PRJNA1140720 SRP522883
Microbiome transmission in a nursery cohort, Italy
Modelling human microbiome transmission in a nursery setting
Longitudinal cohort study of 1163 samples from Italy, examining microbiome transmission among one-year-old babies and their close social contacts (family members, pets, nursery teachers) in a nursery setting. machine-written summary
1,163 samples · 1,163 runs · IT · Infant / toddler · 2024 · 13.72 Gbp / sample
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Sources
✓ Sequence archive 9,246 ○ Abstract / description✓ Full text 2,326 ✓ Supplementary tables 5 – External resources– User contribution– Human verified
Checked this project's papers and archive records yourself? Mark it human-verified .
what each source gave ✓ Sequence archive9,246 sample values (age, antibiotic exposure, country, family id, family role, sex, shared setting id, shared setting type) ○ Abstract / descriptionread; no usable statement ✓ Full text2,326 sample values (collection date, location locality) · PMC12960237 ✓ Supplementary tables5 sample values (age) – External resourcesnot covered by the external resources we ingest – User contributionnothing uploaded yet · share metadata – Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
Age
unknown 1,008
adult 148
infant 5
child 2
Body site
primary 1,013
excluded 150
Sequencing depth per sample ·
all projects, 0–0.03 Gbp: 25,080 samples (4 %) all projects, 0.03–0.1 Gbp: 17,066 samples (3 %) this project, 0.03–0.1 Gbp: 4 samples all projects, 0.1–0.3 Gbp: 29,179 samples (5 %) this project, 0.1–0.3 Gbp: 3 samples all projects, 0.3–1 Gbp: 47,044 samples (8 %) this project, 0.3–1 Gbp: 13 samples all projects, 1–3 Gbp: 124,983 samples (22 %) this project, 1–3 Gbp: 40 samples all projects, 3–10 Gbp: 253,728 samples (44 %) this project, 3–10 Gbp: 286 samples all projects, 10–30 Gbp: 72,533 samples (13 %) this project, 10–30 Gbp: 776 samples all projects, 30–100 Gbp: 3,024 samples (1 %) this project, 30–100 Gbp: 41 samples all projects, 100–300 Gbp: 106 samples (0 %) all projects, ≥ 300 Gbp: 9 samples (0 %) project median 13.72 Gbp per sample 0 1 30 Gbp
Sampling design and relatedness
longitudinal — not resolved daycare / school families father–child mother–infant siblings
126 of 132 people sampled more than once (1,007 samples; median 5, up to 34 per person).
41 families in 3 nurseries: 43 babies, 39 mothers, 29 fathers, 7 siblings, plus 10 nursery educators and pets · 38 families with 115 sampled people (38 with a parent and a child) · 3 shared settings.
mother M father F child C 21 × mother + father + child
mother M father F child C sibling S 7 × mother + father + child + sibling
mother M child C 7 × mother + child
mother M child C child C 1 × mother + child×2
mother M mother M child C 1 × mother×2 + child
mother M father F child C child C 1 × mother + father + child×2
family B1 B1_BA5002 — child · 33 samples C BA5002 B1_FA5000 — father · 7 samples F FA5000 B1_MO5001 — mother · 6 samples M MO5001 B1… family B10 B10_BA5032 — child · 28 samples C BA5032 B10_FA5031 — father · 2 samples F FA5031 B10_MO5030 — mother · 2 samples M MO5030 B10_SI5033 — sibling · 2 samples S SI5033 B10… family B11 B11_BA5034 — child · 20 samples C BA5034 B11_MO5035 — mother · 9 samples M MO5035 B11… family B15 B15_BA5044 — child · 17 samples C BA5044 B15_BA5045 — child · 19 samples C BA5045 B15_MO5046 — mother · 5 samples M MO5046 B15… family B5 B5_BA5016 — child · 31 samples C BA5016 B5_MO5015 — mother · 6 samples M MO5015 B5_MO5010 — mother · 1 sample M MO5010 B5… family T5 T5_BA1019 — child · 14 samples C BA1019 T5_BA1020 — child · 14 samples C BA1020 T5_FA1018 — father · 7 samples F FA1018 T5_MO1017 — mother · 8 samples M MO1017 T5… family B2 B2_BA5005 — child · 28 samples C BA5005 B2_FA5004 — father · 6 samples F FA5004 B2_MO5003 — mother · 6 samples M MO5003 B2… family B7 B7_BA5021 — child · 10 samples C BA5021 B7_FA5022 — father · 5 samples F FA5022 B7_MO5020 — mother · 4 samples M MO5020 B7_SI5011 — sibling · 2 samples S SI5011 B7… family B12 B12_BA5037 — child · 12 samples C