Preterm infant gut metagenomes, NICU cohort, Pittsburgh
305 longitudinal fecal samples from premature infants in a Pittsburgh, PA NICU, including preterm NICU, necrotizing enterocolitis (NEC), and healthy control groups. machine-written summary
305 samples · 305 runs · US · Infant / toddler · 2017 · 7.19 Gbp / sample
One study deposited as 2 BioProjects (574 catalog samples together): PRJNA396794 · PRJNA417343 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 611 sample values (age, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 329 sample values (antibiotic exposure, location site, preterm status) · PMC10175488, PMC5758725, PMC6905865 |
| ✓ Supplementary tables | 3,118 sample values (antibiotic exposure, birth weight grams, delivery mode, feeding mode, gestational age weeks, health condition, maternal antibiotics, nec status) |
| ✓ External resources | 306 sample values (health condition detail, sex) · from GMrepo v3, MicrobiomeDB (VEuPathDB) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
57 of 58 people sampled more than once (304 samples; median 5, up to 9 per person) · follow-up median 27 d (max 2 mo) · median interval between samples 6 d (time from age at collection). Schedule stated by the source: “Serial stool samples collected at multiple days of life (DOL) during NICU stay; up to 9 samples per infant”.
Each row is one person (36 shown of 57); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 275 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 | 305 | 100% | ||||
| country | 305 | 100% | 305 | |||
| health_condition | 305 | 100% | 305 | |||
| subject_id | 305 | 100% | 1 | 304 | ||
| age_at_collection_days | 305 | 100% | 305 | |||
| antibiotic_exposure | 305 | 100% | 303 | 2 | ||
| detailed_location | 305 | 100% | ||||
| health_condition_detail | 305 | 100% | 305 | |||
| location_site | 305 | 100% | 305 | |||
| preterm_status | 305 | 100% | 283 | 22 | ||
| sex | 305 | 100% | 305 | |||
| birth_weight_grams | 304 | 100% | 304 | |||
| delivery_mode | 304 | 100% | 304 | |||
| gestational_age_weeks | 304 | 100% | 304 | |||
| feeding_mode | 303 | 99% | 303 | |||
| nec_status | 303 | 99% | 303 | |||
| timepoint_label | 60 | 20% | 60 | |||
| maternal_antibiotics | 41 | 13% | 41 |
- Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome. PMID 29359195 PMC5758725 curated
- Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria. PMID 31844663 PMC6905865 curated
- Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load. PMID 34677583 PMC8827105 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
5 more
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488
- 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
- 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
Time-series fecal samples for a cohort of premature infants in NICU
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 study.title · “preterm infant gut metagenomes (NIH Y4”
- body site study.description · “Time-series fecal samples for a”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “preterm infant gut metagenomes (NIH”
- life stage study.title · “preterm infant gut metagenomes”
- life stage study.description · “a cohort of premature infants in NICU”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07501037 | age_at_collection_days | 8 | R1 | 0.90 | biosample_attr | 8 |
| SAMN07501037 | antibiotic_exposure | yes | R2 | 0.75 | paper.supp.table | Infant antibiotics=yes |
| SAMN07501290 | antibiotic_exposure | yes | R3 | 0.80 | paper.fulltext.results | All 107 infants received gentamicin and ampicillin during the first week |
| SAMN07501037 | birth_weight_grams | 1411 | R2 | 0.75 | paper.supp.table | Birth weight (gram)=1411 |
| SAMN07501037 | country | US | R1 | 0.90 | biosample_attr | USA: Pittsburgh, PA |
| SAMN07501037 | delivery_mode | c_section | R2 | 0.75 | paper.supp.table | Delivery mode=CS |
| SAMN07501037 | feeding_mode | formula | R2 | 0.75 | paper.supp.table | Feeding pattern=formula |
| SAMN07501037 | gestational_age_weeks | 32.0 | R2 | 0.75 | paper.supp.table | Gestational age (weeks)=32 |
| SAMN07501037 | health_condition | preterm_nicu | R2 | 0.70 | paper.supp.table | Pre_term_nec=Preterm |
| SAMN07501037 | health_condition_detail | Premature Birth | R2 | 0.75 | external.gmrepo source | phenotype: Premature Birth |
| SAMN07501037 | location_site | Magee-Women's Hospital NICU | R3 | 0.70 | paper.fulltext.methods | neonatal intensive care unit (NICU) at the Magee-Women’s Hospital in Pittsburgh, PA |
| SAMN07501037 | maternal_antibiotics | yes | R2 | 0.75 | paper.supp.table | Mat_AB=True |
| SAMN07501037 | nec_status | no | R2 | 0.75 | paper.supp.table | PreNEC=noNEC |
| SAMN07501037 | preterm_status | preterm | R2 | 0.75 | paper.supp.table | Pre_term_nec=Preterm |
| SAMN07501079 | preterm_status | preterm | R3 | 0.80 | paper.fulltext.results | A total of 107 premature infants were studied |
| SAMN07501037 | sex | female | R2 | 0.75 | paper.supp.table | Sex=female |
| SAMN07501302 | sex | male | R2 | 0.75 | external.microbiomedb source | Sex: Male |
| SAMN07501302 | subject_id | N4_115 | R1 | 0.85 | biosample.attribute:infant | N4_115 |
| SAMN07501037 | subject_id | PRJNA396794_N4_005 | R2 | 0.75 | paper.supp.table | Host ID=PRJNA396794_N4_005 |
| SAMN07501040 | timepoint_label | 0 | R2 | 0.75 | paper.supp.table | Window=0 |
Sequencing
305 runs over 305 samples · mean 11.44 Gbp per run (median 7.19 Gbp, total 3,489.32 Gbp; 305 runs with a base count) · layout PAIRED 305 · platform ILLUMINA 305 · models Illumina HiSeq 3000 (305) · 90% of runs with a Sandpiper profile · first public 2017-11-09
Authors (88)
Rahman SF first · Olm MR · Morowitz MJ · Banfield JF last · Bhattacharya N · Crits-Christoph A · Firek BA · Baker R · Song YS · Pärnänen KMM first · Hultman J · Markkanen M · Satokari R · Rautava S · Lamendella R · Wright J · McLimans CJ · Kelleher SL · Virta MP 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 · 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 · 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
PRJNA396794.csv.gz (11.5 KB) · parquet (85.0 KB) — all 305 samples, every field with route and confidence · PRJNA396794_determinations.csv.gz (36.2 KB) — 4,364 evidence rows