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PRJEB108612 ERP189448

Infant and parent gut metagenomes, Hong Kong, longitudinal cohort

MOMmy-Microbiome_Epigenome_Neurodevelopment

5,328 gut metagenome samples from infants and parents in the MOMmy cohort, Hong Kong, collected as part of a longitudinal cohort study. machine-written summary

5,328 samples · 5,328 runs · HK · Infant / toddler · 2026 · 6.37 Gbp / sample

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Sources
✓Sequence archive 26,622○Abstract / description✓Full text 5,328○Supplementary tables–External resources–User contribution–Human verified

Checked this project's papers and archive records yourself? Mark it human-verified.

what each source gave
✓ Sequence archive26,622 sample values (country, family id, family role, subject id, timepoint)
○ Abstract / descriptionread; no usable statement
✓ Full text5,328 sample values (collection date) · PMC12806111
○ Supplementary tablesfiles read; no table could be matched to the samples
– 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
1 country
Age
unknown5,328
Country
HK5,328
Body site
primary5,328
Sequencing depth per sample · this project all projects
all projects, 0–0.03 Gbp: 25,080 samples (4 %)this project, 0–0.03 Gbp: 296 samplesall projects, 0.03–0.1 Gbp: 17,066 samples (3 %)this project, 0.03–0.1 Gbp: 326 samplesall projects, 0.1–0.3 Gbp: 29,179 samples (5 %)this project, 0.1–0.3 Gbp: 99 samplesall projects, 0.3–1 Gbp: 47,044 samples (8 %)this project, 0.3–1 Gbp: 45 samplesall projects, 1–3 Gbp: 124,983 samples (22 %)this project, 1–3 Gbp: 213 samplesall projects, 3–10 Gbp: 253,728 samples (44 %)this project, 3–10 Gbp: 3,049 samplesall projects, 10–30 Gbp: 72,533 samples (13 %)this project, 10–30 Gbp: 1,286 samplesall projects, 30–100 Gbp: 3,024 samples (1 %)this project, 30–100 Gbp: 14 samplesall projects, 100–300 Gbp: 106 samples (0 %)all projects, ≥ 300 Gbp: 9 samples (0 %)project median 6.37 Gbp per sample0130Gbp
Sampling design and relatedness

longitudinalfamiliesfather–childmother–infant

925 of 2,754 people sampled more than once (3,490 samples; median 4, up to 4 per person) · follow-up median 12 mo (max 12 mo) · median interval between samples 4 mo (time from visit codes mapped to the stated schedule). Schedule stated by the source: “Pregnancy, delivery, and postnatal months 1, 2, 6, 12, 18, and years 2 to 7” (time origin: delivery); stated follow-up 7.0 y.

