Preterm infant gut microbiome: antibiotics vs probiotics, UK
92 longitudinal faecal metagenome samples from very-low-birth-weight preterm infants in London and Norwich, UK, studying antibiotic and probiotic effects on gut microbiome/resistome in a nonrandomized longitudinal cohort design. machine-written summary
92 samples · 92 runs · GB · Infant / toddler · 2025 · 1.41 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 460 sample values (collection date, country, intervention, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 184 sample values (feeding mode, preterm status) · PMC12354744 |
| ✓ Supplementary tables | 184 sample values (antibiotic exposure, gestational age weeks) |
| – 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 resolved
5 people have samples in more than one arm.
Antibiotic given as the study intervention (incl. eradication therapy Probiotic (live microorganisms; single strain or mixture) design observational_with_procedure · population preterm_nicu · Probiotic (Bifidobacterium) cohort vs non-probiotic; antibiotics benzylpenicillin/gentamicin in some infants
“one cohort receiving probiotics” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinal
46 of 46 people sampled more than once (92 samples; median 2, up to 2 per person) · follow-up median 7 d (max 14 d) · median interval between samples 7 d (time from timepoint labels). Schedule stated by the source: “Each infant sampled at up to 3 weekly timepoints (W1, W2, W3); median 2, max 2 samples per subject.”.
Each row is one person (29 shown of 46); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 90 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 | 92 | 100% | ||||
| country | 92 | 100% | 92 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 92 | 100% | 92 | |||
| antibiotic_exposure | 92 | 100% | 92 | |||
| collection_date | 92 | 100% | 92 | |||
| feeding_mode | 92 | 100% | 92 | |||
| gestational_age_weeks | 92 | 100% | 92 | |||
| intervention | 92 | 100% | 92 | |||
| preterm_status | 92 | 100% | 92 | |||
| timepoint_label | 92 | 100% | 92 |
- Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants. PMID 40813371 PMC12354744 curated
Archive description
Preterm infants (<37 weeks gestation) are often administered broad-spectrum antibiotics in hospitals due to their vulnerability to severe infections, including necrotising enterocolitis and sepsis. However, antibiotics can disrupt the development of early-life microbiota, potentially impairing gut immunity and colonisation resistance. Evidence shows that probiotics (e.g., Bifidobacterium) may help restore healthy gut microbiota. In this study, we examined the effects of probiotics and antibiotics on the preterm gut microbiome and resistome in two unique cohorts of 34 very-low-birth-weight, human-milk-fed preterm infants (moderate to very preterm), with one cohort receiving probiotics. Within each group, some infants were treated with antibiotics (benzylpenicillin and/or gentamicin) while others served as controls. We performed shotgun metagenome sequencing on 93 longitudinal faecal samples, generated >300 metagenome-assembled genomes, and obtained ~90 isolate genomes through targeted culturomics, enabling analysis of the microbiome/resistome at species and strain levels. Additionally, we investigated in vitro horizontal gene transfer (HGT) capacity of the multidrug-resistant (MDR) pathogen Enterococcus via infant gut models. Overall, probiotic supplementation significantly reduced antibiotic resistance gene prevalence, MDR pathogen load, and helped restore a typical early-life microbiota. However, the persistence of MDR pathogens like Enterococcus, with high HGT potential, highlights the need for ongoing surveillance in neonatal care. Our findings underscore the complex interactions among antibiotics, probiotics, and HGT in shaping the neonatal microbiome and support further research into probiotics for antimicrobial stewardship in preterm populations.
How this project entered the registry
Classified as human gut / stool / human milk 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 · “probiotic treatment on gut microbiome and resistome”
- body site study.description · “microbiota, potentially impairing gut immunity and colonisation”
- body site study.description · “of 34 very-low-birth-weight, human-milk -fed preterm infants”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Impact of early life antibiotic and probiotic”
- life stage study.title · “and resistome of preterm infants (metagenome samples)”
- life stage study.description · “Preterm infants (<37 weeks”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN46357202 | antibiotic_exposure | no | R2 | 0.85 | paper.supp.table | Antibiotic=No |
| SAMN46357202 | collection_date | 2012 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2012 |
| SAMN46357202 | country | GB | R1 | 0.90 | biosample_attr | United Kingdom: London |
| SAMN46357202 | feeding_mode | exclusive_breast | R3 | 0.40 | paper.fulltext.methods | infants were all fed with breastmilk and/or donor breastmilk |
| SAMN46357202 | gestational_age_weeks | 28.0 | R2 | 0.85 | paper.supp.table | Gestational Age=28 |
| SAMN46357202 | intervention | no_intervention | R1 | 0.70 | sample.name_rule:sample_alias | N01-W1 |
| SAMN46357202 | preterm_status | preterm | R3 | 0.80 | paper.fulltext.abstract | 34 very-low-birth-weight, human-milk-fed preterm infants |
| SAMN46357202 | subject_id | 22 | R1 | 0.70 | run.library_name | 21989_5#22 |
| SAMN46357202 | timepoint_label | W1 | R1 | 0.70 | sample.title | Gut metagenome of preterm infant N01-W1 |
Sequencing
92 runs over 92 samples · mean 1.42 Gbp per run (median 1.41 Gbp, total 130.99 Gbp; 92 runs with a base count) · layout PAIRED 92 · platform ILLUMINA 92 · models Illumina HiSeq 2500 (92) · 98% of runs with a Sandpiper profile · first public 2025-09-21
Authors (13)
Kiu R first · Darby EM · Alcon-Giner C · Acuna-Gonzalez A · Camargo A · Lamberte LE · Phillips S · Sim K · Shaw AG · Clarke P · van Schaik W · Kroll JS · Hall LJ last
Downloads
PRJNA1191223.csv.gz (3.5 KB) · parquet (74.1 KB) — all 92 samples, every field with route and confidence · PRJNA1191223_determinations.csv.gz (7.2 KB) — 828 evidence rows