PRJEB45799 ERP129957
Person-to-person gut and oral microbiome transmission cohort
The person-to-person transmission landscape of the gut and oral microbiomes
Longitudinal cohort study of 2394 gut and oral metagenome samples spanning adults, children, adolescents, infants, and others, examining person-to-person microbial transmission across interpersonal relationships. machine-written summary
2,394 samples · 2,394 runs · US, GW, IT · Infant / toddler · 2022 · 8.77 Gbp / sample
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Sources
✓ Sequence archive 9,589 ○ Abstract / description○ Full text✓ Supplementary tables 6,333 ✓ External resources 1,358 – User contribution– Human verified
Checked this project's papers and archive records yourself? Mark it human-verified .
what each source gave ✓ Sequence archive9,589 sample values (age, health condition, health condition detail, sex, subject id) ○ Abstract / descriptionread; no usable statement ○ Full textread; no usable statement or table · PMC13288982, PMC9892008 ✓ Supplementary tables6,333 sample values (country, family id, family role, shared setting id, shared setting type) ✓ External resources1,358 sample values (antibiotic exposure, bmi, country, health condition) · from curatedMetagenomicData 3 (cMD 3) – User contributionnothing uploaded yet – Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
Age
adult 1,441
child 481
adolescent 222
infant 200
unknown 21
neonate 18
+1 more
Condition
healthy_control 424
preterm_nicu 47
Country
US 1,260
GW 340
IT 48
CN 27
AR 26
CO 24
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 %) all projects, 0.1–0.3 Gbp: 29,179 samples (5 %) all projects, 0.3–1 Gbp: 47,044 samples (8 %) this project, 0.3–1 Gbp: 12 samples all projects, 1–3 Gbp: 124,983 samples (22 %) this project, 1–3 Gbp: 192 samples all projects, 3–10 Gbp: 253,728 samples (44 %) this project, 3–10 Gbp: 1,128 samples all projects, 10–30 Gbp: 72,533 samples (13 %) this project, 10–30 Gbp: 859 samples all projects, 30–100 Gbp: 3,024 samples (1 %) this project, 30–100 Gbp: 197 samples all projects, 100–300 Gbp: 106 samples (0 %) this project, 100–300 Gbp: 6 samples all projects, ≥ 300 Gbp: 9 samples (0 %) project median 8.77 Gbp per sample 0 1 30 Gbp
Sampling design and relatedness
longitudinal community families households mother–infant parent–child partners / couples twins
8 of 2,358 people sampled more than once (44 samples; median 6, up to 7 per person) · follow-up median 24 mo (max 24 mo) · median interval between samples 4 mo (time from age at collection) .
C10050_2 C10050_2 (twin): day 0 C10050_2 (twin): day 90 C10050_2 (twin): day 210 C10050_2 (twin): day 335 C10050_2 (twin): day 700 C10050_1 C10050_1 (twin): day 0 C10050_1 (twin): day 118 C10050_1 (twin): day 363 C10050_1 (twin): day 728 C10071_1 C10071_1 (twin): day 0 C10071_1 (twin): day 5 C10071_1 (twin): day 28 C10071_1 (twin): day 118 C10071_1 (twin): day 238 C10071_1 (twin): day 363 C10071_1 (twin): day 728 C10071_2 C10071_2 (twin): day 0 C10071_2 (twin): day 5 C10071_2 (twin): day 28 C10071_2 (twin): day 118 C10071_2 (twin): day 238 C10071_2 (twin): day 363 C10071_2 (twin): day 728 C10075_1 C10075_1 (twin): day 0 C10075_1 (twin): day 23 C10075_1 (twin): day 113 C10075_1 (twin): day 233 C10075_1 (twin): day 358 C10075_2 C10075_2 (twin): day 0 C10075_2 (twin): day 23 C10075_2 (twin): day 113 C10075_2 (twin): day 358 C10076_1 C10076_1 (twin): day 0 C10076_1 (twin): day 28 C10076_1 (twin): day 118 C10076_1 (twin): day 238 C10076_1 (twin): day 363 C10076_1 (twin): day 728 C10076_2 C10076_2 (twin): day 0 C10076_2 (twin): day 5 C10076_2 (twin): day 28 C10076_2 (twin): day 238 C10076_2 (twin): day 363 C10076_2 (twin): day 728 0 d 6 mo 12 mo 18 mo 24 mo
Each row is one person (8 shown); 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 ).
