Infant Gut, Skin, and ICU Environment Microbiome Study
86 samples from an intensive care unit meta-analysis of infant gut, skin, and environmental microbiomes; country and age data are not reported. Design combines case-control and longitudinal cohort elements. machine-written summary
86 samples · 86 runs · Infant / toddler · 2018 · 4.65 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 258 sample values (location locality, location region, location site) · PMC6026636 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Other administered intervention (see intervention_detail) design observational_with_procedure · population preterm_nicu · NICU environment comparison (shared-space vs single-family room); antibiotics observed, not assigned
“infants in a shared-space NICU (old NICU) and a single-family room NICU” — abstract:29988506 (study level; per-sample arms are in the intervention column below)
Genera, mean relative abundance over 80 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 | 0 | 0% | ||||
| country | 0 | 0% | ||||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| detailed_location | 86 | 100% | ||||
| location_locality | 86 | 100% | 86 | |||
| location_region | 86 | 100% | 86 | |||
| location_site | 86 | 100% | 86 |
- Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome Between Neonatal Intensive Care Unit (NICU) Environments. PMID 29988506 PMC6026636 curated
- (no title) curated
- Colibactin genes are highly prevalent in the developing infant gut microbiome. PMID 41405404 PMC12716031 curated
Archive description
Meta-analysis of Infant Gut, Skin, and Environmental Microbiome from an Intensive Care Unit
How this project entered the registry
Classified as human gut / stool / skin / other human site shotgun DNA metagenome of infant / toddler by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
- host run.host_tax_id · “9606”
- host run.scientific_name · “human metagenome”
- body site study.description · “Infant Gut, Skin, and Environmental Microbiome”
- life stage study.description · “Infant Gut, Skin, and Environmental Microbiome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN08616968 | location_locality | Falls Church | R3 | 0.70 | paper.fulltext.methods | Inova Fairfax Hospital, Falls Church, Virginia |
| SAMN08616968 | location_region | Virginia | R3 | 0.70 | paper.fulltext.methods | Inova Fairfax Hospital, Falls Church, Virginia |
| SAMN08616968 | location_site | Inova Fairfax Hospital NICU | R3 | 0.70 | paper.fulltext.methods | Inova Fairfax Hospital, Falls Church, Virginia |
Sequencing
86 runs over 86 samples · mean 4.96 Gbp per run (median 4.65 Gbp, total 426.79 Gbp; 86 runs with a base count) · layout SINGLE 86 · platform ILLUMINA 86 · models Illumina HiSeq 2500 (86) · 93% of runs with a Sandpiper profile · first public 2018-03-03
Authors (25)
Hourigan SK first · Subramanian P · Hasan NA · Ta A · Klein E · Chettout N · Huddleston K · Deopujari V · Levy S · Baveja R · Clemency NC · Baker RL · Niederhuber JE · Colwell RR last · Chaudhary PP first · O'Laughlin B · Kumar PS · Dabdoub SM · Myles IA · McCauley KE · Strength R · Robbins ES · Chen Q · Namasivyam S · Maxwell G
Help complete this project
4 of the 4 core fields are below 50% coverage: age_category, country, health_condition, subject_id. Share metadata
Downloads
PRJNA417283.csv.gz (2.8 KB) · parquet (73.0 KB) — all 86 samples, every field with route and confidence · PRJNA417283_determinations.csv.gz (1.4 KB) — 258 evidence rows