Italian mother-child microbiome, neuroblastoma subgroup
254 gut microbiome samples from Italian mother/child pairs (including siblings and twins), with a subgroup of children with neuroblastoma sampled at onset and during therapy; longitudinal cohort design. machine-written summary
254 samples · 254 runs · IT · Infant / toddler · 2022 · 7.35 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,297 sample values (age, antibiotic exposure, country, family id, family role, health condition, health condition detail, sex) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10234599, PMC11322291, PMC12963580, PMC9892008 |
| ✓ Supplementary tables | 57 sample values (age, delivery mode) |
| ✓ External resources | 89 sample values (age) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
age: supplementary table and curatedMetagenomicData disagree for 37 samples (e.g. 79 vs 730.5) — withheld.
The sources disagree on 37 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (37)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN18473790 | age | 79 (supplementary table) | 730.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473799 | age | 216 (supplementary table) | 2556.75 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473804 | age | 85 (supplementary table) | 730.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473809 | age | 46 (supplementary table) | 547.88 (GMrepo) | withheld: neither value published |
| SAMN18473819 | age | 15 (supplementary table) | 182.62 (GMrepo) | withheld: neither value published |
| SAMN18473820 | age | 122 (supplementary table) | 1461.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473822 | age | 137 (supplementary table) | 1461.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473823 | age | 137 (supplementary table) | 1461.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473832 | age | 9 (supplementary table) | 109.58 (GMrepo) | withheld: neither value published |
| SAMN18473836 | age | 195 (supplementary table) | 2191.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473837 | age | 88 (supplementary table) | 730.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473838 | age | 234 (supplementary table) | 2556.75 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473839 | age | 85 (supplementary table) | 730.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473841 | age | 24 (supplementary table) | 292.2 (GMrepo) | withheld: neither value published |
| SAMN18473842 | age | 201 (supplementary table) | 2191.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473843 | age | 140 (supplementary table) | 1461.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473844 | age | 326 (supplementary table) | 3652.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473845 | age | 198 (supplementary table) | 2191.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473846 | age | 70 (supplementary table) | 730.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473847 | age | 195 (supplementary table) | 2191.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473848 | age | 76 (supplementary table) | 730.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473849 | age | 228 (supplementary table) | 2556.75 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473850 | age | 207 (supplementary table) | 2191.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473852 | age | 237 (supplementary table) | 2556.75 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473853 | age | 207 (supplementary table) | 2191.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473854 | age | 320 (supplementary table) | 3652.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473855 | age | 265 (supplementary table) | 2922.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473856 | age | 347 (supplementary table) | 4017.75 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473857 | age | 85 (supplementary table) | 730.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473858 | age | 213 (supplementary table) | 2556.75 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473859 | age | 292 (supplementary table) | 3287.25 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473860 | age | 177 (supplementary table) | 1826.25 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473861 | age | 177 (supplementary table) | 1826.25 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473863 | age | 180 (supplementary table) | 1826.25 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473864 | age | 180 (supplementary table) | 1826.25 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473865 | age | 180 (supplementary table) | 1826.25 (curatedMetagenomicData) | withheld: neither value published |
| SAMN18473903 | age | 12565 (sequence archive) | 9861.75 (curatedMetagenomicData) | withheld: neither value published |
longitudinal — not resolvedfamiliesmother–infantparent–childsiblingstwins
19 of 217 people sampled more than once (56 samples; median 3, up to 4 per person). Schedule stated by the source: “onset (T0) and during therapy (T1, T2, T3) for NB patients” (time origin: diagnosis).
85 families (BioSample host_family_relationship): 86 mothers, 113 children incl. 11 twins/triplets; 1 cousin; neuroblastoma patients and controls · 85 families with 200 sampled people (85 with a parent and a child), 12 twin sets.
motherchildtwinsiblingother relative · 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: 6 linked groups from explicit relations · 18 of 84 families (one per family structure, then more). 217 people in the project overall.