670 mothers, 625 fathers, 698 children (4 DZ twin pairs) in 729 families incl. Guinea-Bissau households in villages · 729 families with 2,318 sampled people (676 with a parent and a child), 8 twin sets · 17 shared settings.
mother M father F child C 609 × mother + father + child
mother M child C 46 × mother + child
unknown ? unknown ? 7 × unknown×2
unknown ? unknown ? unknown ? 6 × unknown×3
unknown ? unknown ? unknown ? unknown ? unknown ? 6 × unknown×5
mother M father F child C child C 6 × mother + father + child×2
partner Pt partner Pt 6 × partner×2
father F child C 6 × father + child
twin dz: C10050_1, C10050_2 DZ C10050_1 — twin · 4 samples T 1 C10050_2 — twin · 5 samples T 2 C10050… twin dz: C10071_1, C10071_2 DZ C10071_1 — twin · 7 samples T 1 C10071_2 — twin · 7 samples T 2 C10071… twin dz: C10075_1, C10075_2 DZ C10075_1 — twin · 5 samples T 1 C10075_2 — twin · 4 samples T 2 C10075… twin dz: C10076_1, C10076_2 DZ C10076_1 — twin · 6 samples T 1 C10076_2 — twin · 6 samples T 2 C10076… partner: SP0082673, SP0082685 SP0082673 — partner · 1 sample Pt 73 SP0082685 — partner · 1 sample Pt 85 SP00826… partner: SP0101678, SP0103081 SP0101678 — partner · 1 sample Pt 1678 SP0103081 — partner · 1 sample Pt 3081 SP010… partner: SP0105860, SP0110673 SP0105860 — partner · 1 sample Pt 05860 SP0110673 — partner · 1 sample Pt 10673 SP01… partner: SP0109198, SP0123482 SP0109198 — partner · 1 sample Pt 09198 SP0123482 — partner · 1 sample Pt 23482 SP01… partner: SP0159937, SP0160412 SP0159937 — partner · 1 sample Pt 59937 SP0160412 — partner · 1 sample Pt 60412 SP01… partner: SP0163363, SP0163395 SP0163363 — partner · 1 sample Pt 63 SP0163395 — partner · 1 sample Pt 95 SP01633… family SF0002375 SP0002406 — child · 1 sample C 2406 SP0003259 — father · 1 sample F 3259 SP0002342 — mother · 1 sample M 2342 SP000… family ARG_10 ARG_B10 — child · 1 sample C B10 ARG_M10 — mother · 1 sample M M10 ARG… family GUI_HH_00804 family GUI_HH_00804 GUI_0080403 — member · 1 sample 03 GUI_0080417 — member · 1 sample 17 GUI_00804… family GUI_HH_00801 family GUI_HH_00801 GUI_0080101 — member · 1 sample 1 GUI_0080103 — member · 1 sample 3 GUI_0080105 — member · 1 sample 5 GUI_008010… family GUI_HH_00903 family GUI_HH_00903 GUI_0090301 — member · 1 sample 1 GUI_0090302 — member · 1 sample 2 GUI_0090303 — member · 1 sample 3 GUI_0090304 — member · 1 sample 4 GUI_0090305 — member · 1 sample 5 GUI_009030… family SF0007020 SP0007521 — child · 1 sample C 007521 SP0007599 — child · 1 sample C 007599 SP0153276 — father · 1 sample F 153276 SP0006940 — mother · 1 sample M 006940 SP0… family SF0094296 SP0094297 — child · 1 sample C 4297 SP0097543 — father · 1 sample F 7543 SP009… family GUI_HH_01404 family GUI_HH_01404 GUI_0140403 — member · 1 sample 03 GUI_0140404 — member · 1 sample 04 GUI_0140408 — member · 1 sample 08 GUI_0140411 — member · 1 sample 11 GUI_01404… family GUI_HH_00905 family GUI_HH_00905 GUI_0090501 — member · 1 sample 01 GUI_0090502 — member · 1 sample 02 GUI_0090504 — member · 1 sample 04 GUI_0090506 — member · 1 sample 06 GUI_0090508 — member · 1 sample 08 GUI_0090511 — member · 1 sample 11 GUI_0090512 — member · 1 sample 12 GUI_00905… family caritro_twins_C10050 C10050_1 — twin · 4 samples T 1 C10050_2 — twin · 5 samples T 2 C10050_mo — mother · 1 sample M mo C10050… family GUI_HH_01403 family GUI_HH_01403 GUI_0140303 — member · 1 sample 03 GUI_0140305 — member · 1 sample 05 GUI_0140306 — member · 1 sample 06 GUI_0140307 — member · 1 sample 07 GUI_0140308 — member · 1 sample 08 GUI_0140311 — member · 1 sample 11 GUI_01403… family GUI_HH_02101 family GUI_HH_02101 GUI_0210101 — member · 1 sample 01 GUI_0210104 — member · 1 sample 04 GUI_0210105 — member · 1 sample 05 GUI_0210107 — member · 1 sample 07 GUI_0210109 — member · 1 sample 09 GUI_0210111 — member · 1 sample 11 GUI_0210117 — member · 1 sample 17 GUI_0210118 — member · 1 sample 18 GUI_0210119 — member · 1 sample 19 GUI_0210121 — member · 1 sample 21 GUI_0210122 — member · 1 sample 22 GUI_0210124 — member · 1 sample 24 GUI_0210125 — member · 1 sample 25 GUI_0210126 — member · 1 sample 26 GUI_0210127 — member · 1 sample 27 GUI_02101… family GUI_HH_02104 family GUI_HH_02104 GUI_0210402 — member · 1 sample 02 GUI_0210403 — member · 1 sample 03 GUI_0210404 — member · 1 sample 04 GUI_0210405 — member · 1 sample 05 GUI_0210406 — member · 1 sample 06 GUI_0210408 — member · 1 sample 08 GUI_0210410 — member · 1 sample 10 GUI_0210411 — member · 1 sample 11 GUI_02104… family GUI_HH_1101 family GUI_HH_1101 GUI_110101 — member · 1 sample 01 GUI_110102 — member · 1 sample 02 GUI_110103 — member · 1 sample 03 GUI_110104 — member · 1 sample 04 GUI_110105 — member · 1 sample 05 GUI_110106 — member · 1 sample 06 GUI_110108 — member · 1 sample 08 GUI_110109 — member · 1 sample 09 GUI_110110 — member · 1 sample 10 GUI_1101… village or community GUI_014 · 53 people village or community GUI_014 GUI_0140101 — member · 1 sample 101 GUI_0140102 — member · 1 sample 102 GUI_0140103 — member · 1 sample 103 GUI_0140104 — member · 1 sample 104 GUI_0140107 — member · 1 sample 107 GUI_0140108 — member · 1 sample 108 GUI_0140110 — member · 1 sample 110 GUI_0140111 — member · 1 sample 111 GUI_0140112 — member · 1 sample 112 GUI_0140113 — member · 1 sample 113 GUI_0140115 — member · 1 sample 115 GUI_0140116 — member · 1 sample 116 GUI_0140117 — member · 1 sample 117 GUI_0140118 — member · 1 sample 118 GUI_0140119 — member · 1 sample 119 GUI_0140121 — member · 1 sample 121 GUI_0140122 — member · 1 sample 122 GUI_0140303 — member · 1 sample 303 GUI_0140305 — member · 1 sample 305 GUI_0140306 — member · 1 sample 306 GUI_0140… +33 village or community GUI_020 · 48 people village or community GUI_020 GUI_200101 — member · 1 sample 101 GUI_200105 — member · 1 sample 105 GUI_200106 — member · 1 sample 106 GUI_200107 — member · 1 sample 107 GUI_200108 — member · 1 sample 108 GUI_200109 — member · 1 sample 109 GUI_200110 — member · 1 sample 110 GUI_200111 — member · 1 sample 111 GUI_200112 — member · 1 sample 112 GUI_200114 — member · 1 sample 114 GUI_200205 — member · 1 sample 205 GUI_200207 — member · 1 sample 207 GUI_200208 — member · 1 sample 208 GUI_200209 — member · 1 sample 209 GUI_200210 — member · 1 sample 210 GUI_200211 — member · 1 sample 211 GUI_200212 — member · 1 sample 212 GUI_200214 — member · 1 sample 214 GUI_200301 — member · 1 sample 301 GUI_200302 — member · 1 sample 302 GUI_200… +28 village or community GUI_008 · 46 people village or community GUI_008 GUI_0080101 — member · 1 sample 101 GUI_0080103 — member · 1 sample 103 GUI_0080105 — member · 1 sample 105 GUI_0080201 — member · 1 sample 201 GUI_0080302 — member · 1 sample 302 GUI_0080304 — member · 1 sample 304 GUI_0080307 — member · 1 sample 307 GUI_0080308 — member · 1 sample 308 GUI_0080309 — member · 1 sample 309 GUI_0080310 — member · 1 sample 310 GUI_0080311 — member · 1 sample 311 GUI_0080312 — member · 1 sample 312 GUI_0080315 — member · 1 sample 315 GUI_0080318 — member · 1 sample 318 GUI_0080320 — member · 1 sample 320 GUI_0080324 — member · 1 sample 324 GUI_0080403 — member · 1 sample 403 GUI_0080417 — member · 1 sample 417 GUI_0080506 — member · 1 sample 506 GUI_0080508 — member · 1 sample 508 GUI_0080… +26 village or community GUI_021 · 44 people village or community GUI_021 GUI_0210101 — member · 1 sample 101 GUI_0210104 — member · 1 sample 104 GUI_0210105 — member · 1 sample 105 GUI_0210107 — member · 1 sample 107 GUI_0210109 — member · 1 sample 109 GUI_0210111 — member · 1 sample 111 GUI_0210117 — member · 1 sample 117 GUI_0210118 — member · 1 sample 118 GUI_0210119 — member · 1 sample 119 GUI_0210121 — member · 1 sample 121 GUI_0210122 — member · 1 sample 122 GUI_0210124 — member · 1 sample 124 GUI_0210125 — member · 1 sample 125 GUI_0210126 — member · 1 sample 126 GUI_0210127 — member · 1 sample 127 GUI_0210202 — member · 1 sample 202 GUI_0210203 — member · 1 sample 203 GUI_0210204 — member · 1 sample 204 GUI_0210205 — member · 1 sample 205 GUI_0210301 — member · 1 sample 301 GUI_0210… +24 village or community GUI_018 · 28 people village or community GUI_018 GUI_180101 — member · 1 sample 101 GUI_180102 — member · 1 sample 102 GUI_180103 — member · 1 sample 103 GUI_180104 — member · 1 sample 104 GUI_180105 — member · 1 sample 105 GUI_180106 — member · 1 sample 106 GUI_180107 — member · 1 sample 107 GUI_180108 — member · 1 sample 108 GUI_180109 — member · 1 sample 109 GUI_180202 — member · 1 sample 202 GUI_180204 — member · 1 sample 204 GUI_180205 — member · 1 sample 205 GUI_180206 — member · 1 sample 206 GUI_180208 — member · 1 sample 208 GUI_180301 — member · 1 sample 301 GUI_180302 — member · 1 sample 302 GUI_180303 — member · 1 sample 303 GUI_180304 — member · 1 sample 304 GUI_180305 — member · 1 sample 305 GUI_180306 — member · 1 sample 306 GUI_180… +8 village or community GUI_007 · 17 people village or community GUI_007 GUI_0070123 — member · 1 sample 00701… GUI_70102 — member · 1 sample 70102 GUI_70103 — member · 1 sample 70103 GUI_70105 — member · 1 sample 70105 GUI_70108 — member · 1 sample 70108 GUI_70109 — member · 1 sample 70109 GUI_70110 — member · 1 sample 70110 GUI_70111 — member · 1 sample 70111 GUI_70112 — member · 1 sample 70112 GUI_70113 — member · 1 sample 70113 GUI_70114 — member · 1 sample 70114 GUI_70116 — member · 1 sample 70116 GUI_70117 — member · 1 sample 70117 GUI_70119 — member · 1 sample 70119 GUI_70120 — member · 1 sample 70120 GUI_70122 — member · 1 sample 70122 GUI_70202 — member · 1 sample 70202 GUI… village or community GUI_009 · 16 people village or community GUI_009 GUI_0090301 — member · 1 sample 00903… GUI_0090302 — member · 1 sample 00903… GUI_0090303 — member · 1 sample 00903… GUI_0090304 — member · 1 sample 00903… GUI_0090305 — member · 1 sample 00903… GUI_0090401 — member · 1 sample 00904… GUI_0090501 — member · 1 sample 00905… GUI_0090502 — member · 1 sample 00905… GUI_0090504 — member · 1 sample 00905… GUI_0090506 — member · 1 sample 00905… GUI_0090508 — member · 1 sample 00905… GUI_0090511 — member · 1 sample 00905… GUI_0090512 — member · 1 sample 00905… GUI_90101 — member · 1 sample 90101 GUI_90203 — member · 1 sample 90203 GUI_90404 — member · 1 sample 90404 GUI… village or community GUI_019 · 16 people village or community GUI_019 GUI_190101 — member · 1 sample 101 GUI_190102 — member · 1 sample 102 GUI_190104 — member · 1 sample 104 GUI_190105 — member · 1 sample 105 GUI_190106 — member · 1 sample 106 GUI_190107 — member · 1 sample 107 GUI_190108 — member · 1 sample 108 GUI_190301 — member · 1 sample 301 GUI_190302 — member · 1 sample 302 GUI_190303 — member · 1 sample 303 GUI_190305 — member · 1 sample 305 GUI_190401 — member · 1 sample 401 GUI_190402 — member · 1 sample 402 GUI_190403 — member · 1 sample 403 GUI_190404 — member · 1 sample 404 GUI_190406 — member · 1 sample 406 GUI_190…
Families (25 of 729) How longitudinal and relatedness information is derived
Community composition
Streptococcus 13.1%Prevotella 11.0%Neisseria 6.4%Rothia 4.9%Veillonella 4.6%Haemophilus_D 4.1%Gemella 3.0%Nanosynbacter 2.7%Porphyromonas 2.4%Pauljensenia 2.2%Fusobacterium 2.1%Actinomyces 2.0%