004-B004-B (child): day 0004-B (child): day 183004-B (child): day 365007-B007-B (child): day 0007-B (child): day 61007-B (child): day 365008-B008-B (child): day 0008-B (child): day 61008-B (child): day 183008-B (child): day 365010-B010-B (child): day 0010-B (child): day 61010-B (child): day 183010-B (child): day 365017-B017-B (child): day 0017-B (child): day 61017-B (child): day 183017-B (child): day 365018-B018-B (child): day 0018-B (child): day 122018-B (child): day 304021-B021-B (child): day 0021-B (child): day 183023-B023-B (child): day 0023-B (child): day 61023-B (child): day 183024-B024-B (child): day 0024-B (child): day 61024-B (child): day 183024-B (child): day 365025-B025-B (child): day 0025-B (child): day 122025-B (child): day 304027-B027-B (child): day 0027-B (child): day 61027-B (child): day 183027-B (child): day 365028-B028-B (child): day 0028-B (child): day 61028-B (child): day 183028-B (child): day 365029-B029-B (child): day 0029-B (child): day 61029-B (child): day 183032-B032-B (child): day 0032-B (child): day 61032-B (child): day 183032-B (child): day 365034-B034-B (child): day 0034-B (child): day 61034-B (child): day 183034-B (child): day 365035-B035-B (child): day 0035-B (child): day 61035-B (child): day 183035-B (child): day 365037-B037-B (child): day 0037-B (child): day 61037-B (child): day 183038-B038-B (child): day 0038-B (child): day 61038-B (child): day 183038-B (child): day 365039-B039-B (child): day 0039-B (child): day 61039-B (child): day 183039-B (child): day 365040-B040-B (child): day 0040-B (child): day 61040-B (child): day 183040-B (child): day 365041-B041-B (child): day 0041-B (child): day 61041-B (child): day 183041-B (child): day 365042-B042-B (child): day 0042-B (child): day 61042-B (child): day 183042-B (child): day 365043-B043-B (child): day 0043-B (child): day 61043-B (child): day 183043-B (child): day 365044-B044-B (child): day 0044-B (child): day 61044-B (child): day 183044-B (child): day 365045-B045-B (child): day 0045-B (child): day 61045-B (child): day 183045-B (child): day 365046-B046-B (child): day 0046-B (child): day 61046-B (child): day 183046-B (child): day 365047-B047-B (child): day 0047-B (child): day 183047-B (child): day 365050-B050-B (child): day 0050-B (child): day 61050-B (child): day 183050-B (child): day 365053-B053-B (child): day 0053-B (child): day 61053-B (child): day 183053-B (child): day 365055-B055-B (child): day 0055-B (child): day 61055-B (child): day 183055-B (child): day 365060-B060-B (child): day 0060-B (child): day 61060-B (child): day 183060-B (child): day 365061-B061-B (child): day 0061-B (child): day 61061-B (child): day 183061-B (child): day 365062-B062-B (child): day 0062-B (child): day 61062-B (child): day 183062-B (child): day 365064-B064-B (child): day 0064-B (child): day 61064-B (child): day 183064-B (child): day 365065-B065-B (child): day 0065-B (child): day 61065-B (child): day 183065-B (child): day 365066-B066-B (child): day 0066-B (child): day 61066-B (child): day 183066-B (child): day 3650 d3 mo6 mo9 mo12 mo

Each row is one person (36 shown of 925); 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).

969 families (MOMmy cohort): 968 mothers (MT3), 817 fathers, 969 infants (BD0-BM12); 816 families with both parents · 969 families with 2,763 sampled people (969 with a parent and a child).

motherMfatherFchildC
808 × mother + father + child
motherMchildC
151 × mother + child
motherMfatherFchildCchildC
8 × mother + father + child×2
motherMchildCchildC
1 × mother + child×2
fatherFchildC
1 × father + child
family 007007-M — mother · 1 sampleMM007-F — father · 1 sampleFF007-B — child · 3 samplesCB007…
family 004004-M — mother · 1 sampleMM004-B — child · 3 samplesCB004…
family 076076-M — mother · 1 sampleM076-M076-F — father · 1 sampleF076-Fnan — child · 1 sampleCnan076-B — child · 3 samplesC076-B
family 088088-M — mother · 1 sampleM088-Mnan — child · 1 sampleCnan088-B — child · 3 samplesC088-B
family 136136-F — father · 1 sampleFF136-B — child · 4 samplesCB136…
family 008008-M — mother · 1 sampleMM008-F — father · 1 sampleFF008-B — child · 4 samplesCB008…
family 022022-M — mother · 1 sampleMM022-B — child · 1 sampleCB022…
family 080080-M — mother · 1 sampleM080-M080-F — father · 1 sampleF080-Fnan — child · 1 sampleCnan080-B — child · 3 samplesC080-B
family 010010-M — mother · 1 sampleMM010-F — father · 1 sampleFF010-B — child · 4 samplesCB010…
family 037037-M — mother · 1 sampleMM037-B — child · 3 samplesCB037…
family 081081-M — mother · 1 sampleM081-M081-F — father · 1 sampleF081-Fnan — child · 1 sampleCnan081-B — child · 3 samplesC081-B
family 017017-M — mother · 1 sampleMM017-F — father · 1 sampleFF017-B — child · 4 samplesCB017…
family 040040-M — mother · 1 sampleMM040-B — child · 4 samplesCB040…
family 082082-M — mother · 1 sampleM082-M082-F — father · 1 sampleF082-Fnan — child · 1 sampleCnan082-B — child · 3 samplesC082-B
family 018018-M — mother · 1 sampleMM018-F — father · 1 sampleFF018-B — child · 3 samplesCB018…
family 041041-M — mother · 1 sampleMM041-B — child · 4 samplesCB041…
family 083083-M — mother · 1 sampleM083-M083-F — father · 1 sampleF083-Fnan — child · 1 sampleCnan083-B — child · 3 samplesC083-B
family 021021-M — mother · 1 sampleMM021-F — father · 1 sampleFF021-B — child · 2 samplesCB021…
family 043043-M — mother · 1 sampleMM043-B — child · 4 samplesCB043…
family 084084-M — mother · 1 sampleM084-M084-F — father · 1 sampleF084-Fnan — child · 1 sampleCnan084-B — child · 3 samplesC084-B
family 023023-M — mother · 1 sampleMM023-F — father · 1 sampleFF023-B — child · 3 samplesCB023…
family 059059-M — mother · 1 sampleMM059-B — child · 1 sampleCB059…
family 091091-M — mother · 1 sampleM091-M091-F — father · 1 sampleF091-Fnan — child · 1 sampleCnan091-B — child · 3 samplesC091-B
family 024024-M — mother · 1 sampleMM024-F — father · 1 sampleFF024-B — child · 4 samplesCB024…

