Infant gut metagenomes, early-life antibiotics RCT, NL
12 shotgun-sequenced fecal/rectal swab samples from a randomized controlled trial of infants given antibiotics for suspected neonatal sepsis (penicillin+gentamicin, co-amoxiclav+gentamicin, or amoxicillin+cefotaxime) versus untreated controls, sampled in the western Netherlands. machine-written summary
12 samples · 20 runs · NL · Infant / toddler · 2022 · 0.40 Gbp / sample · cohort Reyman 2022 Netherlands
One study deposited as 2 BioProjects (32 catalog samples together): PRJNA613032 · PRJNA613054 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 48 sample values (collection date, country, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC8850541 |
| ✓ Supplementary tables | 12 sample values (antibiotic exposure, birth weight grams, delivery mode, gestational age weeks, maternal antibiotics, sex) |
| – 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 |
intervention — arms not resolved
Antibiotic given as the study intervention (incl. eradication therapy design randomized_controlled_trial · population sepsis_or_infection · Penicillin+gentamicin vs co-amoxiclav+gentamicin vs amoxicillin+cefotaxime for sEONS
“randomized 1:1:1 to receive three commonly prescribed intravenous antibiotic combinations” — abstract:35173154 (study level; per-sample arms are in the intervention column below)
longitudinal
2 of 2 people sampled more than once (12 samples; median 6, up to 8 per person) · follow-up median 9 mo (max 14 mo) · median interval between samples 50 d (time from collection dates). Schedule stated by the source: “Repeated faecal samples per infant; 2 subjects with median 6, max 8 samples each; timepoint_label has 2 values” (time origin: other).
Each row is one person (2 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 3 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 | 2 | 17% | ||||
| country | 12 | 100% | 12 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 12 | 100% | 12 | |||
| collection_date | 12 | 100% | 12 | |||
| timepoint_label | 12 | 100% | 12 | |||
| antibiotic_exposure | 2 | 17% | 2 | |||
| birth_weight_grams | 2 | 17% | 2 | |||
| delivery_mode | 2 | 17% | 2 | |||
| gestational_age_weeks | 2 | 17% | 2 | |||
| maternal_antibiotics | 2 | 17% | 2 | |||
| sex | 2 | 17% | 2 |
- Effects of early-life antibiotics on the developing infant gut microbiome and resistome: a randomized trial. PMID 35173154 PMC8850541 curated
Archive description
We performed a randomised controlled study in 147 infants requiring broad-spectrum antibiotic treatment for suspected early onset neonatal sepsis in their first week of life. Infants were randomly allocated to either treatment with penicillin + gentamicin, co-amoxiclav + gentamicin or amoxicillin + cefotaxime. Healthy infants not receiving antibiotics in their first week of life served as controls (subset of samples from BioProject ID PRJNA481243). Microbiota of faecal samples and rectal swabs were characterised by 16S rRNA-based sequencing (BioProject ID PRJNA612836). The microbiota of a subset of 20 samples were additionally characterised by whole genome shotgun 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 · “Fecal microbiota in early”
- body site study.description · “PRJNA481243). Microbiota of faecal samples and rectal”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Fecal microbiota in early life and effects of”
- life stage study.description · “suspected early onset neonatal sepsis in their”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11050937 | antibiotic_exposure | no | R2 | 0.85 | paper.supp.table | ab=0 |
| SAMN11050937 | birth_weight_grams | 3340 | R2 | 0.85 | paper.supp.table | bw=3340 |
| SAMN11050926 | collection_date | 2015-09-20 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2015-09-20 |
| SAMN11050926 | country | NL | R1 | 0.90 | biosample_attr | Netherlands: western part |
| SAMN11050937 | delivery_mode | vaginal | R2 | 0.85 | paper.supp.table | birthmode=1 |
| SAMN11050937 | gestational_age_weeks | 38.0 | R2 | 0.85 | paper.supp.table | ga=38 |
| SAMN11050937 | maternal_antibiotics | no | R2 | 0.85 | paper.supp.table | ab.ap=0 |
| SAMN11050937 | sex | male | R2 | 0.85 | paper.supp.table | sex=1 |
| SAMN11050926 | subject_id | 381 | R1 | 0.70 | sample.name_rule:sample_id | 381.199 |
| SAMN11050926 | timepoint_label | 2 | R1 | 0.85 | biosample.attribute:time | time: 2 |
Sequencing
20 runs over 20 samples · mean 0.41 Gbp per run (median 0.40 Gbp, total 8.17 Gbp; 20 runs with a base count) · layout PAIRED 20 · platform ILLUMINA 20 · models Illumina NovaSeq 6000 (20) · 40% of runs with a Sandpiper profile · first public 2022-01-12
Authors (12)
Reyman M first · van Houten MA · Watson RL · Chu MLJN · Arp K · de Waal WJ · Schiering I · Plötz FB · Willems RJL · van Schaik W · Sanders EAM · Bogaert D last
Downloads
PRJNA613032.csv.gz (1.3 KB) · parquet (70.2 KB) — all 12 samples, every field with route and confidence · PRJNA613032_determinations.csv.gz (1.3 KB) — 60 evidence rows