Neonatal gut microbiome in BCG trial, Australia
393 stool samples from neonates (days 5–7 of life) in the MIS BAIR randomised trial in Australia, investigating gut microbiome composition and its relation to BCG vaccination, antibiotic resistance, and allergy/vaccine responses. machine-written summary
393 samples · 393 runs · AU · Neonate · 2023 · 1.49 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,178 sample values (age, collection date, country) |
| ✓ Abstract / description | 1,179 sample values (health condition, location locality, subject id) |
| ○ Full text | read; no usable statement or table · PMC10313230, PMC12993559 |
| ○ 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 |
Genera, mean relative abundance over 343 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 | 392 | 100% | ||||
| country | 393 | 100% | 393 | |||
| health_condition | 393 | 100% | 393 | |||
| subject_id | 393 | 100% | 393 | |||
| collection_date | 393 | 100% | 393 | |||
| detailed_location | 393 | 100% | ||||
| location_locality | 393 | 100% | 393 | |||
| age_at_collection_days | 392 | 100% | 392 |
- Metagenomics analysis of the neonatal intestinal resistome. PMID 37397142 PMC10313230 curated
- The association between the composition of the early-life intestinal microbiome and eczema in the first year of life. PMID 41853385 PMC12993559 curated
Archive description
Metagenomic shotgun sequencing was done on stool samples from a subset of 393 participants from The Melbourne Infant Study: BCG for Allergy and Infection Reduction (MIS BAIR). In this randomised trial, 1272 healthy infants were recruited antenatally to investigate whether Bacille Calmette-Guérin (BCG) immunisation given in the first 10 days of life protects against childhood infection, allergy and asthma. Stool samples were collected 5 to 7 days after birth and stool microbiome composition was investigated in different context (e.g. abundance of genetic antibiotic resistance, influence of BCG on the composition, association with vaccine responses, association with eczema prevalence and allergies, etc.).
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of neonate by opus_adjudicated with confidence 0.85. Assay shotgun_dna.
- host study.description · “1272 healthy infants were recruited antenatally”
- body site study.description · “stool samples”
- life stage study.description · “Stool samples were collected 5 to 7 days after birth”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA112148808 | age_at_collection_days | 7.0 | R1 | 0.70 | sample.name_rule:title | 3126D7_S1 |
| SAMEA112148808 | collection_date | 2018 | R1 | 0.85 | biosample.attribute:collection_date | 2018 |
| SAMEA112148808 | country | AU | R1 | 0.90 | biosample_attr | Australia |
| SAMEA112148808 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | healthy, term-born neonates who did not receive antibiotics |
| SAMEA112148808 | location_locality | Melbourne | R4 | 0.45 | ena.study_description | The Melbourne Infant Study: BCG for Allergy |
| SAMEA112148808 | subject_id | SAMEA112148808 | R4 | 0.60 | design.one_sample_per_subject:description | Metagenomic shotgun sequencing was done on stool samples from a subset of 393 participants |
Sequencing
393 runs over 393 samples · mean 1.58 Gbp per run (median 1.49 Gbp, total 619.15 Gbp; 393 runs with a base count) · layout PAIRED 393 · platform ILLUMINA 393 · models NextSeq 550 (393) · 87% of runs with a Sandpiper profile · first public 2023-01-26
Authors (8)
Leo S first · Cetiner OF · Pittet LF · Messina NL · Jakob W · Falquet L · Curtis N · Zimmermann P last
Downloads
PRJEB55714.csv.gz (11.6 KB) · parquet (89.4 KB) — all 393 samples, every field with route and confidence · PRJEB55714_determinations.csv.gz (16.8 KB) — 2,357 evidence rows