Infant/neonate gut microbiome synbiotic trial, Bangladesh
1,674 samples from infants and neonates in Bangladesh (Dhaka), studying a synbiotic intervention, using a randomized trial design. machine-written summary
1,674 samples · 1,919 runs · BD · Infant / toddler · 2025 · 1.92 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 14,984 sample values (age, country, delivery mode, family id, family role, gestational age weeks, preterm status, sex) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 5,022 sample values (collection date, location locality, location site) · PMC11934310 |
| ○ 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
Synbiotic (probiotic + prebiotic) design randomized_controlled_trial · population preterm_nicu · L. plantarum ATCC 202195 + FOS synbiotic, 7 days, vs placebo
“randomized to receive Lactobacillus plantarum” — bioproject.description (study level; per-sample arms are in the intervention column below)
longitudinalmother–infant
356 of 438 people sampled more than once (1,592 samples; median 5, up to 8 per person) · follow-up median 4 mo (max 7 mo) · median interval between samples 20 d (time from age at collection). Schedule stated by the source: “stool collected during 1-7 day dosing (days 0-4) then post-intervention between days 14 and 60, most infants 2-3 samples” (time origin: birth); stated follow-up 2 mo.
Each row is one person (36 shown of 356); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).
299 families (family_id): 139 mother–infant dyads with both sampled, 160 infant-only; 139 mothers, 299 infants · 139 families with 278 sampled people (139 with a parent and a child).
motherchild · circles are people (pale = no sequenced sample), arrows run donor → recipient and parent → child, curved lines join twins, partners and siblings, squares are shared settings or families without recorded roles. Shown: 24 of 139 families (one per family structure, then more). 438 people in the project overall.
Families (25 of 139)
Genera, mean relative abundance over 1,383 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 | 1,674 | 100% | ||||
| country | 1,674 | 100% | 1,674 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 1,674 | 100% | 1,674 | |||
| age_at_collection_days | 1,674 | 100% | 1,674 | |||
| collection_date | 1,674 | 100% | 1,674 | |||
| delivery_mode | 1,674 | 100% | 1,674 | |||
| detailed_location | 1,674 | 100% | ||||
| family_id | 1,674 | 100% | 1,674 | |||
| family_role | 1,674 | 100% | 1,674 | |||
| location_locality | 1,674 | 100% | 1,674 | |||
| location_site | 1,674 | 100% | 1,674 | |||
| sex | 1,674 | 100% | 1,674 | |||
| gestational_age_weeks | 1,633 | 98% | 1,633 | |||
| preterm_status | 1,633 | 98% | 1,633 |
- Neonatal administration of Lactiplantibacillus plantarum ATCC 202195 with or without fructooligosaccharide in Bangladesh: a placebo-controlled randomized trial. 2025 PMID 39992135 PMC11934310 own_data
Archive description
Recent randomized controlled trials (RCTs) have demonstrated the beneficial effects of probiotics and/or prebiotics, compared to placebo, for preventing infections in preterm and/or LBW infant. Some of the most compelling evidence comes from a recent randomized, double blind, placebo-controlled trial conducted by Panigrahi and colleagues, where newborns (≥ 35 weeks ‘gestation and ≥ 2,000 grams) residing in rural India were randomized to receive Lactobacillus plantarum (L. plantarum) ATCC 202195 plus fructooligosaccharide (FOS), or placebo, once daily for seven consecutive days, starting on day two to four of life. Relative to the placebo group, infants in the synbiotic group had a 40% lower risk of the combined primary outcome of sepsis and all-cause mortality, and a 78% lower risk of culture-confirmed sepsis. As a result of the promising safety profile and strong mechanistic rationale regarding its plausible probiotic effects, L. plantarum has garnered interest as a potential intervention for preventing sepsis and pSBI in infants. Although the Panigrahi et al. study provides strong evidence for the proposed beneficial effects,the effects of L. plantarum administration on the infant microbiome has not been fully described. Most of what we know about the microbiome comes from high-income settings. This is because, low- and middle-income countries (LMICs) are currently underrepresented in global microbiome study. In addition, recent work highlights the influence of geography on the composition and stability of the gut microbiota. This study will examine the effects of neonatal oral administration of Lactobacillus plantarum (L. plantarum) ATCC 202195 (109 CFU/day) with fructooligosaccharide (FOS), versus placebo, on the community structure, diversity and metabolite production of the microbiota of infants in Dhaka, Bangladesh
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.description · “stability of the gut microbiota. This study”
- 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.description · “preterm and/or LBW infant . Some of”
- life stage study.description · “preventing infections in preterm and/or LBW infant.”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA117508454 | age_at_collection_days | 10 | R1 | 0.90 | biosample_attr | 10 |
| SAMEA117508454 | collection_date | 2022-01/2022-04 | R3 | 0.70 | paper.body.methods | Enrollment took place between 7 January 2022 and 24 April 2022 |
| SAMEA117508454 | country | BD | R1 | 0.90 | biosample_attr | Bangladesh |
| SAMEA117508454 | delivery_mode | c_section | R1 | 0.90 | biosample_attr | C-section |
| SAMEA117508454 | family_id | 22154 | R1 | 0.85 | biosample.attribute:family_id | family_id=22154 |
| SAMEA117508454 | family_role | child | R1 | 0.85 | biosample.attribute:host_life_stage | host_life_stage=infant; host_age_mother=18 |
| SAMEA117508454 | gestational_age_weeks | 39.29 | R1 | 0.90 | biosample_attr | 275 |
| SAMEA117508454 | location_locality | Dhaka City | R3 | 0.70 | paper.body.methods | screened for eligibility to enter the study at two government hospitals in Dhaka City, Dhaka, Bangladesh |
| SAMEA117508454 | location_site | MCHTI and MFSTC | R3 | 0.70 | paper.body.methods | at two government hospitals in Dhaka City, Dhaka, Bangladesh: MCHTI and MFSTC |
| SAMEA117508454 | preterm_status | term | R1 | 0.85 | biosample_attr | 275 |
| SAMEA117508454 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMEA117508454 | subject_id | 221541 | R1 | 0.85 | biosample_attr | 221541 |
Sequencing
1,919 runs over 1,674 samples · mean 1.88 Gbp per run (median 1.92 Gbp, total 3,601.94 Gbp; 1,919 runs with a base count) · layout PAIRED 1,919 · platform ILLUMINA 1,919 · models Illumina NovaSeq 6000 (1,919) · 72% of runs with a Sandpiper profile · first public 2025-12-12
Authors (0)
No author record.
Downloads
PRJEB83552.csv.gz (58.9 KB) · parquet (148.7 KB) — all 1,674 samples, every field with route and confidence · PRJEB83552_determinations.csv.gz (150.8 KB) — 20,006 evidence rows