Infant and maternal gut microbiomes after antibiotics, Brisbane
A longitudinal cohort study of 50 gut microbiome samples from infants and mothers in Brisbane, Australia, examining the effect of maternal antibiotics and delivery mode at 6 weeks postpartum. machine-written summary
50 samples · 50 runs · AU · Infant / toddler · 2024 · 4.18 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 225 sample values (collection date, country, family id, family role, sex) |
| ✓ Abstract / description | 75 sample values (age, location region) |
| ✓ Full text | 50 sample values (location site) · PMC11316550 |
| ○ 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 · share metadata |
| – 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 observational_with_procedure · population pregnancy_postpartum · Maternal intrapartum/prophylactic antibiotics and caesarean vs vaginal delivery, cohort comparison
“caesarean section with routine maternal prophylactic antibiotics” — abstract:38995243 (study level; per-sample arms are in the intervention column below)
mother–infant
25 mother–infant dyads sampled at 6 weeks postpartum (library names MotherX/InfantX share letter X) · 25 families with 50 sampled people (25 with a parent and a child).
motherchild · 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 25 families (one per family structure, then more).
Families (25)
Genera, mean relative abundance over 21 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 | 25 | 50% | ||||
| country | 50 | 100% | 50 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| collection_date | 50 | 100% | 50 | |||
| detailed_location | 50 | 100% | ||||
| family_id | 50 | 100% | 50 | |||
| family_role | 50 | 100% | 50 | |||
| location_region | 50 | 100% | 50 | |||
| location_site | 50 | 100% | 50 | |||
| age_at_collection_days | 25 | 50% | 25 | |||
| sex | 25 | 50% | 25 |
- Delivery mode is a larger determinant of infant gut microbiome composition at 6 weeks than exposure to peripartum antibiotics. PMID 38995243 PMC11316550 curated
Archive description
This study aimed to evaluate the effect of maternal antibiotics and delivery mode on the gut microbiome of infants and their mothers at 6 weeks postpartum.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Infant and maternal gut microbiomes”
- body site study.description · “mode on the gut microbiome of infants”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Infant and maternal gut”
- life stage study.title · “Infant and maternal gut microbiomes”
- life stage study.description · “the effect of maternal antibiotics and delivery”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN39956494 | age_at_collection_days | 42 | R4 | 0.40 | study.description | at 6 weeks postpartum |
| SAMN39956494 | collection_date | 2019 | R1 | 0.85 | biosample.attribute:collection_date | 2019 |
| SAMN39956494 | country | AU | R1 | 0.90 | biosample_attr | Australia: Brisbane |
| SAMN39956494 | family_id | B | R1 | 0.70 | sample.name_rule:library_name | InfantB |
| SAMN39956494 | family_role | child | R1 | 0.70 | sample.name_rule:library_name | InfantB |
| SAMN39956494 | location_region | Queensland | R4 | 0.40 | paper.abstract | Queensland Family Cohort Study |
| SAMN39956494 | location_site | Queensland Family Cohort (QFC) pilot study | R3 | 0.70 | paper.fulltext.methods | selected from the Queensland Family Cohort |
| SAMN39956519 | sex | female | R1 | 0.70 | sample.name_rule:sample_title | maternal_stool |
Sequencing
50 runs over 50 samples · mean 4.84 Gbp per run (median 4.18 Gbp, total 242.13 Gbp; 50 runs with a base count) · layout PAIRED 50 · platform ILLUMINA 50 · models Illumina NovaSeq 6000 (50) · 84% of runs with a Sandpiper profile · first public 2024-02-24 – 2024-03-19
Authors (6)
Leech SM first · Borg DJ · Rae KM · Kumar S · Clifton VL · Dekker Nitert M last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA1076911.csv.gz (2.5 KB) · parquet (72.4 KB) — all 50 samples, every field with route and confidence · PRJNA1076911_determinations.csv.gz (3.4 KB) — 350 evidence rows