Breastmilk microbiome in preterm infants, Virginia, USA
Longitudinal cohort of 156 samples from 36 preterm infants (mean gestational age 29 weeks) and their maternal/donor breastmilk, collected in Virginia, USA, examining microbiome dynamics with maternal antibiotic exposure as an intervention factor. machine-written summary
156 samples · 156 runs · US · Infant / toddler · 2023 · 2.26 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 610 sample values (country, family id, family role, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| ✓ Supplementary tables | 74 sample values (subject id) |
| – 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 |
Other administered intervention (see intervention_detail) · population preterm_nicu · Observational study of maternal/donor breastmilk and infant microbiome; no assigned intervention
“serial breastmilk samples collected approximately 2 weeks apart” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal — not resolvedmother–infant
27 of 37 people sampled more than once (65 samples; median 2, up to 4 per person). Schedule stated by the source: “breastmilk samples collected approximately 2 weeks apart from each other” (time origin: birth).
36 preterm infant stool series each paired with breastmilk (sample_pair_id); milk may be maternal or donor milk · 36 families with 72 sampled people.
child · 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 36 families (one per family structure, then more). 37 people in the project overall.
Families (25 of 36)
Genera, mean relative abundance over 71 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 | 0 | 0% | ||||
| country | 156 | 100% | 156 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 156 | 100% | 82 | 74 | ||
| timepoint_label | 150 | 96% | 150 | |||
| family_id | 148 | 95% | 148 | |||
| family_role | 74 | 47% | 74 |
Archive description
A total of 36 infants were included in the study, with 74 serial breastmilk samples collected approximately 2 weeks apart from each other. The mean infant gestational age was 29 weeks (range 23-39 weeks). The mean maternal age was 33 years ( range 21-42 years). 11/36 (31%) of infants were born by vaginal delivery. 22/36 (61%) of mothers received antibiotics during delivery. 11/36 (31%) of mothers received antibiotics prenatally.
How this project entered the registry
Classified as human human milk / gut / stool / vaginal / urogenital 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 · “maternal and donor breastmilk and infants”
- body site study.description · “with 74 serial breastmilk samples collected approximately”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.description · “were born by vaginal delivery. 22/36 (61%)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “donor breastmilk and infants”
- life stage study.title · “microbiome dynamics among maternal and donor breastmilk”
- life stage study.description · “weeks). The mean maternal age was 33”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN31893194 | country | US | R1 | 0.90 | biosample_attr | USA: Virginia |
| SAMN31893194 | family_id | 15 | R1 | 0.85 | biosample.attribute:sample_pair_id | TITLE 15a-m; sample_pair_id 15; sample_type Breastmilk |
| SAMN31893249 | family_role | child | R1 | 0.85 | biosample.attribute:sample_type | TITLE 16a-f; sample_pair_id 16; sample_type Fecal |
| SAMN31893214 | subject_id | NegativeControlS12 | R1 | 0.85 | biosample.attribute:sample_pair_id | sample_pair_id: NegativeControlS12 |
| SAMN31893194 | subject_id | 15-m | R2 | 0.80 | archive | |
| SAMN31893194 | timepoint_label | a | R1 | 0.80 | biosample_attr | a |
| SAMN31893214 | timepoint_label | 01-m | R1 | 0.70 | sample.title | negative-01-m-S12 |
Sequencing
156 runs over 156 samples · mean 3.09 Gbp per run (median 2.26 Gbp, total 481.46 Gbp; 156 runs with a base count) · layout SINGLE 156 · platform ILLUMINA 156 · models NextSeq 500 (156) · 92% of runs with a Sandpiper profile · first public 2023-12-02
Authors (0)
No author record.
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA906107.csv.gz (5.6 KB) · parquet (76.5 KB) — all 156 samples, every field with route and confidence · PRJNA906107_determinations.csv.gz (6.6 KB) — 684 evidence rows