Antibiotic exposure & vaccine immune response in infants
Longitudinal cohort of 459 gut microbiome samples from healthy neonates and infants in Adelaide, Australia, studying immune responses to routine vaccinations in relation to antibiotic exposure. machine-written summary
459 samples · 459 runs · AU · Infant / toddler · 2025 · 4.85 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,836 sample values (age, collection date, country, feeding mode, sex, subject id, timepoint) |
| ✓ Abstract / description | 459 sample values (health condition) |
| ✓ Full text | 2,088 sample values (collection date, delivery mode, location locality, location site, preterm status) · PMC12058517 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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
Vaccination as the study intervention design observational_with_procedure · population healthy_control · Routine infant vaccination (PCV13, 6-in-1 Infanrix Hexa); observed antibiotic exposure
“immune responses to vaccination” — abstract:40175554 (study level; per-sample arms are in the intervention column below)
longitudinal
187 of 224 people sampled more than once (422 samples; median 2, up to 3 per person) · follow-up median 38 d (max 52 d) · median interval between samples 38 d (time from age at collection). Schedule stated by the source: “Neonatal timepoint and Week 6 timepoint per infant” (time origin: birth); stated follow-up 42 d.
Each row is one person (36 shown of 187); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 412 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 | 459 | 100% | ||||
| country | 459 | 100% | 459 | |||
| health_condition | 459 | 100% | 459 | |||
| subject_id | 459 | 100% | 459 | |||
| age_at_collection_days | 459 | 100% | 459 | |||
| collection_date | 459 | 100% | 207 | 252 | ||
| delivery_mode | 459 | 100% | 459 | |||
| detailed_location | 459 | 100% | ||||
| location_locality | 459 | 100% | 459 | |||
| location_site | 459 | 100% | 459 | |||
| preterm_status | 459 | 100% | 459 | |||
| timepoint_label | 459 | 100% | 459 | |||
| feeding_mode | 456 | 99% | 456 | |||
| sex | 337 | 73% | 337 |
- Bifidobacteria support optimal infant vaccine responses. PMID 40175554 PMC12058517 curated
Archive description
The Antibiotics and Immune Responses (AIR) Clinical study will examine the effect of antibiotic exposure on immune responses to routine vaccinations given during the first six months of life. The study will consent participants shortly after birth with the aim of achieving enrolment of approximately 200 infants, with or without intrapartum/neonatal antibiotic exposure).
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.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “of approximately 200 infants , with or”
- life stage study.description · “or without intrapartum/ neonatal antibiotic exposure).”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN25982051 | age_at_collection_days | 4 | R1 | 0.90 | biosample_attr | 4 |
| SAMN25982051 | collection_date | 2018-01-01 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2018-01-01 |
| SAMN34063078 | collection_date | 2017-04/2021-03 | R3 | 0.70 | paper.fulltext.methods | Adelaide, Australia, between April 2017 and March 2021 |
| SAMN25982051 | country | AU | R1 | 0.90 | biosample_attr | Australia: Adelaide |
| SAMN25982051 | delivery_mode | vaginal | R3 | 0.80 | paper.fulltext.abstract | healthy, vaginally born, term infants from birth to 15 months |
| SAMN25982051 | feeding_mode | exclusive_breast | R1 | 0.85 | biosample_attr | Exclusive |
| SAMN25982051 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | prospectively followed 191 healthy, vaginally born, term infants |
| SAMN25982051 | location_locality | Adelaide | R3 | 0.70 | paper.fulltext.methods | Women’s and Children’s Hospital Adelaide, Australia, between April 2017 |
| SAMN25982051 | location_site | Women's and Children's Hospital | R3 | 0.70 | paper.fulltext.methods | Women’s and Children’s Hospital Adelaide, Australia, between April 2017 |
| SAMN25982051 | preterm_status | term | R3 | 0.80 | paper.fulltext.abstract | healthy, vaginally born, term infants |
| SAMN25982051 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN25982051 | subject_id | WCH001 | R1 | 0.85 | biosample_attr | WCH001 |
| SAMN46715476 | subject_id | WCH200 | R1 | 0.70 | sample.name_rule:library_name | WCH200_6W |
| SAMN25982051 | timepoint_label | neonatal | R1 | 0.70 | sample.name_rule:title | WCH001_Neonatal_faecal |
| SAMN34063078 | timepoint_label | Neonatal | R1 | 0.80 | biosample_attr | Neonatal |
| SAMN46715476 | timepoint_label | 6W | R1 | 0.70 | run.library_name | WCH200_6W |
| SAMN46715477 | timepoint_label | neonatal | R1 | 0.70 | sample.name_rule:library_name | WCH200_B |
Sequencing
459 runs over 459 samples · mean 5.48 Gbp per run (median 4.85 Gbp, total 2,514.57 Gbp; 459 runs with a base count) · layout PAIRED 459 · platform ILLUMINA 459 · models Illumina NovaSeq 6000 (459) · 90% of runs with a Sandpiper profile · first public 2025-01-21 – 2025-02-15
Authors (24)
Ryan FJ first · Clarke M · Lynn MA · Benson SC · McAlister S · Giles LC · Choo JM · Rossouw C · Ng YY · Semchenko EA · Richard A · Leong LEX · Taylor SL · Blake SJ · Mugabushaka JI · Walker M · Wesselingh SL · Licciardi PV · Seib KL · Tumes DJ · Richmond P · Rogers GB · Marshall HS · Lynn DJ last
Downloads
PRJNA807448.csv.gz (15.2 KB) · parquet (90.4 KB) — all 459 samples, every field with route and confidence · PRJNA807448_determinations.csv.gz (30.7 KB) — 5,383 evidence rows