Mother-Infant Vertical Transmission Pilot, Trento, Italy
A longitudinal cohort pilot study of 24 samples from mothers and infants in Trento, Italy, assessing feasibility of strain-level tracking of shared microbiome members; 16 samples from healthy infants. machine-written summary
24 samples · 24 runs · IT · Infant / toddler · 2016 · 2.11 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 148 sample values (collection date, country, family id, family role, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC11733223, PMC5264247, PMC8115609, PMC9542798 |
| ✓ Supplementary tables | 47 sample values (age, delivery mode, diet, feeding mode, subject id) |
| ✓ External resources | 32 sample values (health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
age: supplementary table and Meta2DB disagree for 3 samples (e.g. 90 vs 365.2) — withheld; sex differs between samples of the same subject id (2 subjects, 4 samples) — sex withheld; subject ids shared by samples of both sexes (4 ids, 14 samples) — ids withheld.
The sources disagree on 14 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 (21)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN05615099 | age | 90 (supplementary table) | 365.2 (Meta2DB) | withheld: neither value published |
| SAMN05615101 | age | 90 (supplementary table) | 365.2 (Meta2DB) | withheld: neither value published |
| SAMN05615103 | age | 480 (supplementary table) | 365.2 (Meta2DB) | withheld: neither value published |
| SAMN05615097 | sex | male (sequence archive) | subject 2: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMN05615098 | sex | male (sequence archive) | subject 3: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMN05615105 | sex | female (sequence archive) | subject 2: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMN05615106 | sex | female (sequence archive) | subject 3: male in 1 sample, female in 1 sample | withheld: neither value published |
| SAMN05615097 | subject id | 2 | male (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMN05615098 | subject id | 3 | male (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMN05615099 | subject id | 4 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN05615100 | subject id | 4 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN05615101 | subject id | 5 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN05615102 | subject id | 5 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN05615103 | subject id | 5 | male (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN05615105 | subject id | 2 | female (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMN05615106 | subject id | 3 | female (sequence archive) | subject id withheld (samples of both sexes share it) |
| SAMN05615107 | subject id | 4 | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN05615108 | subject id | 4 | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN05615109 | subject id | 5 | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN05615110 | subject id | 5 | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
| SAMN05615111 | subject id | 5 | female (sequence archive) | subject id withheld (samples of both sexes share it); sex kept |
longitudinal — not resolvedmother–infant
Schedule stated by the source: “Samples at T1, T2, T3 (up to 3 timepoints per subject, collected in 2014 and 2015)”.
5 mother–infant pairs (couple 1–5): mother stool, mother milk and infant stool, up to 3 time points · 5 families with 17 sampled people (5 with a parent and a child).
motherchild · 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: 5 linked groups from explicit relations · 5 families. 1 people in the project overall.
Families (5)
| family | members | samples |
|---|---|---|
| 5 | mother×2 + child×3 | SAMN05615101 · SAMN05615102 · SAMN05615103 · SAMN05615109 · SAMN05615110 · SAMN05615111 · SAMN05615117 · SAMN05615118 · SAMN05615119 |
| 4 | mother×2 + child×2 | SAMN05615099 · SAMN05615100 · SAMN05615107 · SAMN05615108 · SAMN05615115 · SAMN05615116 |
| 1 | mother + child | SAMN05615096 · SAMN05615104 · SAMN05615112 |
| 2 | mother×2 + child | SAMN05615097 · SAMN05615105 · SAMN05615113 |
| 3 | mother×2 + child | SAMN05615098 · SAMN05615106 · SAMN05615114 |
Genera, mean relative abundance over 8 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 | 16 | 67% | ||||
| country | 24 | 100% | 24 | |||
| health_condition | 16 | 67% | 16 | |||
| subject_id | 10 | 42% | 8 | 2 | ||
| collection_date | 24 | 100% | 24 | |||
| family_id | 24 | 100% | 24 | |||
| family_role | 24 | 100% | 24 | |||
| timepoint_label | 24 | 100% | 24 | |||
| sex | 20 | 83% | 20 | |||
| delivery_mode | 16 | 67% | 16 | |||
| health_condition_detail | 16 | 67% | 16 | |||
| age_at_collection_days | 13 | 54% | 13 | |||
| diet | 8 | 33% | 8 | |||
| feeding_mode | 8 | 33% | 8 |
- Studying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling. PMID 28144631 PMC5264247 curated
- Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures. PMID 33960282 PMC8115609 curated
- Investigating the infant gut microbiota in developing countries: worldwide metagenomic meta-analysis involving infants living in sub-urban areas of Côte d'Ivoire. PMID 34152069 PMC8518733 curated
- A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID 36050292 PMC9437082 curated
- Lactic acid bacteria and bifidobacteria deliberately introduced into the agro-food chain do not significantly increase the antimicrobial resistance gene pool. PMID 36170451 PMC9542798 curated
11 more
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645
- Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium. PMID 36316342 PMC9622858
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646
- Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut. PMID 37259063 PMC10230729
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871
- A metagenomic catalog of the early-life human gut virome. PMID 38424077 PMC10904392
- Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life. PMID 38882494 PMC11170968
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892
- Early life microbial succession in the gut follows common patterns in humans across the globe. PMID 39809768 PMC11733223
Archive description
This is a pilot study whose aim is to assess the feasibility of strain-level tracking of microbiome members shared by mothers and their children.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- 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.description · “mothers and their children .”
