Preterm neonate mouth, skin, gut microbiome, Pittsburgh
Case series of 45 samples from the mouth, skin, and gut microbiomes of premature infants (37 preterm NICU) at Magee-Womens Hospital of UPMC, Pittsburgh, USA, sampled longitudinally during the first month of life. machine-written summary
45 samples · 45 runs · US · Infant / toddler · 2016 · 3.10 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 180 sample values (age, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10175488, PMC10269646, PMC10769871, PMC10904392, PMC11019788, PMC11170968, PMC11322291, PMC12677589, PMC5378178, PMC9437082, PMC9445129 |
| ✓ Supplementary tables | 333 sample values (antibiotic exposure, birth weight grams, delivery mode, diet, feeding mode, gestational age weeks, health condition, nec status) |
| ✓ External resources | 43 sample values (antibiotic exposure, health condition detail) · from curatedMetagenomicData 3 (cMD 3), Meta2DB (LLNL) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
2 of 2 people sampled more than once (37 samples; median 18, up to 20 per person) · follow-up median 20 d (max 23 d) · median interval between samples 1 d (time from age at collection). Schedule stated by the source: “sampled longitudinally during the first month of life” (time origin: birth); stated follow-up 30 d.
Each row is one person (2 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 37 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 | 45 | 100% | ||||
| country | 45 | 100% | 45 | |||
| health_condition | 37 | 82% | 37 | |||
| subject_id | 45 | 100% | 45 | |||
| age_at_collection_days | 45 | 100% | 45 | |||
| timepoint_label | 45 | 100% | 45 | |||
| antibiotic_exposure | 43 | 96% | 43 | |||
| birth_weight_grams | 37 | 82% | 37 | |||
| delivery_mode | 37 | 82% | 37 | |||
| diet | 37 | 82% | 37 | |||
| feeding_mode | 37 | 82% | 37 | |||
| gestational_age_weeks | 37 | 82% | 37 | |||
| health_condition_detail | 37 | 82% | 37 | |||
| nec_status | 37 | 82% | 37 | |||
| preterm_status | 37 | 82% | 37 |
- Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. PMID 28073918 PMC5378178 curated
- A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID 36050292 PMC9437082 curated
- Metabolic model of necrotizing enterocolitis in the premature newborn gut resulting from enteric dysbiosis. PMID 36081629 PMC9445129 curated
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488 curated
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646 curated
6 more
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871
- A metagenomic catalog of the early-life human gut virome. PMID 38424077 PMC10904392
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788
- Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life. PMID 38882494 PMC11170968
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291
- The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset. PMID 41025564 PMC12677589
Archive description
Simultaneous longitudinal metagenomic sequencing of the mouth, skin, and gut microbiomes of two premature infants during the first month 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 two”
- 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 · “microbiomes of two premature infants during the”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN05301464 | age_at_collection_days | 6 | R1 | 0.85 | sample.title | DOL 6 |
| SAMN05301464 | antibiotic_exposure | yes | R2 | 0.70 | external.meta2db source | antibiotics: TRUE |
| SAMN05301466 | antibiotic_exposure | yes | R2 | 0.75 | paper.supp.table | antibiotic_treatment=1 |
| SAMN05301466 | birth_weight_grams | 2847 | R2 | 0.75 | paper.supp.table | Birth weight (gram)=2847 |
| SAMN05301464 | country | US | R1 | 0.90 | biosample_attr | USA: Pittsburgh, Magee-Womens Hospital of UPMC |
| SAMN05301466 | delivery_mode | vaginal | R2 | 0.75 | paper.supp.table | delivery_mode=vaginal |
| SAMN05301466 | diet | formula | R2 | 0.85 | paper.supp.Table_3.XLSX[mapping_global.txt!feeding_practice] | SRR3726349 | feeding_practice: formula |
| SAMN05301466 | feeding_mode | formula | R2 | 0.75 | paper.supp.table | Feeding pattern=formula |
| SAMN05301466 | gestational_age_weeks | 28.0 | R2 | 0.75 | paper.supp.table | gestational_age_week=28 |
| SAMN05301466 | health_condition | preterm_nicu | R2 | 0.70 | paper.supp.table | Pre_term_nec=Preterm |
| SAMN05301466 | health_condition_detail | Preterm Birth | R2 | 0.75 | external.cmd source | disease: Preterm Birth |
| SAMN05301466 | nec_status | no | R2 | 0.75 | paper.supp.table | NEC=No |
| SAMN05301466 | preterm_status | preterm | R2 | 0.75 | paper.supp.table | Pre_term_nec=Preterm |
| SAMN05301464 | subject_id | 1 | R1 | 0.70 | sample.title | Infant 1 DOL 6 skin |
| SAMN05301464 | timepoint_label | DOL 6 | R1 | 0.70 | sample.title | Infant 1 DOL 6 skin |
Sequencing
45 runs over 45 samples · mean 3.00 Gbp per run (median 3.10 Gbp, total 134.78 Gbp; 45 runs with a base count) · layout PAIRED 45 · platform ILLUMINA 45 · models Illumina HiSeq 2500 (45) · 100% of runs with a Sandpiper profile · first public 2016-09-02
Authors (108)
Olm MR first · Brown CT · Brooks B · Firek B · Baker R · Burstein D · Soenjoyo K · Thomas BC · Morowitz M · Banfield JF last · Tisza MJ first · Buck CB last · Zeng S first · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Stanton C · Wang S last · Casaburi G first · Wei J · Kazi S · Liu J · Wang K · Tao GZ · Lin PY · Dunn JCY · Henrick BM · Frese SA · Sylvester KG last · Lugli GA first · Mancabelli L · Milani C · Fontana F · Tarracchini C · Alessandri G · van Sinderen D · Turroni F · Ventura M last · Rizzo SM first · Viappiani A · Bianchi MG · Bussolati O · Hall B first · Levy S · Dufault-Thompson K · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Jiang X last · Li S · Ying J · Wang H · Qu Y · Niu X · De Biase R · Bocchio F · De Conto F · Nouvenne A · Ticinesi A · Meschi T · Cecchi R · Xu X first · Feng Q · Zhang T · Gao Y · Cheng Q · Zhang W · Wu Q · Xu K · Li Y · Nguyen N · Taft DH · Mills DA · Lemay DG · Zhu W · Mao S · Zhang A · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Zhang L · Yuan Y · Tian M · Zhou M · Hu Y · Huang J · Zou R · Zhao F · Su X · Liu Q · He Y · Feng J · Huang W · Luo Y · Shen W
Downloads
PRJNA327106.csv.gz (2.4 KB) · parquet (72.2 KB) — all 45 samples, every field with route and confidence · PRJNA327106_determinations.csv.gz (6.3 KB) — 556 evidence rows