BA5037 B12_MO5038 — mother · 8 samples M MO5038 B12… family B3 B3_BA5007 — child · 14 samples C BA5007 B3_FA5008 — father · 8 samples F FA5008 B3_MO5006 — mother · 8 samples M MO5006 B3… family B8 B8_BA5023 — child · 33 samples C BA5023 B8_FA5026 — father · 8 samples F FA5026 B8_MO5024 — mother · 9 samples M MO5024 B8_SI5025 — sibling · 5 samples S SI5025 B8… family B13 B13_BA5039 — child · 6 samples C BA5039 B13_MO5040 — mother · 8 samples M MO5040 B13… family B9 B9_BA5029 — child · 34 samples C BA5029 B9_FA5028 — father · 3 samples F FA5028 B9_MO5027 — mother · 3 samples M MO5027 B9… family G11 G11_BA3038 — child · 5 samples C BA3038 G11_FA3040 — father · 5 samples F FA3040 G11_MO3037 — mother · 5 samples M MO3037 G11_SI3039 — sibling · 3 samples S SI3039 G11… family B14 B14_BA5042 — child · 8 samples C BA5042 B14_MO5043 — mother · 4 samples M MO5043 B14… family G1 G1_BA3001 — child · 10 samples C BA3001 G1_FA3000 — father · 3 samples F FA3000 G1_MO3002 — mother · 4 samples M MO3002 G1… family T10 T10_BA1030 — child · 12 samples C BA1030 T10_FA1032 — father · 7 samples F FA1032 T10_MO1031 — mother · 8 samples M MO1031 T10_SI1033 — sibling · 5 samples S SI1033 T10… family B4 B4_BA5009 — child · 9 samples C BA5009 B4_MO5010 — mother · 2 samples M MO5010 B4… family G12 G12_BA3044 — child · 9 samples C BA3044 G12_FA3045 — father · 7 samples F FA3045 G12_MO3043 — mother · 8 samples M MO3043 G12… family T3 T3_BA1007 — child · 17 samples C BA1007 T3_FA1008 — father · 8 samples F FA1008 T3_MO1006 — mother · 8 samples M MO1006 T3_SI1009 — sibling · 6 samples S SI1009 T3… family B6 B6_BA5018 — child · 33 samples C BA5018 B6_MO5017 — mother · 8 samples M MO5017 B6… family G13 G13_BA3046 — child · 9 samples C BA3046 G13_FA3047 — father · 7 samples F FA3047 G13_MO3048 — mother · 8 samples M MO3048 G13… family T7 T7_BA1023 — child · 11 samples C BA1023 T7_FA1024 — father · 7 samples F FA1024 T7_MO1025 — mother · 6 samples M MO1025 T7_SI1026 — sibling · 4 samples S SI1026 T7… family T2 T2_BA1005 — child · 16 samples C BA1005 T2_MO1004 — mother · 7 samples M MO1004 T2… daycare or school Nursery B · 48 people daycare or school Nursery B G0_ED3022 — member · 7 samples G0_ED3023 — member · 7 samples G0_ED3024 — member · 8 samples G10_BA3036 — member · 9 samples G11_BA3038 — member · 5 samples G11_FA3040 — member · 5 samples G11_MO3037 — member · 5 samples G11_SI3039 — member · 3 samples G12_BA3044 — member · 9 samples G12_FA3045 — member · 7 samples G12_MO3043 — member · 8 samples G13_BA3046 — member · 9 samples G13_FA3047 — member · 7 samples G13_MO3048 — member · 8 samples G14_BA3050 — member · 12 samples G14_FA3051 — member · 4 samples G14_MO3049 — member · 4 samples G15_BA3052 — member · 12 samples G15_FA3054 — member · 3 samples G15_MO3053 — member · 3 samples +28 daycare or school Nursery A · 45 people daycare or school Nursery A B0_ED5012 — member · 12 samples B0_ED5013 — member · 5 samples B0_ED5014 — member · 8 samples B10_BA5032 — member · 28 samples B10_FA5031 — member · 2 samples B10_MO5030 — member · 2 samples B10_SI5033 — member · 2 samples B11_BA5034 — member · 20 samples B11_MO5035 — member · 9 samples B12_BA5037 — member · 12 samples B12_MO5038 — member · 8 samples B13_BA5039 — member · 6 samples B13_MO5040 — member · 8 samples B14_BA5042 — member · 8 samples B14_MO5043 — member · 4 samples B15_BA5044 — member · 17 samples B15_BA5045 — member · 19 samples B15_MO5046 — member · 5 samples B1_BA5002 — member · 33 samples B1_FA5000 — member · 7 samples +25 daycare or school Nursery C · 35 people daycare or school Nursery C T0_ED1013 — member · 6 samples T0_ED… T0_ED1014 — member · 5 samples T0_ED… T0_ED1015 — member · 4 samples T0_ED… T0_ED1016 — member · 7 samples T0_ED… T10_BA1030 — member · 12 samples T10_B… T10_FA1032 — member · 7 samples T10_F… T10_MO1031 — member · 8 samples T10_M… T10_SI1033 — member · 5 samples T10_S… T1_BA1003 — member · 15 samples T1_BA… T1_FA1002 — member · 7 samples T1_FA… T1_MO1001 — member · 8 samples T1_MO… T2_BA1005 — member · 16 samples T2_BA… T2_MO1004 — member · 7 samples T2_MO… T3_BA1007 — member · 17 samples T3_BA… T3_FA1008 — member · 8 samples T3_FA… T3_MO1006 — member · 8 samples T3_MO… T3_SI1009 — member · 6 samples T3_SI… T4_BA1012 — member · 15 samples T4_BA… T4_FA1010 — member · 8 samples T4_FA… T4_MO1011 — member · 8 samples T4_MO… +15
