Long. gut, skin, & mouth microbiome in preemies, Pittsburgh
Cohort longitudinal study of 140 samples from premature infants' mouth, skin, and gut microbiomes, collected at Magee-Womens Hospital of UPMC, Pittsburgh, USA, over the first two months of life. machine-written summary
140 samples · 146 runs · US · Infant / toddler · 2022 · 1.42 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 840 sample values (age, country, health condition, health condition detail, subject id, timepoint) |
| ✓ Abstract / description | 46 sample values (preterm status) |
| ○ Full text | read; no usable statement or table · PMC9979413 |
| ○ 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 |
longitudinal
15 of 16 people sampled more than once (45 samples; median 3, up to 3 per person) · follow-up median 42 d (max 48 d) · median interval between samples 20 d (time from age at collection). Schedule stated by the source: “Repeated sampling of mouth, skin, and gut at multiple day-of-life (DOL) timepoints per infant over the first two months of life; 27 distinct timepoint labels across 140 samples from 16 infants.”.
Each row is one person (15 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 39 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 | 140 | 100% | ||||
| country | 140 | 100% | 140 | |||
| health_condition | 140 | 100% | 140 | |||
| subject_id | 140 | 100% | 140 | |||
| age_at_collection_days | 140 | 100% | 140 | |||
| health_condition_detail | 140 | 100% | 140 | |||
| timepoint_label | 140 | 100% | 140 | |||
| preterm_status | 46 | 33% | 46 |
- Using strain-resolved analysis to identify contamination in metagenomics data. 2023 PMID 36864482 PMC9979413 cites_accession
Archive description
Simultaneous longitudinal metagenomic sequencing of the mouth, skin, and gut microbiomes of premature infants during the first two months of life
How this project entered the registry
Classified as human gut / stool / skin / oral cavity 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 study.title · “mouth, skin, and gut”
- body site study.description · “mouth, skin, and gut microbiomes of premature”
- body site study.title · “premature infant mouth, skin , and gut”
- body site study.description · “of the mouth, skin , and gut”
- body site run.scientific_name · “human oral metagenome”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “microbiota of premature infant mouth, skin, and”
- life stage study.title · “the microbiota of premature infant mouth, skin,”
- life stage study.description · “gut microbiomes of premature infants during the”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN31253590 | age_at_collection_days | 13 | R1 | 0.85 | sample.title | DOL 13 |
| SAMN31253590 | country | US | R1 | 0.90 | biosample_attr | USA: Pittsburgh, Magee-Womens Hospital of UPMC |
| SAMN31253590 | health_condition | preterm_nicu | R1 | 0.70 | sample.name_rule:title | Infant Mouth #11 DOL 13 |
| SAMN31253590 | health_condition_detail | Infant | R1 | 0.70 | sample.name_rule:title | Infant Mouth #11 DOL 13 |
| SAMN31253623 | preterm_status | preterm | R4 | 0.40 | paper.abstract | microbiota of premature infant |
| SAMN31253590 | subject_id | 11 | R1 | 0.70 | sample.title | Infant Mouth #11 DOL 13 |
| SAMN31253590 | timepoint_label | DOL 13 | R1 | 0.70 | sample.title | Infant Mouth #11 DOL 13 |
Sequencing
146 runs over 140 samples · mean 2.77 Gbp per run (median 1.42 Gbp, total 404.35 Gbp; 146 runs with a base count) · layout PAIRED 146 · platform ILLUMINA 146 · models Illumina NovaSeq 6000 (146) · 82% of runs with a Sandpiper profile · first public 2022-10-15 – 2022-10-16
Authors (0)
No author record.
Downloads
PRJNA889771.csv.gz (5.0 KB) · parquet (75.9 KB) — all 140 samples, every field with route and confidence · PRJNA889771_determinations.csv.gz (9.5 KB) — 886 evidence rows