Preterm infant gut metagenomes, Pittsburgh NICU cohort
407 longitudinal gut metagenome samples from preterm infants at Magee Womens Hospital, Pittsburgh, USA, characterizing colonization patterns; most samples are from NICU preterm infants (some with necrotizing enterocolitis) versus healthy controls. machine-written summary
407 samples · 408 runs · US · Infant / toddler · 2017 · 3.36 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 814 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 408 sample values (health condition detail, location site) · PMC10175488, PMC10769871, PMC10904392, PMC11170968, PMC11322291, PMC12677589, PMC5703836, PMC5893878, PMC6011520, PMC6905865, PMC8549755, PMC9437082, PMC9445129, PMC9720133 |
| ✓ Supplementary tables | 4,317 sample values (age, antibiotic exposure, birth weight grams, delivery mode, diet, gestational age weeks, health condition, nec status) |
| ✓ External resources | 410 sample values (health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolvedhospital ward
Schedule stated by the source: “Infants' fecal samples collected repeatedly across hospitalization, from day of life 5 to day of life 86, over an ~3-year study period” (time origin: birth); stated follow-up 3 mo.
Preterm infants of one NICU; 2 rooms (C5, D10) each occupied sequentially by 2 sampled infants; room–infant strain-sharing study2 shared settings.
member · 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 shared settings. 407 people in the project overall.
Genera, mean relative abundance over 351 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 | 407 | 100% | ||||
| country | 407 | 100% | 407 | |||
| health_condition | 407 | 100% | 407 | |||
| subject_id | 407 | 100% | 407 | |||
| age_at_collection_days | 407 | 100% | 407 | |||
| collection_date | 407 | 100% | 407 | |||
| detailed_location | 407 | 100% | ||||
| health_condition_detail | 407 | 100% | 406 | 1 | ||
| location_site | 407 | 100% | 407 | |||
| antibiotic_exposure | 403 | 99% | 403 | |||
| delivery_mode | 403 | 99% | 403 | |||
| gestational_age_weeks | 403 | 99% | 403 | |||
| nec_status | 403 | 99% | 403 | |||
| sex | 403 | 99% | 403 | |||
| birth_weight_grams | 387 | 95% | 387 | |||
| preterm_status | 328 | 81% | 328 | |||
| timepoint_label | 119 | 29% | 119 | |||
| diet | 99 | 24% | 99 | |||
| shared_setting_id | 76 | 19% | 76 | |||
| shared_setting_type | 76 | 19% | 76 |
- Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome. PMID 29180750 PMC5703836 curated
- Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles. PMID 29636439 PMC5893878 curated
- The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms. PMID 29925423 PMC6011520 curated
- Necrotizing enterocolitis is preceded by increased gut bacterial replication, Klebsiella, and fimbriae-encoding bacteria. PMID 31844663 PMC6905865 curated
- Unraveling the Microbiome of Necrotizing Enterocolitis: Insights in Novel Microbial and Metabolomic Biomarkers. PMID 34704805 PMC8549755 curated
9 more
- A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID 36050292 PMC9437082
- Metabolic model of necrotizing enterocolitis in the premature newborn gut resulting from enteric dysbiosis. PMID 36081629 PMC9445129
- Antibiotic resistance and host immune system-induced metal bactericidal control are key factors for microbial persistence in the developing human preterm infant gut microbiome. PMID 36478853 PMC9720133
- 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
- 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
The data was generated to characterize colonization patterns in the preterm infant gut.
