MinION diagnostics for NEC in pre-term babies (case series)
17 gut microbiome samples from pre-term infants, studied for Necrotising EnteroColitis using MinION-based diagnostics, in a case series design. machine-written summary
18 samples · 24 runs · GB · Infant / toddler · 2017 · 0.47 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 20 sample values (subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 69 sample values (antibiotic exposure, country, location locality, location region, probiotic exposure) · PMC10769871, PMC7044117 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 — not resolvedhospital ward — not resolved
3 of 8 people sampled more than once (11 samples; median 3, up to 6 per person). Schedule stated by the source: “Repeated faecal sampling per infant over time (e.g., patient P10 samples N, R, V) linked to clinical events like probiotics/antibiotics/sepsis; no fixed day schedule stated”.
Preterm infants co-located and sampled while admitted to the same Neonatal Intensive Care Unit.
Genera, mean relative abundance over 4 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 | 1 | 6% | ||||
| country | 17 | 94% | 17 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 16 | 89% | 16 | |||
| detailed_location | 18 | 100% | ||||
| location_locality | 18 | 100% | 18 | |||
| location_region | 18 | 100% | 18 | |||
| antibiotic_exposure | 8 | 44% | 8 | |||
| probiotic_exposure | 8 | 44% | 8 | |||
| timepoint_label | 4 | 22% | 4 |
- Real-time analysis and visualization of nanopore metagenomic samples with MARTi. 2025 PMID 41145216 PMC12581910 cites_accession
- Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens. PMID 31844297 PMC7044117 curated
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871 curated
- Rapid profiling of the preterm infant gut microbiota using nanopore sequencing aids pathogen diagnostics curated
- Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens. 2020 PMID 31844297 PMC7044117 own_data
Archive description
We show how the MinION can be used as a tool for diagnostics of infections in pre-term babies suffering from Necrotising EnteroColitis (NEC).
How this project entered the registry
Classified as human gut / stool mixed assays of infant / toddler by sonnet_x2 with confidence 0.72. Assay mixed.
- host run.scientific_name · “Homo sapiens”
- body site study.title · “Gut microbiome diagnostics”
- life stage study.title · “pre-term babies”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA104219959 | antibiotic_exposure | yes | R3 | 0.40 | paper.fulltext.results | days of antibiotic treatment |
| SAMEA104219959 | country | GB | R3 | 0.80 | paper.fulltext.methods | Norfolk and Norwich University Hospital NHS |
| SAMEA104219959 | location_locality | Norwich | R3 | 0.70 | paper.fulltext.methods | Norfolk and Norwich University Hospital NHS Foundation Trust |
| SAMEA104219959 | location_region | Norfolk | R3 | 0.70 | paper.fulltext.methods | Norfolk and Norwich University Hospital NHS Foundation Trust |
| SAMEA104219959 | probiotic_exposure | yes | R3 | 0.40 | paper.fulltext.results | days of probiotic treatment |
| SAMEA104219959 | subject_id | P10 | R1 | 0.70 | sample.name_rule:title | BAMBI patient P10, sample N |
| SAMEA4895124 | timepoint_label | 1D | R1 | 0.70 | run.library_name | 20180112_1459_BAMBI_P49A_1D_12012018 |
Sequencing
24 runs over 18 samples · mean 3.48 Gbp per run (median 0.37 Gbp, total 83.51 Gbp; 24 runs with a base count) · layout SINGLE 20, PAIRED 4 · platform OXFORD_NANOPORE 20, ILLUMINA 4 · models MinION (16), GridION (4), Illumina HiSeq 2500 (4) · 17% of runs with a Sandpiper profile · first public 2017-08-21 – 2019-09-13
Authors (29)
Leggett RM first · Alcon-Giner C · Heavens D · Caim S · Brook TC · Kujawska M · Martin S · Peel N · Acford-Palmer H · Hoyles L · Clarke P · Hall LJ · Clark MD 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
Downloads
PRJEB22207.csv.gz (1.5 KB) · parquet (70.3 KB) — all 18 samples, every field with route and confidence · PRJEB22207_determinations.csv.gz (1.6 KB) — 89 evidence rows