Infant gut microbiome & rotavirus vaccine efficacy
835 samples from infants and neonates in Panama City, Lima, and Los Angeles, in a longitudinal cohort study examining how the gut microbiome relates to rotavirus vaccine efficacy. machine-written summary
835 samples · 928 runs · PA, PE, US · Infant / toddler · 2026 · 1.43 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 6,552 sample values (age, country, delivery mode, diet, feeding mode, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| – Full text | no open-access full text linked |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 |
longitudinal
312 of 337 people sampled more than once (810 samples; median 3, up to 3 per person) · follow-up median 4 mo (max 5 mo) · median interval between samples 57 d (time from age at collection). Schedule stated by the source: “Not explicitly defined; sample titles use per-infant ID with timepoint suffix (e.g., M1, M2, M4) implying repeated sampling, but schedule not stated”.
Each row is one person (36 shown of 312); dots are samples at days since that person's first sample.
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 835 | 100% | ||||
| country | 835 | 100% | 835 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 835 | 100% | 835 | |||
| age_at_collection_days | 835 | 100% | 835 | |||
| sex | 835 | 100% | 835 | |||
| timepoint_label | 835 | 100% | 835 | |||
| delivery_mode | 827 | 99% | 827 | |||
| diet | 775 | 93% | 775 | |||
| feeding_mode | 775 | 93% | 775 |
Archive description
The Rotavirus vaccine works well to provide protection from the virus in high-income countries, however it does not work as well in middle to low income countries. This research study investigates why this happens, looking at the role of early life exposures such as breast milk and infant nutrition in how the gut microbiome is formed. This study also investigates the role that the gut microbome plays in how well the Rotavirus vaccine works.
How this project entered the registry
Classified as human gut / stool / human milk 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 · “of the infant gut microbiome in rotavirus”
- body site study.description · “in how the gut microbiome is formed.”
- body site study.description · “exposures such as breast milk and infant nutrition”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “role of the infant gut microbiome in”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN54719829 | age_at_collection_days | 115 | R1 | 0.85 | sample.attr.host_age | 115 |
| SAMN54719829 | country | PA | R1 | 0.90 | biosample_attr | Panama: Panama City |
| SAMN54719829 | delivery_mode | vaginal | R1 | 0.90 | biosample_attr | vaginal |
| SAMN54719829 | diet | other_diet | R1 | 0.85 | biosample.attribute:host_diet | host_diet: Both |
| SAMN54719829 | feeding_mode | mixed | R1 | 0.85 | biosample_attr | Both |
| SAMN54719829 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN54719829 | subject_id | RB016 | R1 | 0.85 | biosample_attr | RB016 |
| SAMN54719829 | timepoint_label | M4 | R1 | 0.70 | sample.title | Infant gut microbiome, [RB016_M4] |
Sequencing
928 runs over 835 samples · mean 2.09 Gbp per run (median 1.43 Gbp, total 1,943.29 Gbp; 928 runs with a base count) · layout PAIRED 928 · platform ILLUMINA 928 · models Illumina NovaSeq 6000 (928) · 0% of runs with a Sandpiper profile · first public 2026-01-20
Authors (0)
No author record.
Downloads
PRJNA1404625.csv.gz (27.0 KB) · parquet (108.0 KB) — all 835 samples, every field with route and confidence · PRJNA1404625_determinations.csv.gz (39.1 KB) — 6,552 evidence rows