Preterm infant oral feeding and gut/oral microbiome, San Diego
135 stool, saliva, and milk samples from preterm infants (<34 weeks gestational age) and mothers in San Diego, USA, examining how feeding route affects microbiome and metabolome across 4 longitudinal timepoints; longitudinal cohort design. machine-written summary
135 samples · 193 runs · US · Infant / toddler · 2024 · 0.14 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,620 sample values (antibiotic exposure, birth weight grams, collection date, country, delivery mode, family id, family role, feeding mode) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 174 sample values (age, location locality) · PMC12055563 |
| ○ 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 |
antibiotic exposure: two sequence archives disagree for 100 samples (e.g. no vs yes) — withheld.
The sources disagree on 100 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (40 of 100)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN40407659 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407660 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407661 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407662 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407663 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407664 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407665 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407666 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407667 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407668 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407669 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407670 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407671 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407672 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407673 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407674 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407675 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407676 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407677 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407678 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407679 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407680 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407681 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407682 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407683 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407684 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407685 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407686 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407687 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407688 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407689 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407690 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407691 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407692 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407693 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407694 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407695 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407696 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407697 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN40407698 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
longitudinalmother–infanttwins
11 of 11 people sampled more than once (39 samples; median 4, up to 4 per person) · follow-up median 2 mo (max 2 mo) · median interval between samples 21 d (time from age at collection). Schedule stated by the source: “Weekly samples collected throughout NICU course; 4 longitudinal timepoints selected (2 pre- and 2 post-oral feeding initiation)”.
Each row is one person (11 shown); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).
11 maternal-infant dyads; twin_pair attribute shows 2 twin pairs among the 11 infants · 2 families with 4 sampled people, 2 twin sets.
twin · 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: 2 families. 11 people in the project overall.
Families (2)
| family | members | samples |
|---|---|---|
| P4 | twin×2 | SAMN40407682 · SAMN40407683 · SAMN40407684 · SAMN40407685 · SAMN40407686 · SAMN40407687 · SAMN40407688 · SAMN40407689 · SAMN40407690 · SAMN40407691 · SAMN40407692 · SAMN40407693 |
| P9 | twin×2 | SAMN40407768 · SAMN40407769 · SAMN40407770 · SAMN40407771 · SAMN40407772 · SAMN40407773 · SAMN40407774 · SAMN40407775 · SAMN40407776 · SAMN40407777 · SAMN40407778 · SAMN40407779 |
Genera, mean relative abundance over 35 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 | 83 | 61% | ||||
| country | 135 | 100% | 135 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 135 | 100% | 135 | |||
| birth_weight_grams | 135 | 100% | 135 | |||
| collection_date | 135 | 100% | 135 | |||
| delivery_mode | 135 | 100% | 135 | |||
| detailed_location | 135 | 100% | ||||
| feeding_mode | 135 | 100% | 135 | |||
| gestational_age_weeks | 135 | 100% | 135 | |||
| location_locality | 135 | 100% | 135 | |||
| maternal_antibiotics | 135 | 100% | 135 | |||
| preterm_status | 135 | 100% | 135 | |||
| sex | 135 | 100% | 135 | |||
| timepoint_label | 135 | 100% | 135 | |||
| family_id | 50 | 37% | 50 | |||
| family_role | 50 | 37% | 50 | |||
| age_at_collection_days | 39 | 29% | 39 | |||
| antibiotic_exposure | 35 | 26% | 35 |
- The impact of breastfeeding on the preterm infant's microbiome and metabolome: a pilot study. PMID 39138352 PMC12055563 curated
Archive description
The purpose of this study is to determine how the route of a preterm infant's feeding impacts their oral and gut microbiome and metabolome. This study analyzed stool, saliva, and milk samples collected from a cohort of preterm infants enrolled in the MAP (Microbiome, Atopic disease, and Prematurity) Study. This study recruited babies <34 weeks gestational age and collected weekly samples throughout their NICU course. A sub cohort of 11 maternal-infant dyads that met criteria for orogastric/nasogastric feeds transitioning to a mix of milk from the bottle and breastfeeding were selected. The microbiome and metabolome of the samples were analyzed from 4 longitudinal sample time points (2 prior to initiating oral feeds and 2 after).
How this project entered the registry
Classified as human oral cavity / gut / stool / human milk shotgun DNA metagenome of infant / toddler and neonate 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 · “The Impact of Oral Feedings on the”
- body site study.description · “feeding impacts their oral and gut microbiome”
- body site study.description · “their oral and gut microbiome and metabolome.”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.description · “stool, saliva, and milk samples collected from”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “on the Preterm Infant Microbiome and Metabolome”
- life stage study.title · “Feedings on the Preterm Infant Microbiome and”
- life stage study.description · “route of a preterm infant's feeding impacts”
- life stage study.description · “cohort of 11 maternal -infant dyads that”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN40407658 | age_at_collection_days | 14 | R3 | 0.70 | paper.fulltext.results | timepoint 1 was collected at 2 weeks of life |
| SAMN40407656 | antibiotic_exposure | yes | R1 | 0.85 | biosample_attr | yes |
| SAMN40407656 | birth_weight_grams | 575 | R1 | 0.90 | biosample_attr | 575 |
| SAMN40407656 | collection_date | 2020 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2020 |
| SAMN40407656 | country | US | R1 | 0.90 | biosample_attr | USA:CA,San Diego |
| SAMN40407656 | delivery_mode | c_section | R1 | 0.90 | biosample_attr | cesarian |
| SAMN40407682 | family_id | P4 | R1 | 0.85 | biosample.attribute:parent | P4 |
| SAMN40407682 | family_role | twin | R1 | 0.85 | biosample.attribute:twin_pair | Pair 1 |
| SAMN40407656 | feeding_mode | exclusive_breast | R1 | 0.85 | biosample_attr | Breastmilk |
| SAMN40407656 | gestational_age_weeks | 28.3 | R1 | 0.90 | biosample_attr | 28.3 |
| SAMN40407656 | location_locality | San Diego | R3 | 0.70 | paper.fulltext.methods | two level III NICUs at University of California San Diego |
| SAMN40407656 | maternal_antibiotics | yes | R1 | 0.85 | biosample_attr | yes |
| SAMN40407656 | preterm_status | preterm | R1 | 0.85 | biosample_attr | 28.3 |
| SAMN40407656 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN40407656 | subject_id | J13 | R1 | 0.85 | biosample_attr | J13 |
| SAMN40407656 | timepoint_label | 1 | R1 | 0.80 | biosample_attr | 1 |
Sequencing
193 runs over 135 samples · mean 0.72 Gbp per run (median 0.14 Gbp, total 139.85 Gbp; 193 runs with a base count) · layout PAIRED 193 · platform ILLUMINA 193 · models Illumina NovaSeq 6000 (193) · 47% of runs with a Sandpiper profile · first public 2024-03-24
Authors (13)
Schulkers Escalante K first · Bai-Tong SS · Allard SM · Ecklu-Mensah G · Sanchez C · Song SJ · Gilbert J · Bode L · Dorrestein P · Knight R · Gonzalez DJ · Leibel SA · Leibel SL last
Downloads
PRJNA1086674.csv.gz (4.8 KB) · parquet (76.8 KB) — all 135 samples, every field with route and confidence · PRJNA1086674_determinations.csv.gz (11.3 KB) — 1,794 evidence rows