Preterm infant gut microbiome, pro/prebiotics, Finland, RCT
181 stool samples from Finnish moderate/late preterm infants (plus full-term reference infants), followed from birth to 12 months in a randomized controlled trial testing probiotic (L. rhamnosus GG) and prebiotic (GOS/polydextrose) interventions versus placebo. machine-written summary
181 samples · 181 runs · FI · Infant / toddler · 2023 · 8.61 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,943 sample values (age, collection date, country, delivery mode, health condition, health condition detail, intervention, preterm status) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 362 sample values (location locality, location site) · PMC10730193 |
| ○ 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 |
intervention — arms not resolved
Prebiotic / dietary fibre supplement Probiotic (live microorganisms; single strain or mixture) design randomized_controlled_trial · population preterm_nicu · Lactobacillus rhamnosus GG probiotic and GOS/polydextrose prebiotic vs placebo, days 3-60
“a probiotic ( Lactobacillus rhamnosus GG” — abstract:38010080 (study level; per-sample arms are in the intervention column below)
longitudinal
52 of 52 people sampled more than once (181 samples; median 4, up to 4 per person) · follow-up median 12 mo (max 12 mo) · median interval between samples 5 mo (time from age at collection). Schedule stated by the source: “stool at birth, 1, 6 and 12 months” (time origin: birth); stated follow-up 12 mo.
Each row is one person (36 shown of 52); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 165 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 | 181 | 100% | ||||
| country | 181 | 100% | 181 | |||
| health_condition | 181 | 100% | 181 | |||
| subject_id | 181 | 100% | 181 | |||
| age_at_collection_days | 181 | 100% | 181 | |||
| collection_date | 181 | 100% | 181 | |||
| delivery_mode | 181 | 100% | 181 | |||
| detailed_location | 181 | 100% | ||||
| health_condition_detail | 181 | 100% | 181 | |||
| location_locality | 181 | 100% | 181 | |||
| location_site | 181 | 100% | 181 | |||
| preterm_status | 181 | 100% | 181 | |||
| probiotic_exposure | 181 | 100% | 181 | |||
| timepoint_label | 173 | 96% | 173 | |||
| intervention | 141 | 78% | 141 |
- Reversible aberrancies in gut microbiome of moderate and late preterm infants: results from a randomized, controlled trial. PMID 38010080 PMC10730193 curated
Archive description
The aim of this study was to obtain insight into the deviant and distinctive gut microbiome composition and function throughout infancy in children born moderately and late preterm and their response to microbiome modulation. We characterized the longitudinal development of the gut microbiome from birth to the age of 12 months by metagenomic sequencing in 43 moderate and late preterm children participating in a randomized, controlled trial (ClinicalTrials.gov/no.NCT00167700) assessing the impact of a probiotic (Lactobacillus rhamnosus GG, ATCC 53103, currently Lacticaseibacillus rhamnosus GG) and a prebiotic (galacto-oligosaccharide and polydextrose mixture, 1:1) intervention as compared to a placebo given from 3 to 60 days of life. In addition, 9 full-term, vaginally delivered, breast-fed infants, who also remained healthy long-term were included for reference. Significant differences in taxonomy, but not in functional potential, were found when comparing preterm and full-term infants gut microbiome composition during the first month of life. However, this aberrancy was transient the gut microbiome of preterm infants resembled that of full-term infants by the age of 6 months. Pro- and prebiotic treatment were found to mitigate the shift in microbiome of preterm infants by accelerating Bifidobacteria-dominated gut microbiome composition in a beta diversity analysis. This study provides intriguing information about the establishment of the gut microbiome in children born moderate and late preterm, representing the majority of children born preterm. Specific pro- and prebiotics may reverse the pro-inflammatory gut microbiome composition during the vulnerable period, when the microbiome is low in resilience and susceptible to environmental exposures and also simultaneously promotes immunological and metabolic maturation.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and neonate and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Infant stool , moderate and”
- body site study.description · “deviant and distinctive gut microbiome composition and”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Infant stool, moderate and”
- life stage study.title · “moderate and late preterm infants, probiotic and”
- life stage study.description · “moderately and late preterm and their response”
- life stage study.description · “throughout infancy in children born moderately and”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA113578983 | age_at_collection_days | 0 | R1 | 0.90 | biosample_attr | 0 months |
| SAMEA113578983 | collection_date | 2012 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2012 |
| SAMEA113578983 | country | FI | R1 | 0.90 | biosample_attr | Finland |
| SAMEA113578983 | delivery_mode | c_section | R1 | 0.90 | biosample_attr | Cesarean |
| SAMEA113578983 | health_condition | preterm_nicu | R1 | 0.85 | biosample.attribute:intervention_group | intervention_group: preterm probiotics |
| SAMEA113578983 | health_condition_detail | preterm probiotics | R1 | 0.85 | biosample.attribute:intervention_group | intervention_group: preterm probiotics |
| SAMEA113578983 | intervention | probiotic | R1 | 0.85 | biosample.attribute:intervention_group | intervention_group: preterm probiotics |
| SAMEA113578983 | location_locality | Turku | R3 | 0.70 | paper.fulltext.methods | treated at Turku University Hospital, Turku, Finland |
| SAMEA113578983 | location_site | Turku University Hospital | R3 | 0.70 | paper.fulltext.methods | treated at Turku University Hospital, Turku, Finland |
| SAMEA113578983 | preterm_status | preterm | R1 | 0.60 | biosample_attr | preterm probiotics |
| SAMEA113578983 | probiotic_exposure | yes | R1 | 0.60 | biosample_attr | preterm probiotics |
| SAMEA113578983 | subject_id | 23 | R1 | 0.85 | biosample_attr | 23 |
| SAMEA113578983 | timepoint_label | 0 months | R1 | 0.70 | sample.name_rule:library_names | L23_F0kk |
Sequencing
181 runs over 181 samples · mean 8.89 Gbp per run (median 8.61 Gbp, total 1,609.74 Gbp; 181 runs with a base count) · layout PAIRED 181 · platform ILLUMINA 181 · models Illumina HiSeq 2000 (181) · 91% of runs with a Sandpiper profile · first public 2023-06-21
Authors (5)
Luoto R first · Pärtty A · Vogt JK · Rautava S · Isolauri E last
Downloads
PRJEB62848.csv.gz (6.9 KB) · parquet (79.1 KB) — all 181 samples, every field with route and confidence · PRJEB62848_determinations.csv.gz (14.9 KB) — 2,305 evidence rows