Preterm infant gut resistome, UK longitudinal cohort
15 gut metagenome samples from premature infants (neonates and infants) in the United Kingdom, healthy controls, studied via shotgun metagenomics to assess antibiotic resistome; cohort/longitudinal case-series design. machine-written summary
15 samples · 15 runs · GB · Infant / toddler · 2016 · 2.68 Gbp / sample · cohort Stewart/Rose UK preterm infant cohort
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 45 sample values (collection date, country, subject id) |
| ✓ Abstract / description | 15 sample values (health condition) |
| ✓ Full text | 60 sample values (feeding mode, location locality, location site, nec status) · PMC10269646, PMC11322291, PMC5270596, PMC8343889 |
| ✓ Supplementary tables | 44 sample values (age, antibiotic exposure, delivery mode, gestational age weeks, maternal antibiotics) |
| ✓ External resources | 15 sample values (health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal — not resolved
4 of 11 people sampled more than once (8 samples; median 2, up to 2 per person). Schedule stated by the source: “Not explicitly stated; catalog shows 4 of 11 subjects sampled >=2 times (repeat gut samples from same infants).”.
Genera, mean relative abundance over 13 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 | 15 | 100% | ||||
| country | 15 | 100% | 15 | |||
| health_condition | 15 | 100% | 15 | |||
| subject_id | 15 | 100% | 15 | |||
| collection_date | 15 | 100% | 15 | |||
| detailed_location | 15 | 100% | ||||
| feeding_mode | 15 | 100% | 15 | |||
| health_condition_detail | 15 | 100% | 15 | |||
| location_locality | 15 | 100% | 15 | |||
| location_site | 15 | 100% | 15 | |||
| nec_status | 15 | 100% | 15 | |||
| age_at_collection_days | 11 | 73% | 11 | |||
| delivery_mode | 11 | 73% | 11 | |||
| gestational_age_weeks | 11 | 73% | 11 | |||
| antibiotic_exposure | 8 | 53% | 8 | |||
| maternal_antibiotics | 3 | 20% | 3 |
- Antibiotic resistance potential of the healthy preterm infant gut microbiome. PMID 28149696 PMC5270596 curated
- Premature neonatal gut microbial community patterns supporting an epithelial TLR-mediated pathway for necrotizing enterocolitis. PMID 34362295 PMC8343889 curated
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646 curated
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291 curated
Archive description
These samples were generated to quantify and interrogate the antibiotic resistome within a cohort of premature infants, using shotgun metagenomic sequencing.
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 · “the preterm infant gut microbiome measured using”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “of the preterm infant gut microbiome measured”
- life stage study.title · “potential of the preterm infant gut microbiome”
- life stage study.description · “a cohort of premature infants, using shotgun”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA4413037 | age_at_collection_days | 5 | R2 | 0.85 | paper.supp.table | DOL of Sample=5 |
| SAMEA4413037 | antibiotic_exposure | yes | R2 | 0.85 | paper.supp.table | Antibiotic (Course 1)=Co-amoxiclav |
| SAMEA4413037 | collection_date | 2010 | R1 | 0.85 | biosample.attribute:collection_date | 2010 |
| SAMEA4413037 | country | GB | R1 | 0.90 | biosample_attr | United Kingdom |
| SAMEA4413037 | delivery_mode | c_section | R2 | 0.85 | paper.supp.table | Delivery=CS |
| SAMEA4413037 | feeding_mode | mixed | R3 | 0.40 | paper.fulltext.methods | received donor breast milk and/or mother's breast milk |
| SAMEA4413037 | gestational_age_weeks | 28.71 | R2 | 0.85 | paper.supp.table | Gestation at birth=28+5 |
| SAMEA4413037 | health_condition | healthy_control | R4 | 0.50 | paper.abstract | gut microbiomes from preterm but healthy infants |
| SAMEA4413037 | health_condition_detail | Premature Birth | R2 | 0.75 | external.gmrepo source | phenotype: Premature Birth |
| SAMEA4413037 | location_locality | London | R3 | 0.70 | paper.fulltext.methods | Imperial College Healthcare National Health Service Trust neonatal intensive care unit |
| SAMEA4413037 | location_site | Queen Charlotte's and Chelsea Hospital NICU | R3 | 0.70 | paper.fulltext.methods | neonatal intensive care unit (NICU), at Queen Charlotte's and Chelsea Hospital |
| SAMEA4413038 | maternal_antibiotics | yes | R2 | 0.85 | paper.supp.table | Maternal antibiotics in pregnancy=Erythromycin and augmentin |
| SAMEA4413037 | nec_status | no | R3 | 0.80 | paper.fulltext.methods | no diagnosis of necrotising enterocolitis or blood-stream infection |
| SAMEA4413037 | subject_id | 19 | R1 | 0.70 | sample.name_rule:library_name | Q19_110319_S11 |
Sequencing
15 runs over 15 samples · mean 2.77 Gbp per run (median 2.68 Gbp, total 41.54 Gbp; 15 runs with a base count) · layout PAIRED 15 · platform ILLUMINA 15 · models Illumina MiSeq (15) · 87% of runs with a Sandpiper profile · first public 2016-09-23
Authors (26)
Rose G first · Shaw AG · Sim K · Wooldridge DJ · Li MS · Gharbia S · Misra R · Kroll JS last · Misra RV · Rizzo SM first · Alessandri G · Lugli GA · Fontana F · Tarracchini C · Mancabelli L · Viappiani A · Bianchi MG · Bussolati O · van Sinderen D · Ventura M · Turroni F last · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last
Downloads
PRJEB15257.csv.gz (1.6 KB) · parquet (71.4 KB) — all 15 samples, every field with route and confidence · PRJEB15257_determinations.csv.gz (3.0 KB) — 179 evidence rows