Mother-infant microbiome transmission cohort, Trento, Italy
Longitudinal cohort of 230 shotgun metagenome samples (stool, tongue dorsum, vagina, skin) from 25 mother/infant pairs in Trento, Italy, studying vertical transmission of microbiome members; most samples from neonates, 118 healthy controls. machine-written summary
230 samples · 230 runs · IT · Infant / toddler · 2018 · 1.59 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,318 sample values (age, collection date, country, family id, family role, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 244 sample values (collection date, location locality) · PMC6716579 |
| ✓ Supplementary tables | 944 sample values (age, antibiotic exposure, birth weight grams, delivery mode, feeding mode, maternal antibiotics, preterm status, sex) |
| ✓ External resources | 258 sample values (bmi, 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 |
intervention — arms not resolved
design observational_with_procedure
longitudinalmother–infant
10 of 122 people sampled more than once (21 samples; median 2, up to 3 per person) · follow-up median 4 d (max 23 d) · median interval between samples 4 d (time from age at collection). Schedule stated by the source: “Longitudinal timepoints t0-t5/T6-T7 per subject; infant_age values observed: not applicable, 1 day, 3 days, 7 days, 1 month, 4 months.” (time origin: birth).
Each row is one person (4 shown of 10); dots are samples at days since that person's first sample; rows of one family are adjacent and coloured by role (mother, father, child, twin).
25 mother–infant couples (couple_id), mothers and infants both sampled; gut samples of 216 linked · 25 families with 145 sampled people (25 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: 24 of 25 families (one per family structure, then more). 122 people in the project overall.
Families (25)
Genera, mean relative abundance over 100 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 | 160 | 70% | ||||
| country | 230 | 100% | 230 | |||
| health_condition | 118 | 51% | 118 | |||
| subject_id | 230 | 100% | 14 | 216 | ||
| collection_date | 230 | 100% | 216 | 14 | ||
| detailed_location | 230 | 100% | ||||
| location_locality | 230 | 100% | 230 | |||
| timepoint_label | 230 | 100% | 230 | |||
| family_id | 216 | 94% | 216 | |||
| family_role | 216 | 94% | 216 | |||
| age_at_collection_days | 159 | 69% | 137 | 22 | ||
| delivery_mode | 151 | 66% | 151 | |||
| maternal_antibiotics | 138 | 60% | 138 | |||
| preterm_status | 138 | 60% | 138 | |||
| health_condition_detail | 118 | 51% | 118 | |||
| feeding_mode | 97 | 42% | 97 | |||
| antibiotic_exposure | 90 | 39% | 90 | |||
| sex | 80 | 35% | 59 | 21 | ||
| birth_weight_grams | 71 | 31% | 71 | |||
| bmi | 22 | 10% | 22 |
- Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome. PMID 30001516 PMC6716579 curated
- Impact of Microbiota Transplant on Resistome of Gut Microbiota in Gnotobiotic Piglets and Human Subjects. PMID 32508773 PMC7248251 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
- Deterministic transition of enterotypes shapes the infant gut microbiome at an early age. PMID 34429130 PMC8383385 curated
20 more
- Rapid evolution and strain turnover in the infant gut microbiome. PMID 35545448 PMC9248880
- A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID 36050292 PMC9437082
- Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach. PMID 36123315 PMC10092070
- 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
- Microbial bile salt hydrolase activity influences gene expression profiles and gastrointestinal maturation in infant mice. PMID 36420990 PMC9704388
- Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population. PMID 37116481 PMC10234599
- 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
- BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen. PMID 38172624 PMC10769871
- Longitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition. PMID 38291346 PMC10827747
- A metagenomic catalog of the early-life human gut virome. PMID 38424077 PMC10904392
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788
- 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
- Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome. PMID 39866568 PMC11758915
- Dynamics of gut resistome and mobilome in early life: a meta-analysis. PMID 40048849 PMC11929092
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
- CLMB: deep contrastive learning for robust metagenomic binning
Archive description
The study investigates the potential transmission of the human microbiome members from mothers to infants using shotgun metagenomics. We targeted 25 mother/infant pairs, considering multiple bodysides (stool, tongue dorsum, vagina and skin).
How this project entered the registry
Classified as human gut / stool / oral cavity / skin / vaginal / urogenital shotgun DNA metagenome of infant / toddler and adult by deterministic_prior with confidence 0.90. Assay shotgun_dna.
- host external_curation.infant_catalog · “infant triage verdict include”
- body site study.description · “multiple bodysides ( stool , tongue dorsum,”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site study.description · “multiple bodysides (stool, tongue dorsum, vagina and”
- body site study.description · “dorsum, vagina and skin ).”
