Gut microbiome in neuroblastoma and healthy children, Italy
Cross-sectional study of 288 gut microbiome samples from children in Italy, comparing healthy controls (225 samples) and children with other cancer (63 samples), examining maternal-to-child microbiome seeding and transmission. machine-written summary
288 samples · 288 runs · IT · Infant / toddler · 2023 · 7.05 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 576 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 576 sample values (location locality, location site) · PMC10731604 |
| ✓ Supplementary tables | 962 sample values (age, antibiotic exposure, delivery mode, feeding mode, sex) |
| ✓ External resources | 576 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
mother–infant — not resolved
Maternal-seeding design: children (neuroblastoma, other cancer, healthy) and mothers; archive has no per-sample mother/child link.
Genera, mean relative abundance over 253 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 | 86 | 30% | ||||
| country | 288 | 100% | 288 | |||
| health_condition | 288 | 100% | 288 | |||
| subject_id | 0 | 0% | ||||
| collection_date | 288 | 100% | 288 | |||
| detailed_location | 288 | 100% | ||||
| health_condition_detail | 288 | 100% | 288 | |||
| location_locality | 288 | 100% | 288 | |||
| location_site | 288 | 100% | 288 | |||
| sex | 288 | 100% | 288 | |||
| antibiotic_exposure | 274 | 95% | 274 | |||
| delivery_mode | 157 | 55% | 157 | |||
| feeding_mode | 157 | 55% | 157 | |||
| age_at_collection_days | 86 | 30% | 86 |
- Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal microbial seeding. PMID 38104504 PMC10731604 curated
Archive description
Neuroblastoma accounts for approximately 15% of all deaths due to cancer in childhood, being the most frequent extracranial tumour in children often present as an abdominal formation. It remains uncovered whether the gut microbiome, which is seeded at birth and shaped during the first childhood, plays a role in the tumorigenesis of neuroblastoma, and if non-usual microbiome transmission from mother to child may represent a differential aspect from healthy children to children diagnosed with neuroblastoma.
How this project entered the registry
Classified as human gut / stool / blood / tissue / internal fluids shotgun DNA metagenome of infant / toddler and adult 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 · “with alterations in gut microbiome composition subsequent”
- body site study.description · “uncovered whether the gut microbiome, which is”
- body site study.description · “most frequent extracranial tumour in children often”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “composition subsequent to maternal seeding”
- life stage study.description · “to cancer in childhood , being the”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA113904353 | age_at_collection_days | 950 | R2 | 0.85 | paper.supp.table | age_years=2.6 |
| SAMEA113904353 | antibiotic_exposure | no | R2 | 0.85 | paper.supp.table | antibiotic_intake=no |
| SAMEA113904353 | collection_date | 2018 | R1 | 0.85 | biosample.attribute:collection_date | 2018 |
| SAMEA113904353 | country | IT | R1 | 0.90 | biosample_attr | Italy |
| SAMEA113904353 | delivery_mode | vaginal | R2 | 0.85 | paper.supp.table | mode_delivery=vaginal |
| SAMEA113904353 | feeding_mode | exclusive_breast | R2 | 0.85 | paper.supp.table | feeding_mode=breastmilk |
| SAMEA113904353 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMEA113904353 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMEA113904353 | location_locality | Genoa | R3 | 0.70 | paper.fulltext.methods | enrolled at the IRCCS Istituto Giannina Gaslini in Genoa |
| SAMEA113904353 | location_site | IRCCS Istituto Giannina Gaslini | R3 | 0.70 | paper.fulltext.methods | enrolled at the IRCCS Istituto Giannina Gaslini |
| SAMEA113904353 | sex | male | R2 | 0.85 | paper.supp.table | sex=M |
Sequencing
288 runs over 288 samples · mean 7.67 Gbp per run (median 7.05 Gbp, total 2,208.33 Gbp; 288 runs with a base count) · layout PAIRED 288 · platform ILLUMINA 288 · models unspecified (288) · 88% of runs with a Sandpiper profile · first public 2023-08-20
Authors (14)
Valles-Colomer M first · Manghi P · Cumbo F · Masetti G · Armanini F · Asnicar F · Blanco-Miguez A · Pinto F · Punčochář M · Garaventa A · Amoroso L · Ponzoni M · Corrias MV · Segata N last
Help complete this project
2 of the 4 core fields are below 50% coverage: age_category, subject_id. Share metadata
Downloads
PRJEB63351.csv.gz (9.2 KB) · parquet (83.5 KB) — all 288 samples, every field with route and confidence · PRJEB63351_determinations.csv.gz (17.9 KB) — 2,690 evidence rows