- life stage study.description · “members shared by mothers and their children.”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN05615096 | age_at_collection_days | 90 | R2 | 0.85 | paper.supp.table | Sampling, day=90 |
| SAMN05615096 | collection_date | 2014 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2014 |
| SAMN05615096 | country | IT | R1 | 0.90 | biosample_attr | Italy: Trento |
| SAMN05615096 | delivery_mode | vaginal | R2 | 0.85 | paper.supp.table | Mode of delivery=vaginal |
| SAMN05615096 | diet | other_diet | R2 | 0.85 | paper.supp.Table S1.xlsx[Asnicar et al.!Feeding regimen] | SRR4052021: Feeding regimen=combined |
| SAMN05615096 | family_id | 1 | R1 | 0.85 | biosample.attribute:couple | couple: 1 |
| SAMN05615096 | family_role | child | R1 | 0.85 | biosample.attribute:env_material | env_material: Human infant stool |
| SAMN05615096 | feeding_mode | mixed | R2 | 0.85 | paper.supp.table | Feeding regimen=combined |
| SAMN05615096 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN05615096 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN05615096 | sex | female | R1 | 0.90 | biosample_attr | female |
| SAMN05615112 | subject_id | M1 | R1 | 0.70 | sample.name_rule:library_name | MV_MIM1_t1M14; couple 1; Human mother milk |
| SAMN05615096 | subject_id | 1 | R2 | 0.85 | paper.supp.Table S1.xlsx[Asnicar et al.!PersonID] | SRR4052021: PersonID=1 |
| SAMN05615096 | timepoint_label | T1 | R1 | 0.80 | biosample_attr | T1 |
Sequencing
24 runs over 24 samples · mean 1.86 Gbp per run (median 2.11 Gbp, total 44.57 Gbp; 24 runs with a base count) · layout PAIRED 24 · platform ILLUMINA 24 · models Illumina HiSeq 2500 (24) · 62% of runs with a Sandpiper profile · first public 2016-10-01
Authors (127)
Asnicar F first · Manara S · Zolfo M · Truong DT · Scholz M · Armanini F · Ferretti P · Gorfer V · Pedrotti A · Tett A · Segata N last · Wang S first · Zeng S · Egan M · Cherry P · Strain C · Morais E · Boyaval P · Ryan CA · M Dempsey E · Ross RP · Stanton C last · Fontana F first · Mancabelli L · Lugli GA · Taracchini C · Alessandri G · Longhi G · Anzalone R · Viappiani A · Famo R · Brognan M · Micondo KH · Turroni F · Ventura M · D'Alfonso R · Milani C last · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Rozman V first · Mohar Lorbeg P · Treven P · Accetto T · Golob M · Zdovc I · Bogovič Matijašić B last · Tarracchini C first · Argentini C · van Sinderen D · Rizzo SM first · Bianchi MG · Bussolati O · Ormaasen I first · Rudi K · Diep DB · Snipen L last · Hall B first · Levy S · Dufault-Thompson K · Arp G · Zhong A · Ndjite GM · Weiss A · Braccia D · Jenkins C · Grant MR · Abeysinghe S · Yang Y · Jermain MD · Wu CH · Ma B · Jiang X last · Li S · Ying J · Wang H · Qu Y · Niu X · Xu X first · Feng Q · Zhang T · Gao Y · Cheng Q · Zhang W · Wu Q · Xu K · Li Y · Nguyen N · Taft DH · Mills DA · Lemay DG · Zhu W · Mao S · Zhang A · Liu J last · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Fahur Bottino G first · Bonham KS · Patel F · McCann S · Zieff M · Naspolini N · Ho D · Portlock T · Joos R · Midani FS · Schüroff P · Das A · Shennon I · Wilson BC · O'Sullivan JM · Britton RA · Murray DM · Kiely ME · Taddei CR · Beltrão-Braga PCB · Campos AC · Polanczyk GV · Huttenhower C · Donald KA · Klepac-Ceraj V last
Downloads
PRJNA339914.csv.gz (1.8 KB) · parquet (71.6 KB) — all 24 samples, every field with route and confidence · PRJNA339914_determinations.csv.gz (3.1 KB) — 227 evidence rows