- body site study.description · “(stool, tongue dorsum, vagina and skin).”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Mother- infant microbiome vertical transmission”
- life stage study.description · “microbiome members from mothers to infants using”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN06350023 | age_at_collection_days | 1 | R1 | 0.70 | biosample_attr | 1 day |
| SAMN06350029 | age_at_collection_days | 0 | R2 | 0.85 | paper.supp.table | Sampling, day=0 |
| SAMN06350023 | antibiotic_exposure | no | R2 | 0.75 | paper.supp.table | abx_ever=no |
| SAMN06350023 | birth_weight_grams | 3210 | R2 | 0.75 | paper.supp.table | birth_weight=3210 |
| SAMN06350029 | bmi | 22.8 | R2 | 0.75 | external.cmd source | bmi: 22.8 |
| SAMN06350021 | collection_date | 2015 | R1 | 0.85 | biosample.attribute:collection_date | 2015 |
| SAMN18395666 | collection_date | 2015-04/2016-07 | R3 | 0.70 | paper.fulltext.methods | recruited by Santa Chiara Hospital in Trento, Italy, between April 2015 and |
| SAMN06350021 | country | IT | R1 | 0.90 | biosample_attr | Italy: Trento |
| SAMN06350023 | delivery_mode | vaginal | R2 | 0.75 | paper.supp.table | Mode of delivery=vaginal |
| SAMN06350021 | family_id | 10001 | R1 | 0.85 | biosample.attribute:couple_id | 10001 |
| SAMN06350021 | family_role | mother | R1 | 0.85 | biosample.attribute:donor | mother |
| SAMN06350023 | feeding_mode | exclusive_breast | R2 | 0.75 | paper.supp.table | Nutrition=breast-fed |
| SAMN06350023 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN06350023 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN06350021 | location_locality | Trento | R3 | 0.70 | paper.fulltext.methods | recruited by Santa Chiara Hospital in Trento, Italy |
| SAMN06350023 | maternal_antibiotics | yes | R2 | 0.75 | paper.supp.table | maternal_abx=yes |
| SAMN06350023 | preterm_status | term | R2 | 0.75 | paper.supp.table | premature=no |
| SAMN06350021 | sex | female | R1 | 0.85 | biosample.attribute:donor | mother |
| SAMN06350029 | sex | female | R2 | 0.85 | paper.supp.table | Gender=female |
| SAMN18395666 | subject_id | 10006I | R1 | 0.70 | sample.name_rule:alias | 10006I |
| SAMN06350021 | subject_id | PRJNA352475_10001_M | R2 | 0.75 | paper.supp.table | Host ID=PRJNA352475_10001_M |
| SAMN06350021 | timepoint_label | t0 | R1 | 0.70 | run.library_name | 2003_t0 |
| SAMN18395666 | timepoint_label | T6 | R1 | 0.70 | sample.name_rule:alias | T6 |
Sequencing
230 runs over 230 samples · mean 2.43 Gbp per run (median 1.59 Gbp, total 558.03 Gbp; 230 runs with a base count) · layout PAIRED 230 · platform ILLUMINA 230 · models Illumina HiSeq 2500 (230) · 55% of runs with a Sandpiper profile · first public 2018-02-03 – 2022-04-04
Authors (188)
Ferretti P first · Pasolli E · Tett A · Asnicar F · Gorfer V · Fedi S · Armanini F · Truong DT · Manara S · Zolfo M · Beghini F · Bertorelli R · De Sanctis V · Bariletti I · Canto R · Clementi R · Cologna M · Crifò T · Cusumano G · Gottardi S · Innamorati C · Masè C · Postai D · Savoi D · Duranti S · Lugli GA · Mancabelli L · Turroni F · Ferrario C · Milani C · Mangifesta M · Anzalone R · Viappiani A · Yassour M · Vlamakis H · Xavier R · Collado CM · Koren O · Tateo S · Soffiati M · Pedrotti A · Ventura M · Huttenhower C · Bork P · Segata N last · Liu H first · Wang HH 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 · Taracchini C · Alessandri G · Longhi G · Famo R · Brognan M · Micondo KH · D'Alfonso R · Xiao L first · Wang J · Zheng J · Li X · Zhao F last · Chen DW first · Garud NR last · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Tarracchini C · Bianchi MG · Rizzo SM · Argentini C · Vergna LM · Taurino G · Chiu M · Bussolati O · van Sinderen D · Núñez-Sánchez MA first · Herisson FM · Keane JM · García-González N · Rossini V · Pinhiero J · Daly J · Bustamante-Garrido M · Hueston CM · Patel S · Canela N · Herrero P · Claesson MJ · Melgar S · Nally K · Caplice NM · Gahan CGM last · Selma-Royo M · Huang KD · Blanco-Miguez A · Cumbo F · Golzato D · Manghi P · Pinto F · Valles-Colomer M · Amoroso L · Corrias MV · Ponzoni M · Raffaetà R · Cabrera-Rubio R · Olcina M · Collado MC · 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 · Ennis D first · Shmorak S · Jantscher-Krenn E · Li S · Ying J · Wang H · Qu Y · Niu X · De Biase R · Bocchio F · De Conto F · Nouvenne A · Ticinesi A · Meschi T · Cecchi R · 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 · Pucci N first · Ujčič-Voortman J · Verhoeff AP · Mende DR last · Bargheet A first · Noordzij HT · Ponsero AJ · Jian C · Korpela K · Debelius J · Kurilshikov A · Pettersen VK last · Gennaioli E · Muscò A · Vitale SG · Angioni S
Downloads
PRJNA352475.csv.gz (8.8 KB) · parquet (83.7 KB) — all 230 samples, every field with route and confidence · PRJNA352475_determinations.csv.gz (28.2 KB) — 2,764 evidence rows