Genera, mean relative abundance over 2,180 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 2,373 99% country 1,725 72% 1,725 health_condition 471 20% 47 424 subject_id 2,394 100% 2,394 health_condition_detail 2,394 100% 2,394 sex 2,381 99% 2,381 age_at_collection_days 2,373 99% 2,373 family_id 2,354 98% 2,354 family_role 2,041 85% 2,041 antibiotic_exposure 465 19% 465 shared_setting_id 339 14% 339 shared_setting_type 339 14% 339 bmi 4 0% 4
Papers (2)
The person-to-person transmission landscape of the gut and oral microbiomes. PMID 36653448 PMC9892008 curated Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis. PMID 42171373 PMC13288982 curated
Details
Archive description The human microbiome is an integral component of our body and a co-determinant of several health conditions. However, how the human microbiome is shaped via person-to-person microbial transmission and the extent to which interpersonal relations impact the individual genetic makeup of the microbiome and its spread within and across populations remain largely unknown. We assessed this in >9700 gut and oral metagenomes.
How this project entered the registry Classified as human gut / stool / oral cavity 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 study.title · “landscape of the gut and oral microbiomes”body site study.description · “this in >9700 gut and oral metagenomes.”body site study.title · “the gut and oral microbiomes”body site study.description · “>9700 gut and oral metagenomes.”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
SAMEA10739526 age_at_collection_days 120 R1 0.85 biosample_attr male_subject_of_0.328767123_years SAMEA10739527 age_at_collection_days 10958.0 R1 0.85 biosample.attribute:phenotype phenotype: female_subject_of_30.0_years SAMEA10739526 antibiotic_exposure no R2 0.75 external.cmd source antibiotics_current_use: No SAMEA10739955 bmi 22.65 R2 0.75 external.cmd source bmi: 22.65 SAMEA10739526 country AR R2 0.75 external.cmd source country: Argentina SAMEA10739994 country US R2 0.75 paper.supp.table country=USA SAMEA10739526 family_id ARG_10 R2 0.85 paper.supp.41586_2022_5620_MOESM3_ESM.xlsx[Table S2!familyID] subjectID ARG_B10 familyID ARG_10 SAMEA10739526 family_role child R2 0.85 paper.supp.41586_2022_5620_MOESM3_ESM.xlsx[Table S2!mother_subjectID] subjectID ARG_B10 role derived from mother_subjectID SAMEA10739526 health_condition preterm_nicu R1 0.80 biosample.attribute:phenotype phenotype: male_subject_of_0.328767123_years SAMEA10739527 health_condition healthy_control R2 0.75 external.cmd source disease: Healthy SAMEA10739526 health_condition_detail male_subject_of_0.328767123_years R1 0.90 biosample.attribute:phenotype phenotype: male_subject_of_0.328767123_years SAMEA10739526 sex male R1 0.90 biosample_attr male_subject_of_0.328767123_years SAMEA10739604 shared_setting_id GUI_007 R2 0.85 paper.supp.41586_2022_5620_MOESM3_ESM.xlsx[Table S2!village] subjectID GUI_0070123 village GUI_007 SAMEA10739604 shared_setting_type village_or_community R2 0.85 paper.supp.41586_2022_5620_MOESM3_ESM.xlsx[Table S2!village] subjectID GUI_0070123 village GUI_007 SAMEA10739526 subject_id ARG_B10 R1 0.85 biosample_attr ARG_B10
Sequencing 2,394 runs over 2,394 samples · mean 13.26 Gbp per run (median 8.77 Gbp, total 31,740.20 Gbp; 2,394 runs with a base count) · layout PAIRED 2,394 · platform ILLUMINA 2,394 · models unspecified (2,394) · 91% of runs with a Sandpiper profile · first public 2022-03-29
Authors (48) 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 · Schroer HW first · Beghini F · Raygoza Garay JA · Christakis NA · Bosch DE last
Downloads PRJEB45799.csv.gz (99.5 KB) · parquet (213.6 KB) — all 2,394 samples, every field with route and confidence · PRJEB45799_determinations.csv.gz (221.8 KB) — 17,280 evidence rows
Samples (2,394 · every field this project has values for · hover a cell for its source)
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