Families (25 of 38) How longitudinal and relatedness information is derived
Community composition
Bifidobacterium 18.5%Bacteroides 8.7%Phocaeicola 7.9%Faecalibacterium 7.7%Prevotella 5.3%Blautia_A 3.9%Roseburia 3.3%Alistipes 2.4%Lachnospira 1.9%Mediterraneibacter 1.7%Ruminococcoides 1.6%Veillonella 1.6%
Genera, mean relative abundance over 935 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Field coverage
field samples coverage R1 R2 R3 R4
age_category 155 13% country 1,163 100% 1,163 health_condition 0 0% subject_id 1,163 100% 1,163 collection_date 1,163 100% 1,163 detailed_location 1,163 100% location_locality 1,163 100% 1,163 timepoint_label 1,163 100% 1,163 shared_setting_id 1,152 99% 1,152 shared_setting_type 1,152 99% 1,152 family_id 1,083 93% 1,083 family_role 1,083 93% 1,083 antibiotic_exposure 987 85% 987 age_at_collection_days 155 13% 150 5 sex 150 13% 150
Details
Archive description The goal of microTOUCH-baby is to study the dynamics of microbiome transmission among babies of about one year of age and their close social interactions network including their family members and pets, and nursery teachers.
How this project entered the registry Classified as human gut / stool shotgun DNA metagenome of infant / toddler 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 · “goal of microTOUCH- baby is to study”Evidence examples (one per field × route)
sample field value route conf. source quote
SAMN50690761 age_at_collection_days 11323 R1 0.85 sample.attr.age age=31 SAMN50690792 age_at_collection_days 15705.75 R1 0.85 biosample.attribute:age 43 SAMN42843001 age_at_collection_days 13605.56 R2 0.75 paper.supp.41586_2025_9983_MOESM1_ESM.xlsx[ST3!age_months] 447 SAMN42842963 antibiotic_exposure no R1 0.85 biosample.attribute:during_atb_atf No SAMN42842963 collection_date 2022-06 R3 0.70 paper.fulltext.methods recruited and enroled across 3 nursery schools SAMN42842963 country IT R1 0.90 biosample_attr Italy SAMN50690761 country IT R1 0.90 sample.attr.geo_loc_name geo_loc_name=Italy SAMN42842976 family_id B1 R1 0.85 biosample.attribute:family_id family_id: B1 SAMN42842976 family_role child R1 0.85 biosample.attribute:participant_type participant_type: Baby SAMN42842963 location_locality Trento R3 0.70 paper.fulltext.methods municipality of Trento (Italy) in June 2022 SAMN50690761 sex male R1 0.90 sample.attr.sex sex=male SAMN42842963 shared_setting_id Nursery A R1 0.85 biosample.attribute:nursery nursery: Nursery A SAMN42842963 shared_setting_type daycare_or_school R1 0.85 biosample.attribute:nursery nursery: Nursery A SAMN42842963 subject_id B0_ED5012 R1 0.85 biosample_attr B0_ED5012 SAMN50690761 subject_id B1_FA5000 R1 0.85 sample.attr.subjectid family_id=B1 subjectid=FA5000 SAMN42842963 timepoint_label T01 R1 0.80 biosample_attr T01 SAMN50690761 timepoint_label T01 R1 0.80 sample.attr.timepoint timepoint=T01
Sequencing 1,163 runs over 1,163 samples · mean 14.46 Gbp per run (median 13.72 Gbp, total 16,813.83 Gbp; 1,163 runs with a base count) · layout PAIRED 1,163 · platform ILLUMINA 1,163 · models Illumina NovaSeq 6000 (1,163) · 80% of runs with a Sandpiper profile · first public 2024-10-11 – 2026-09-02
Authors (13) Ricci L first · Heidrich V · Punčochář M · Armanini F · Ciciani M · Nabinejad A · Fazaeli F · Piperni E · Servais C · Pinto F · Valles-Colomer M · Asnicar F · Segata N last
Help complete this project 2 of the 4 core fields are below 50% coverage: age_category , health_condition . Share metadata
Downloads PRJNA1140720.csv.gz (35.1 KB) · parquet (118.7 KB) — all 1,163 samples, every field with route and confidence · PRJNA1140720_determinations.csv.gz (74.0 KB) — 11,577 evidence rows
Samples (1,163 · every field this project has values for · hover a cell for its source)
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