in a longitudinal cohort study of acute antibiotic effects on the infant gut microbiome. machine-written summary
94 samples · 94 runs · CA · Infant / toddler · 2023 · 0.64 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 95 sample values (country, intervention) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 376 sample values (collection date, location locality, location region, location site) · PMC13291269 |
| ✓ Supplementary tables | 1,058 sample values (age, antibiotic exposure, birth weight grams, delivery mode, diet, feeding mode, gestational age weeks, maternal antibiotics) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy design single_arm_before_after · population healthy_control · Antibiotic treatment in infants, sampled before and after
“samples before and after antibiotic treatment” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
47 of 47 people sampled more than once (94 samples; median 2, up to 2 per person).
Genera, mean relative abundance over 4 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 94 | 100% | ||||
| country | 94 | 100% | 94 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 94 | 100% | 94 | |||
| age_at_collection_days | 94 | 100% | 94 | |||
| antibiotic_exposure | 94 | 100% | 94 | |||
| birth_weight_grams | 94 | 100% | 94 | |||
| collection_date | 94 | 100% | 94 | |||
| delivery_mode | 94 | 100% | 94 | |||
| detailed_location | 94 | 100% | ||||
| feeding_mode | 94 | 100% | 94 | |||
| gestational_age_weeks | 94 | 100% | 94 | |||
| location_locality | 94 | 100% | 94 | |||
| location_region | 94 | 100% | 94 | |||
| location_site | 94 | 100% | 94 | |||
| preterm_status | 94 | 100% | 94 | |||
| sex | 94 | 100% | 94 | |||
| timepoint_label | 94 | 100% | 94 | |||
| maternal_antibiotics | 92 | 98% | 92 | |||
| diet | 26 | 28% | 26 | |||
| intervention | 1 | 1% | 1 |
- Antibiotic-induced Malassezia expansion in the infant gut promotes early-life immune dysregulation and airway inflammation in mice. PMID 42336834 PMC13291269 curated
Archive description
Infant antibiotic use impacts the intestinal microbiome and increases the risk of asthma. We performed shallow shotgun sequencing in DNA extracted from infant (<6 month-old) fecal samples before and after antibiotic treatment. This study aimed to characterize the acute effect of antibiotic treatment on the infant microbiome.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Infant stool shallow shotgun sequencing”
- body site study.description · “use impacts the intestinal microbiome and increases”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Infant stool shallow shotgun”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SRR27312506 | age_at_collection_days | 22 | R2 | 0.75 | paper.supp.table | Age_days=22 |
| SRR27312506 | antibiotic_exposure | no | R2 | 0.75 | paper.supp.table | Abx_previous=No |
| SRR27312506 | birth_weight_grams | 3500 | R2 | 0.75 | paper.supp.table | Birth_weight=3.5 |
| SRR27312506 | collection_date | 2018-07/2020-02 | R3 | 0.70 | paper.fulltext.methods | in Calgary, Alberta, from July 2018 to February 2020 |
| SRR27312506 | country | CA | R1 | 0.90 | sample.attr.geo_loc_name | Canada |
| SRR27312506 | delivery_mode | vaginal | R2 | 0.75 | paper.supp.table | Delivery_method=Vaginal |
| SRR27312510 | diet | formula | R2 | 0.80 | paper.supp.41467_2026_74417_MOESM5_ESM.xlsx[ANTIBIO_Metadata!Current_feeding] | Manifest=S00CI.0009; Current_feeding=Formula |
| SRR27312506 | feeding_mode | exclusive_breast | R2 | 0.75 | paper.supp.table | Current_feeding=Breast_Milk |
| SRR27312506 | gestational_age_weeks | 40.0 | R2 | 0.75 | paper.supp.table | Pregnancy_duration=40 |
| SRR27312506 | intervention | antibiotic | R1 | 0.85 | biosample.attribute:chem_administration | chem_administration: antibiotics |
| SRR27312506 | location_locality | Calgary | R3 | 0.70 | paper.fulltext.methods | the ANTIBIO study recruited 47 infants aged <6 months |
| SRR27312506 | location_region | Alberta | R3 | 0.70 | paper.fulltext.methods | evaluated in the ACH-ED, in Calgary, Alberta |
| SRR27312506 | location_site | Alberta Children's Hospital Emergency Department (ACH-ED) | R3 | 0.70 | paper.fulltext.methods | infants aged <6 months evaluated in the ACH-ED |
| SRR27312506 | maternal_antibiotics | no | R2 | 0.75 | paper.supp.table | labour_antibiotics=No |
| SRR27312506 | preterm_status | term | R2 | 0.75 | paper.supp.table | Pregnancy_duration=40 |
| SRR27312506 | sex | female | R2 | 0.75 | paper.supp.table | Sex=F |
| SRR27312506 | subject_id | P42 | R2 | 0.80 | paper.supp.41467_2026_74417_MOESM5_ESM.xlsx[ANTIBIO_Metadata!Patient_ID] | Manifest=S00CI.0084; Patient_ID=P42 |
| SRR27312506 | timepoint_label | Follow_Up | R2 | 0.80 | paper.supp.41467_2026_74417_MOESM5_ESM.xlsx[ANTIBIO_Metadata!Time_point] | Manifest=S00CI.0084; Time_point=Follow_Up |
Sequencing
94 runs over 94 samples · mean 0.60 Gbp per run (median 0.64 Gbp, total 56.87 Gbp; 94 runs with a base count) · layout PAIRED 94 · platform ILLUMINA 94 · models NextSeq 500 (94) · 4% of runs with a Sandpiper profile · first public 2023-12-22
Authors (16)
van Tilburg Bernardes E first · Glatthardt T · Gutierrez MW · Nguyen WNT · Mercer EM · Ramay HR · Thomson CA · Halim TBA · Gopalakrishnan N · MacConnell K · Kalbfleisch K · Patel KD · Corrales-Aguilar E · McCoy KD · Freedman SB · Arrieta MC last
Downloads
PRJNA1055141.csv.gz (3.6 KB) · parquet (75.3 KB) — all 94 samples, every field with route and confidence · PRJNA1055141_determinations.csv.gz (13.7 KB) — 1,529 evidence rows