Metagenomes in preterm infants with/without NEC, Pittsburgh
60 fecal metagenome samples from premature infants hospitalized in Pittsburgh, PA (neonates and infants; 30 healthy control, 23 NEC), in a case-control study comparing strain-level gut colonization between infants with and without necrotizing enterocolitis. machine-written summary
60 samples · 60 runs · US · Infant / toddler · 2015 · 2.89 Gbp / sample · cohort Brown 2018 USA
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 185 sample values (age, collection date, country, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 42 sample values (preterm status) · PMC10175488, PMC10230729, PMC5703836 |
| ✓ Supplementary tables | 557 sample values (age, antibiotic exposure, birth weight grams, delivery mode, feeding mode, gestational age weeks, health condition, nec status) |
| – 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 |
longitudinalhospital ward — not resolved
10 of 12 people sampled more than once (58 samples; median 6, up to 9 per person) · follow-up median 23 d (max 44 d) · median interval between samples 2 d (time from age at collection). Schedule stated by the source: “Repeated fecal sampling per infant over time, labeled sequentially as 'sample 1'..'sample N' with day-of-life (DOL) values increasing per infant (e.g. DOL 11, 31, 39, 45, 51).” (time origin: birth).
Each row is one person (10 shown); dots are samples at days since that person's first sample.
10 co-hospitalized preterm infants in one NICU (whole cohort shares the ward; no sub-units distinguished).
Genera, mean relative abundance over 56 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 | 60 | 100% | ||||
| country | 60 | 100% | 60 | |||
| health_condition | 53 | 88% | 53 | |||
| subject_id | 60 | 100% | 60 | |||
| age_at_collection_days | 60 | 100% | 5 | 55 | ||
| collection_date | 60 | 100% | 60 | |||
| preterm_status | 60 | 100% | 18 | 42 | ||
| timepoint_label | 60 | 100% | 60 | |||
| antibiotic_exposure | 53 | 88% | 53 | |||
| birth_weight_grams | 53 | 88% | 53 | |||
| delivery_mode | 53 | 88% | 53 | |||
| feeding_mode | 53 | 88% | 53 | |||
| gestational_age_weeks | 53 | 88% | 53 | |||
| nec_status | 53 | 88% | 53 | |||
| sex | 53 | 88% | 53 |
- 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
- 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
- A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID 36050292 PMC9437082 curated
8 more
- Metabolic model of necrotizing enterocolitis in the premature newborn gut resulting from enteric dysbiosis. PMID 36081629 PMC9445129
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488
- Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut. PMID 37259063 PMC10230729
- 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
Premature infants are highly vulnerable to aberrant gastrointestinal tract colonization, a process that may lead to diseases like necrotizing enterocolitis. This study compares microbial communities of 10 co-hospitalized infants, five of which had a diagnosis of necrotizing enterocolitis. Surprisingly, while potentially pathogenic bacteria of the same species colonized many infants, a genome-resolved analysis revealed that strains colonizing each baby were typically distinct. In particular, no strain was common to all infants that developed necrotizing enterocolitis. The paucity of shared gut colonizers suggests the existence of significant barriers to spread of bacteria among infants. Importantly, we demonstrate that strain-resolved comprehensive community analysis can be accomplished on potentially medically-relevant time scales.
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 · “from human infant fecal samples with and”
- body site study.description · “vulnerable to aberrant gastrointestinal tract colonization, a”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Metagenomes from human infant fecal samples with”
- life stage study.description · “Premature infants are highly”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN07977757 | age_at_collection_days | 51 | R1 | 0.85 | sample.title | DOL 51 |
| SAMN03295806 | age_at_collection_days | 9 | R2 | 0.75 | paper.supp.table | Host Age (days)=9 |
| SAMN03295806 | antibiotic_exposure | yes | R2 | 0.75 | paper.supp.table | Infant antibiotics=yes |
| SAMN03295806 | birth_weight_grams | 1810 | R2 | 0.75 | paper.supp.table | Birth weight (gram)=1810 |
| SAMN03295806 | collection_date | 2014-07 | R1 | 0.85 | biosample.attribute:collection_date | 2014-07 |
| SAMN03295806 | country | US | R1 | 0.90 | biosample_attr | USA: Pittsburgh, PA |
| SAMN03295806 | delivery_mode | c_section | R2 | 0.75 | paper.supp.table | Delivery mode=CS |
| SAMN03295806 | feeding_mode | mixed | R2 | 0.75 | paper.supp.table | Feeding pattern=combined |
| SAMN03295806 | gestational_age_weeks | 32.0 | R2 | 0.75 | paper.supp.table | Gestational age (weeks)=32 |
| SAMN03295806 | health_condition | healthy_control | R2 | 0.70 | paper.supp.table | PreNEC=noNEC |
| SAMN03295806 | nec_status | no | R2 | 0.75 | paper.supp.table | PreNEC=noNEC |
| SAMN03295826 | preterm_status | preterm | R2 | 0.75 | paper.supp.table | Pre_term_nec=Preterm |
| SAMN03295806 | preterm_status | preterm | R3 | 0.80 | paper.fulltext.results | 35 infants born prematurely and housed in the neonatal intensive care unit |
| SAMN03295806 | sex | male | R2 | 0.75 | paper.supp.table | Sex=male |
| SAMN03295806 | subject_id | 1 | R2 | 0.75 | paper.supp.table | SubjectID=1 |
| SAMN03295806 | timepoint_label | sample 1 | R1 | 0.70 | sample.name_rule:isolation_source | fecal sample 1 from infant 1 |
| SAMN07977757 | timepoint_label | DOL 51 | R1 | 0.70 | sample.title | Infant N3_176 DOL 51 |
Sequencing
60 runs over 60 samples · mean 3.21 Gbp per run (median 2.89 Gbp, total 192.69 Gbp; 60 runs with a base count) · layout PAIRED 60 · platform ILLUMINA 60 · models Illumina HiSeq 2000 (55), Illumina HiSeq 2500 (5) · 93% of runs with a Sandpiper profile · first public 2015-06-05 – 2017-11-05
Authors (116)
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 · 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 · van Sinderen D · Ormaasen I first · Rudi K · Diep DB · Snipen L 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 · 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
PRJNA273761.csv.gz (3.0 KB) · parquet (73.1 KB) — all 60 samples, every field with route and confidence · PRJNA273761_determinations.csv.gz (7.3 KB) — 784 evidence rows