Families (25 of 85)
Genera, mean relative abundance over 228 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 | 211 | 83% | ||||
| country | 254 | 100% | 254 | |||
| health_condition | 221 | 87% | 221 | |||
| subject_id | 254 | 100% | 254 | |||
| health_condition_detail | 254 | 100% | 254 | |||
| sex | 254 | 100% | 254 | |||
| timepoint_label | 253 | 100% | 253 | |||
| antibiotic_exposure | 249 | 98% | 249 | |||
| family_id | 237 | 93% | 237 | |||
| family_role | 237 | 93% | 237 | |||
| age_at_collection_days | 174 | 69% | 84 | 90 | ||
| delivery_mode | 56 | 22% | 56 |
- The person-to-person transmission landscape of the gut and oral microbiomes. PMID 36653448 PMC9892008 curated
- Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population. PMID 37116481 PMC10234599 curated
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291 curated
- Gut microbial signatures expose the westernized lifestyle of urban Ethiopian children. PMID 41620544 PMC12963580 curated
Archive description
human gut microbiome from Italian children and mothers pairs (including siblings and twins). A subgroup of children has Neuroblastoma, sampled at the onset and during therapy.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of child and adult and infant / toddler by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “human gut microbiome from Italian”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- life stage study.title · “Mothers/ children Metagenome”
- life stage study.description · “microbiome from Italian children and mothers pairs”
- life stage study.title · “Mothers /children Metagenome”
- life stage study.description · “Italian children and mothers pairs (including siblings”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN18473884 | age_at_collection_days | 13843 | R1 | 0.80 | sample.attr.host_age | 37.9 |
| SAMN18473791 | age_at_collection_days | 1168.8 | R2 | 0.75 | external.gmrepo source | host_age: 3.2 |
| SAMN18473810 | age_at_collection_days | 0 | R2 | 0.85 | paper.supp.table | age=0 |
| SAMN18473790 | antibiotic_exposure | no | R1 | 0.85 | biosample_attr | no |
| SAMN18473790 | country | IT | R1 | 0.90 | biosample_attr | Italy |
| SAMN18473790 | delivery_mode | vaginal | R2 | 0.85 | paper.supp.table | delivery_mode=vaginal |
| SAMN18473790 | family_id | CTRM1 | R1 | 0.85 | biosample.attribute:host_family_relationship | Brother C2 |
| SAMN18473790 | family_role | child | R1 | 0.85 | biosample.attribute:host_family_relationship | Brother C2 |
| SAMN18473790 | health_condition | healthy_control | R1 | 0.90 | sample.attr.host_disease | host_disease=healthy control |
| SAMN18473884 | health_condition | healthy_control | R1 | 0.80 | biosample.attribute:host_disease | host_disease: Mother_healthy control |
| SAMN18473790 | health_condition_detail | healthy control | R1 | 0.90 | biosample.attribute:host_disease | host_disease: healthy control |
| SAMN18473790 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN18473790 | subject_id | C1 | R1 | 0.85 | biosample_attr | C1 |
| SAMN18473791 | timepoint_label | T0 | R1 | 0.80 | biosample_attr | T0 |
Sequencing
254 runs over 254 samples · mean 7.89 Gbp per run (median 7.35 Gbp, total 2,003.90 Gbp; 254 runs with a base count) · layout PAIRED 254 · platform ILLUMINA 254 · models Illumina NovaSeq 6000 (254) · 90% of runs with a Sandpiper profile · first public 2022-04-04
Authors (57)
Valles-Colomer M first · Blanco-Míguez A · Manghi P · Asnicar F · Dubois L · Golzato D · Armanini F · Cumbo F · Huang KD · Manara S · Masetti G · Pinto F · Piperni E · Punčochář M · Ricci L · Zolfo M · Farrant O · Goncalves A · Selma-Royo M · Binetti AG · Becerra JE · Han B · Lusingu J · Amuasi J · Amoroso L · Visconti A · Steves CM · Falchi M · Filosi M · Tett A · Last A · Xu Q · Qin N · Qin H · May J · Eibach D · Corrias MV · Ponzoni M · Pasolli E · Spector TD · Domenici E · Collado MC · Segata N last · Raffaetà R · Cabrera-Rubio R · Olcina M · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Kirsche L first · Leary P · Blaser MJ · Scharl M · Negussie A · Müller A last
Downloads
PRJNA716780.csv.gz (10.0 KB) · parquet (84.2 KB) — all 254 samples, every field with route and confidence · PRJNA716780_determinations.csv.gz (21.9 KB) — 2,443 evidence rows