Infant gut microbiome, vaccine response cohort
736 stool samples from infants and neonates followed longitudinally over the first year of life, examining microbiome/metabolome maturation in relation to primary vaccination response and antibiotic exposure. machine-written summary
736 samples · 736 runs · US · Infant / toddler · 2023 · 6.21 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,803 sample values (age, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 736 sample values (country) · PMC10654091 |
| ○ 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
design observational_with_procedure
longitudinal — not resolved
Schedule stated by the source: “Repeated stool samples per infant across multiple visits over the first year of life (library names show V1-V12 visit codes)” (time origin: birth); stated follow-up 12 mo.
Genera, mean relative abundance over 658 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 | 659 | 90% | ||||
| country | 736 | 100% | 736 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 736 | 100% | 736 | |||
| sex | 709 | 96% | 709 | |||
| timepoint_label | 699 | 95% | 699 | |||
| age_at_collection_days | 659 | 90% | 659 |
- Very early life microbiome and metabolome correlates with primary vaccination variability in children. PMID 37610205 PMC10654091 curated
Archive description
We show a longitudinal study of stool microbiome in infants and track the microbiome development over the first year of life. We demonstrate that the stool microbiome has divergent timing and patterns in maturation. We also show that that evenness of genera in the stool microbiome correlates with lower vaccine response. Finally, we show that antibiotic exposure was associated with low vaccine response and microbiome features. This work indicates that there may be potential to intervene before first childhood vaccinations to improve later protection
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “longitudinal study of stool microbiome in infants”
- 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.title · “Very Early Life Microbiome and Metabolome”
- life stage study.title · “Vaccination Variability in Children”
- life stage study.description · “intervene before first childhood vaccinations to improve”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN34364944 | age_at_collection_days | 171 | R1 | 0.80 | biosample_attr | age=171; unit from PMC10654091: showing their time in the study by age |
| SAMN34364944 | country | US | R3 | 0.75 | paper.fulltext.methods | Rochester Regional Health System (Bay Creek Pediatrics |
| SAMN34364944 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN34364944 | subject_id | 123_S2F2 | R1 | 0.50 | biosample_attr | 123_S2F2 |
| SAMN34364945 | timepoint_label | S2F | R1 | 0.70 | sample.name_rule:library_names | 123_S2F |
| SAMN34364950 | timepoint_label | V10 | R1 | 0.70 | run.library_name | 123_V10 |
Sequencing
736 runs over 736 samples · mean 6.69 Gbp per run (median 6.21 Gbp, total 4,922.84 Gbp; 736 runs with a base count) · layout PAIRED 736 · platform ILLUMINA 736 · models Illumina HiSeq 2000 (664), Illumina NovaSeq 6000 (72) · 89% of runs with a Sandpiper profile · first public 2023-08-19
Authors (19)
Shaffer M first · Best K · Tang C · Liang X · Schulz S · Gonzalez E · White CH · Wyche TP · Kang J · Wesseling H · Topçuoğlu BD · Cairns T · Sana TR · Kaufhold RM · Maritz JM · Woelk CH · Swaminathan G · Norton JE · Pichichero ME last
Downloads
PRJNA961698.csv.gz (24.4 KB) · parquet (105.7 KB) — all 736 samples, every field with route and confidence · PRJNA961698_determinations.csv.gz (28.2 KB) — 3,539 evidence rows