motherfatherchild · 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 969 families (one per family structure, then more). 2,754 people in the project overall.

Families (25 of 969)
familymemberssamples
303mother + father + childSAMEA121701225 · SAMEA121701226 · SAMEA121701227 · SAMEA121701228 · SAMEA121701229 · SAMEA121701230
433mother + father + childSAMEA121700625 · SAMEA121700626 · SAMEA121700627 · SAMEA121700628 · SAMEA121700629 · SAMEA121700630
922mother + father + childSAMEA121698554 · SAMEA121698555 · SAMEA121698556 · SAMEA121698557 · SAMEA121698558 · SAMEA121698559
437mother + father + childSAMEA121700604 · SAMEA121700605 · SAMEA121700606 · SAMEA121700607 · SAMEA121700608 · SAMEA121700609
438mother + father + childSAMEA121700598 · SAMEA121700599 · SAMEA121700600 · SAMEA121700601 · SAMEA121700602 · SAMEA121700603
439mother + father + childSAMEA121700592 · SAMEA121700593 · SAMEA121700594 · SAMEA121700595 · SAMEA121700596 · SAMEA121700597
442mother + father + childSAMEA121700581 · SAMEA121700582 · SAMEA121700583 · SAMEA121700584 · SAMEA121700585 · SAMEA121700586
443mother + father + childSAMEA121700575 · SAMEA121700576 · SAMEA121700577 · SAMEA121700578 · SAMEA121700579 · SAMEA121700580
445mother + father + childSAMEA121700569 · SAMEA121700570 · SAMEA121700571 · SAMEA121700572 · SAMEA121700573 · SAMEA121700574
446mother + father + childSAMEA121700563 · SAMEA121700564 · SAMEA121700565 · SAMEA121700566 · SAMEA121700567 · SAMEA121700568
447mother + father + childSAMEA121700557 · SAMEA121700558 · SAMEA121700559 · SAMEA121700560 · SAMEA121700561 · SAMEA121700562
449mother + father + childSAMEA121700551 · SAMEA121700552 · SAMEA121700553 · SAMEA121700554 · SAMEA121700555 · SAMEA121700556
450mother + father + childSAMEA121700545 · SAMEA121700546 · SAMEA121700547 · SAMEA121700548 · SAMEA121700549 · SAMEA121700550
453mother + father + childSAMEA121700534 · SAMEA121700535 · SAMEA121700536 · SAMEA121700537 · SAMEA121700538 · SAMEA121700539
454mother + father + childSAMEA121700528 · SAMEA121700529 · SAMEA121700530 · SAMEA121700531 · SAMEA121700532 · SAMEA121700533
455mother + father + childSAMEA121700522 · SAMEA121700523 · SAMEA121700524 · SAMEA121700525 · SAMEA121700526 · SAMEA121700527
456mother + father + childSAMEA121700516 · SAMEA121700517 · SAMEA121700518 · SAMEA121700519 · SAMEA121700520 · SAMEA121700521
457mother + father + childSAMEA121700510 · SAMEA121700511 · SAMEA121700512 · SAMEA121700513 · SAMEA121700514 · SAMEA121700515
459mother + father + childSAMEA121700499 · SAMEA121700500 · SAMEA121700501 · SAMEA121700502 · SAMEA121700503 · SAMEA121700504
460mother + father + childSAMEA121700493 · SAMEA121700494 · SAMEA121700495 · SAMEA121700496 · SAMEA121700497 · SAMEA121700498
462mother + father + childSAMEA121700487 · SAMEA121700488 · SAMEA121700489 · SAMEA121700490 · SAMEA121700491 · SAMEA121700492
463mother + father + childSAMEA121700481 · SAMEA121700482 · SAMEA121700483 · SAMEA121700484 · SAMEA121700485 · SAMEA121700486
464mother + father + childSAMEA121700475 · SAMEA121700476 · SAMEA121700477 · SAMEA121700478 · SAMEA121700479 · SAMEA121700480
434mother + father + childSAMEA121700619 · SAMEA121700620 · SAMEA121700621 · SAMEA121700622 · SAMEA121700623 · SAMEA121700624
432mother + father + childSAMEA121700631 · SAMEA121700632 · SAMEA121700633 · SAMEA121700634 · SAMEA121700635 · SAMEA121700636