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 (S2_2013 and”
- body site study.description · “the preterm infant gut .”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “preterm infant gut metagenomes (S2_2013”
- life stage study.title · “preterm infant gut metagenomes”
- life stage study.description · “patterns in the preterm infant gut.”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN06444306 | age_at_collection_days | 8 | R2 | 0.75 | paper.supp.table | Host Age (days)=8 |
| SAMN06444306 | antibiotic_exposure | yes | R2 | 0.75 | paper.supp.table | antibiotic_treatment=1 |
| SAMN06444306 | birth_weight_grams | 773 | R2 | 0.75 | paper.supp.table | Birth weight (gram)=773 |
| SAMN06444306 | collection_date | 2012 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2012 |
| SAMN06444306 | country | US | R1 | 0.90 | biosample_attr | USA: Pittsburgh, Pennsylvania Magee Womens Hospital |
| SAMN06444306 | delivery_mode | c_section | R2 | 0.75 | paper.supp.table | delivery_mode=c-section |
| SAMN06444394 | diet | exclusive_breast_milk | R2 | 0.75 | paper.supp.Table_3.XLSX[mapping_global.txt!feeding_practice] | breastfed |
| SAMN06444306 | gestational_age_weeks | 26.0 | R2 | 0.75 | paper.supp.table | gestational_age_week=26 |
| SAMN06444306 | health_condition | preterm_nicu | R2 | 0.70 | paper.supp.table | Pre_term_nec=Preterm |
| SAMN06444709 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN06444306 | health_condition_detail | Preterm Birth | R2 | 0.75 | external.cmd source | disease: Preterm Birth |
| SAMN06444308 | health_condition_detail | Control | R3 | 0.75 | paper.body.TABLE 1[Condition] | N2_031: Control |
| SAMN06444306 | location_site | Magee-Womens' Hospital of UPMC | R3 | 0.60 | paper.fulltext.results | NICU of the Magee-Womens' Hospital of UPMC, Pittsburgh |
| SAMN06444306 | nec_status | no | R2 | 0.75 | paper.supp.table | NEC=No |
| SAMN06444306 | preterm_status | preterm | R2 | 0.75 | paper.supp.table | Pre_term_nec=Preterm |
| SAMN06444306 | sex | male | R2 | 0.75 | paper.supp.table | Sex=male |
| SAMN06444475 | shared_setting_id | C5 | R2 | 0.85 | paper.supp.41467_2017_2018_MOESM5_ESM.txt[Supplementary Data 2!nicu_room] | S2_003_005G1 infant Sloan2_3 nicu_room C5 |
| SAMN06444475 | shared_setting_type | hospital_ward | R2 | 0.85 | paper.supp.41467_2017_2018_MOESM5_ESM.txt[Supplementary Data 2!nicu_room] | S2_003_005G1 infant Sloan2_3 nicu_room C5 |
| SAMN06444306 | subject_id | PRJNA376566_N2_031_008G1 | R2 | 0.75 | paper.supp.table | Host ID=PRJNA376566_N2_031_008G1 |
| SAMN06444307 | timepoint_label | 4 | R2 | 0.75 | paper.supp.table | Window=4 |
Sequencing
408 runs over 407 samples · mean 3.63 Gbp per run (median 3.36 Gbp, total 1,482.19 Gbp; 408 runs with a base count) · layout PAIRED 408 · platform ILLUMINA 408 · models Illumina HiSeq 2500 (258), Illumina HiSeq 2000 (150) · 86% of runs with a Sandpiper profile · first public 2017-12-06
Authors (118)
Brooks B first · Olm MR · Firek BA · Baker R · Thomas BC · Morowitz MJ · Banfield JF last · Brown CT first · Xiong W · Firek B · Hettich RL · Geller-McGrath D · Reimer SR · Soenjoyo KR · Yip JS · Dahan D · Bhattacharya N · Crits-Christoph A · Song YS · Tarracchini C first · Milani C · Longhi G · Fontana F · Mancabelli L · Pintus R · Lugli GA · Alessandri G · Anzalone R · Viappiani A · Turroni F · Mussap M · Dessì A · Cesare Marincola F · Noto A · De Magistris A · Vincent M · Bernasconi S · Picaud JC · Fanos V · Ventura M 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 · Peters SL first · van Sinderen D · 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 · 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
PRJNA376566.csv.gz (15.3 KB) · parquet (92.7 KB) — all 407 samples, every field with route and confidence · PRJNA376566_determinations.csv.gz (53.4 KB) — 5,949 evidence rows