Preterm infant fecal metagenome, necrotizing enterocolitis
Shotgun metagenomic sequencing of 47 fecal samples from preterm infants in France, studied in relation to necrotizing enterocolitis, using a case-control design. machine-written summary
47 samples · 47 runs · FR · Infant / toddler · 2021 · 29.6 Mbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 139 sample values (collection date, country, subject id) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 94 sample values (location locality, preterm status) · PMC8549755 |
| – 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 |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
14 of 17 people sampled more than once (42 samples; median 2, up to 6 per person) · follow-up median 27 d (max 42 d) · median interval between samples 9 d (time from collection dates). Schedule stated by the source: “Repeated fecal sampling per infant over study period; median 2, max 6 samples per subject across distinct collection dates.”.
Each row is one person (14 shown); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 47 | 100% | ||||
| country | 47 | 100% | 47 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 45 | 96% | 45 | |||
| collection_date | 47 | 100% | 47 | |||
| detailed_location | 47 | 100% | ||||
| location_locality | 47 | 100% | 47 | |||
| preterm_status | 47 | 100% | 47 |
- Unraveling the Microbiome of Necrotizing Enterocolitis: Insights in Novel Microbial and Metabolomic Biomarkers. PMID 34704805 PMC8549755 curated
Archive description
Shotgun metagenomic sequencing of fecal samples collected from human infants with and without necrotizing enterocolitis
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 fecal metagenome”
- body site study.description · “metagenomic sequencing of fecal samples collected from”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Preterm infant fecal metagenome”
- life stage study.title · “Preterm infant fecal metagenome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN19460943 | collection_date | 2014-09-25 | R1 | 0.85 | biosample.attribute:collection_date | 2014-09-25 |
| SAMN19460943 | country | FR | R1 | 0.90 | biosample_attr | France |
| SAMN19460943 | location_locality | Lyon | R3 | 0.70 | paper.fulltext.methods | Croix Rousse University Hospital of Lyon, France |
| SAMN19460943 | preterm_status | preterm | R3 | 0.80 | paper.fulltext.results | 47 fecal samples of preterm infants from NICU |
| SAMN19460943 | subject_id | 55 | R1 | 0.70 | sample.name_rule:library_names | 55-RIC-LE-2509 |
Sequencing
47 runs over 47 samples · mean 35.0 Mbp per run (median 29.6 Mbp, total 1.65 Gbp; 47 runs with a base count) · layout PAIRED 47 · platform ILLUMINA 47 · models Illumina MiSeq (47) · 0% of runs with a Sandpiper profile · first public 2021-08-25
Authors (21)
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
Downloads
PRJNA733860.csv.gz (2.3 KB) · parquet (71.4 KB) — all 47 samples, every field with route and confidence · PRJNA733860_determinations.csv.gz (2.3 KB) — 233 evidence rows