How longitudinal and relatedness information is derived

Community composition
Bifidobacterium 27.6%Bacteroides 7.8%Phocaeicola 7.6%Escherichia 5.2%Faecalibacterium 3.3%Prevotella 2.7%Streptococcus 2.6%Enterococcus 2.6%Klebsiella 2.4%Blautia_A 2.0%Mediterraneibacter 1.6%Collinsella 1.6%not assigned to a genus 3.2%other genera 29.8%

Genera, mean relative abundance over 4,593 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).

Field coverage
fieldsamplescoverageR1R2R3R4
age_category0 0%
country5,328 100%5,328
health_condition0 0%
subject_id5,319 100%5,319
collection_date5,328 100%5,328
family_id5,328 100%5,328
family_role5,328 100%5,328
timepoint_label5,319 100%5,319
Papers (1)
Details
Archive description

This is a repository of 5,328 gut metagenomes from 969 infants and 1,785 parents in the MOMmy cohort.

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 study.description · “repository of 5,328 gut metagenomes from 969”
  • 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 · “metagenomes from 969 infants and 1,785 parents”
Evidence examples (one per field × route)
samplefieldvaluerouteconf.sourcequote
SAMEA121698248collection_date2019-09/2024-03R30.70paper.fulltext.methodsThe recruitment of pregnant women at trimesters 1, 2, or 3 started since September 2019
SAMEA121698248countryHKR10.90biosample_attrHong Kong
SAMEA121698248family_id508R10.70sample.name_rule:TITLE508-BM6
SAMEA121698248family_rolechildR10.70sample.name_rule:TITLE508-BM6
SAMEA121698248subject_id508-BR10.70sample.name_rule:library_name508-BM6
SAMEA121698250subject_id999-MR10.70sample.name_rule:title999-MT3
SAMEA121698248timepoint_labelBM6R10.70sample.name_rule:title508-BM6
Sequencing

5,328 runs over 5,328 samples · mean 6.57 Gbp per run (median 6.37 Gbp, total 35,022.59 Gbp; 5,328 runs with a base count) · layout PAIRED 5,328 · platform ILLUMINA 5,328 · models Illumina NovaSeq 6000 (5,328) · 86% of runs with a Sandpiper profile · first public 2026-02-22 – 2026-02-25

Authors (0)

No author record.

Help complete this project

2 of the 4 core fields are below 50% coverage: age_category, health_condition. Share metadata

Downloads

PRJEB108612.csv.gz (158.8 KB) · parquet (310.4 KB) — all 5,328 samples, every field with route and confidence · PRJEB108612_determinations.csv.gz (281.3 KB) — 31,950 evidence rows

Samples (5,328 · every field this project has values for · hover a cell for its source)
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