Preterm infant gut microbiota over time (BAMBI cohort)
Longitudinal cohort study characterising the gut microbiota of preterm infants over time, comprising 1392 samples; no location, health condition, or intervention details are specified in the sources. machine-written summary
1,486 samples · 1,908 runs · Infant / toddler · 2018 · 64.8 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,315 sample values (subject id, timepoint) |
| ✓ Abstract / description | 4,364 sample values (health condition, health condition detail, preterm status) |
| ○ Full text | read; no usable statement or table · PMC10234813, PMC12323770, PMC12354744, PMC7044117, PMC7453906, PMC7712117 |
| ✓ Supplementary tables | 2,027 sample values (age, antibiotic exposure, diet, intervention, sex, timepoint) |
| – 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 — not resolved
Schedule stated by the source: “repeated stool sampling of preterm infants over time (exact timepoints not specified)” (time origin: birth).
Genera, mean relative abundance over 121 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 | 1,481 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 1,486 | 100% | 1,486 | |||
| subject_id | 1,297 | 87% | 1,297 | |||
| health_condition_detail | 1,486 | 100% | 1,486 | |||
| preterm_status | 1,392 | 94% | 1,392 | |||
| timepoint_label | 356 | 24% | 18 | 338 | ||
| age_at_collection_days | 338 | 23% | 338 | |||
| antibiotic_exposure | 338 | 23% | 338 | |||
| intervention | 338 | 23% | 338 | |||
| sex | 338 | 23% | 338 | |||
| diet | 337 | 23% | 337 |
Archive description
Study to characterise the microbiota of preterm infants over time These data are part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
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 · “microbiota of preterm infants over time These”
- life stage study.description · “the microbiota of preterm infants over time”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104208808 | age_at_collection_days | 11 | R2 | 0.85 | paper.supp.mmc3.xlsx[recoded_metadata 28.07.2020!daysfrombirth] | 11 |
| SAMEA104208808 | antibiotic_exposure | no | R2 | 0.85 | paper.supp.mmc3.xlsx[recoded_metadata 28.07.2020!antibiotics] | n |
| SAMEA104208808 | diet | other_diet | R2 | 0.85 | paper.supp.mmc3.xlsx[recoded_metadata 28.07.2020!diettype] | BM_DBM |
| SAMEA104208807 | health_condition | preterm_nicu | R4 | 0.50 | archive.study_description | Study to characterise the microbiota of preterm infants over time |
| SAMEA104208807 | health_condition_detail | preterm infants | R4 | 0.50 | archive.study_description | Study to characterise the microbiota of preterm infants over time |
| SAMEA104208808 | intervention | no_intervention | R2 | 0.85 | paper.supp.mmc3.xlsx[recoded_metadata 28.07.2020!Treatment] | Control |
| SAMEA104230826 | preterm_status | preterm | R4 | 0.50 | study.description | microbiota of preterm infants over time |
| SAMEA104208808 | sex | female | R2 | 0.85 | paper.supp.mmc3.xlsx[recoded_metadata 28.07.2020!sex] | F |
| SAMEA104230826 | subject_id | 3662STDY7058113 | R1 | 0.85 | biosample_attr | 3662STDY7058113 |
| SAMEA6262402 | timepoint_label | D8 | R1 | 0.70 | run.library_name | DN589255R:D8 |
| SAMEA104208808 | timepoint_label | 10_29 | R2 | 0.85 | paper.supp.mmc3.xlsx[recoded_metadata 28.07.2020!time_point] | 10_29 |
Sequencing
1,908 runs over 1,486 samples · mean 0.18 Gbp per run (median 65.8 Mbp, total 335.14 Gbp; 1,908 runs with a base count) · layout PAIRED 1,908 · platform ILLUMINA 1,908 · models Illumina MiSeq (1,776), HiSeq X Ten (132) · 6% of runs with a Sandpiper profile · first public 2018-07-24 – 2021-06-22
Authors (0)
No author record.
Downloads
PRJEB9403.csv.gz (37.2 KB) · parquet (137.4 KB) — all 1,486 samples, every field with route and confidence · PRJEB9403_determinations.csv.gz (43.1 KB) — 7,706 evidence rows