Infant gut virome, poliovirus shedding, Bangladesh/US
150 stool samples from a longitudinal cohort of Bangladeshi infants (with age-matched US infants for comparison), examining gut virome composition in relation to poliovirus shedding after oral poliovirus vaccination. machine-written summary
150 samples · 150 runs · BD, US · Infant / toddler · 2020 · 2.13 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 150 sample values (probiotic exposure) · PMC7506025 |
| ✓ Supplementary tables | 376 sample values (country, subject id, timepoint) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
intervention — arms not resolved
Vaccination as the study intervention design observational_with_procedure · population healthy_control · Oral poliovirus vaccine (OPV) administered to infants
“Poliovirus Shedding After Oral Poliovirus Vaccination” — study.title (study level; per-sample arms are in the intervention column below)
longitudinal — not resolved
27 of 27 people sampled more than once (81 samples; median 3, up to 3 per person). Schedule stated by the source: “3 serially collected stool samples per infant following OPV vaccination; timepoints labeled 1, 2, 3” (time origin: intervention start).
Genera, mean relative abundance over 78 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 | 0 | 0% | ||||
| country | 147 | 98% | 147 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 81 | 54% | 81 | |||
| probiotic_exposure | 150 | 100% | 150 | |||
| timepoint_label | 148 | 99% | 148 |
- Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination. PMID 32958861 PMC7506025 curated
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646 curated
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788 curated
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767 curated
Archive description
The potential role of enteric viral infections and the developing infant virome in affecting immune responses to the oral poliovirus vaccine (OPV) is unknown. Here we performed viral metagenomic sequencing on 3 serially collected stool samples from 30 Bangladeshi infants following OPV vaccination and compared findings to stool samples from 16 age-matched infants in the United States (US). In 14 Bangladeshi infants, available post-vaccination serum samples were tested for polio-neutralizing antibodies. The abundance (p=0.006) and richness (p=0.013) of the eukaryotic virome increased with age and were higher than seen in age-matched US infants (p<0.001). In contrast, phage diversity metrics remained stable and were similar to those in US infants. Non-poliovirus eukaryotic virus abundance (3.68 log10 vs. 2.25 log10, p=0.002), particularly from potential viral pathogens (2.78log10 vs. 0.83log10, p=0.002), and richness (p=0.016) were inversely associated with poliovirus shedding. Following vaccination, 28.6% of 14 infants tested developed neutralizing antibodies to all three Sabin types and also exhibited higher rates of poliovirus shedding (p=0.020). No vaccine-derived poliovirus variants were detected. These results reveal an inverse association between eukaryotic virome abundance and poliovirus shedding. Overall gut virome ecology and concurrent viral infections may impact oral vaccine responsiveness in Bangladeshi infants.
How this project entered the registry
Classified as human gut / stool / oral cavity / blood / tissue / internal fluids shotgun DNA metagenome of infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.title · “Metagenomic Sequencing of Stool Samples in Bangladeshi”
- body site study.description · “3 serially collected stool samples from 30”
- body site study.title · “Poliovirus Shedding After Oral Poliovirus Vaccination”
- body site study.description · “responses to the oral poliovirus vaccine (OPV)”
- body site study.description · “infants, available post-vaccination serum samples were tested”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Samples in Bangladeshi Infants : Virome Association”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN15471015 | country | BD | R2 | 0.75 | paper.supp.table | Geography=Bangladesh |
| SAMN15471015 | probiotic_exposure | yes | R3 | 0.70 | paper.fulltext.methods | phase I trial of probiotics in infants |
| SAMN15471078 | subject_id | 2 | R2 | 0.85 | paper.supp.table | Infant=2 |
| SAMN15471015 | timepoint_label | pre-weaning | R2 | 0.75 | paper.supp.table | Time Group=pre-weaning |
Sequencing
150 runs over 150 samples · mean 2.14 Gbp per run (median 2.13 Gbp, total 321.20 Gbp; 150 runs with a base count) · layout PAIRED 150 · platform ILLUMINA 150 · models Illumina HiSeq 2500 (150) · 67% of runs with a Sandpiper profile · first public 2020-07-10 – 2021-07-04
Authors (40)
Tan SK first · Granados AC · Bouquet J · Hoy-Schulz YE · Green L · Federman S · Stryke D · Haggerty TD · Ley C · Yeh MT · Jannat K · Maldonado YA · Andino R · Parsonnet J · Chiu CY last · 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 · Milani C · De Biase R · Bocchio F · De Conto F · Nouvenne A · Ticinesi A · Meschi T · Cecchi R · Longhi G · Gennaioli E · Muscò A · Vitale SG · Angioni S
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata
Downloads
PRJNA644725.csv.gz (4.7 KB) · parquet (75.3 KB) — all 150 samples, every field with route and confidence · PRJNA644725_determinations.csv.gz (4.2 KB) — 526 evidence rows