Infant cystic fibrosis BAL and stool microbiome, Melbourne
96 BAL and stool samples from infants (and a few neonates) with cystic fibrosis in Melbourne, Australia, treated with prophylactic amoxicillin/clavulanate, in a longitudinal cohort study of microbial maturation over the first two years of life. machine-written summary
96 samples · 96 runs · AU · Infant / toddler · 2024 · 2.32 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 576 sample values (age, collection date, country, sex, subject id, timepoint) |
| ✓ Abstract / description | 384 sample values (antibiotic exposure, health condition, health condition detail, location locality) |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
longitudinal
25 of 31 people sampled more than once (90 samples; median 4, up to 6 per person) · follow-up median 10 mo (max 18 mo) · median interval between samples 3 mo (time from age at collection). Schedule stated by the source: “BAL and stool collected repeatedly over first two years of life at 6 distinct timepoints (A-F) per subject” (time origin: birth).
Each row is one person (25 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 83 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 | 96 | 100% | ||||
| country | 96 | 100% | 96 | |||
| health_condition | 96 | 100% | 96 | |||
| subject_id | 96 | 100% | 96 | |||
| age_at_collection_days | 96 | 100% | 96 | |||
| antibiotic_exposure | 96 | 100% | 96 | |||
| collection_date | 96 | 100% | 96 | |||
| detailed_location | 96 | 100% | ||||
| health_condition_detail | 96 | 100% | 96 | |||
| location_locality | 96 | 100% | 96 | |||
| sex | 96 | 100% | 96 | |||
| timepoint_label | 96 | 100% | 96 |
- The longitudinal microbial and metabolic landscape of infant cystic fibrosis: the gut-lung axis. 2024 PMID 38485151 own_data
Archive description
BAL and stool was collected over the first two years of life from infants with cystic fibrosis (CF) in Melbourne, Australia who were treated with ongoing prophylactic amoxicillin/clavulanate to assess microbial maturation over this period. Low biomass BAL samples underwent 16S amplicon sequencing using custom primers for the V1-V2 region (F-27/R-338) and the Illumina MiSeq system. Stool samples underwent Illumina shotgun sequencing via the NovaSeq 6000 system.
How this project entered the registry
Classified as human gut / stool / lower respiratory 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 · “fibrosis BAL and stool microbiome”
- body site study.description · “BAL and stool was collected over”
- body site study.title · “Infant cystic fibrosis BAL and stool microbiome”
- body site study.description · “BAL and stool was”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Infant cystic fibrosis BAL”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN38813636 | age_at_collection_days | 392 | R1 | 0.75 | biosample_attr | host_age=392 (days; U2_unique_admissible_unit) |
| SAMN38813636 | antibiotic_exposure | yes | R4 | 0.50 | study.description | treated with ongoing prophylactic amoxicillin/clavulanate |
| SAMN38813636 | collection_date | 2021-04-23 | R1 | 0.85 | biosample.attribute:collection_date | 2021-04-23 |
| SAMN38813636 | country | AU | R1 | 0.90 | biosample_attr | Australia: Melbourne |
| SAMN38813636 | health_condition | other_disease | R4 | 0.50 | paper.abstract | 39 infants with cystic fibrosis between 0 and 24 months |
| SAMN38813636 | health_condition_detail | cystic fibrosis | R4 | 0.50 | paper.abstract | 39 infants with cystic fibrosis between 0 and 24 months |
| SAMN38813636 | location_locality | Melbourne | R4 | 0.45 | ena.study_description | infants with cystic fibrosis (CF) in Melbourne |
| SAMN38813636 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMN38813636 | subject_id | CFGLA1 | R1 | 0.85 | biosample_attr | CFGLA1 |
| SAMN38813636 | timepoint_label | A | R1 | 0.70 | sample.name_rule:library_name | CFGLA1_Stool_A_WGS |
Sequencing
96 runs over 96 samples · mean 2.62 Gbp per run (median 2.32 Gbp, total 251.18 Gbp; 96 runs with a base count) · layout PAIRED 96 · platform ILLUMINA 96 · models Illumina NovaSeq 6000 (96) · 86% of runs with a Sandpiper profile · first public 2024-05-24 – 2024-06-30
Authors (0)
No author record.
Downloads
PRJNA978345.csv.gz (4.1 KB) · parquet (75.6 KB) — all 96 samples, every field with route and confidence · PRJNA978345_determinations.csv.gz (7.0 KB) — 960 evidence rows