PRJEB89491 ERP172517
Longitudinal infant and parent gut microbiota cohort, Netherlands
LucKi Gut - Longitudinal metagenomic sequencing of infant gut microbiota
929 fecal metagenome samples from infants (collected at 1–2 weeks and 1, 2, 4, 5, 6, 9, 11, and 14 months) and their parents (collected ~1–2 weeks postpartum) in the Netherlands; longitudinal cohort design. machine-written summary
929 samples · 929 runs · NL · Infant / toddler · 2025 · 15.73 Gbp / sample
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Sampling design and relatedness
longitudinal families father–child mother–infant
134 of 260 people sampled more than once (803 samples; median 6, up to 9 per person) · follow-up median 11 mo (max 14 mo) · median interval between samples 2 mo (time from age at collection) .
Schedule stated by the source: “Infant stool at 1-2wks,1,2,4,5,6,9,11,14 months (well-baby clinic visits); parents sampled once ~1-2wks postpartum” (time origin: birth); stated follow-up 14 mo.
ENA_fam_0001_inf ENA_fam_0001_infant (child): day 0 ENA_fam_0001_infant (child): day 18 ENA_fam_0001_infant (child): day 46 ENA_fam_0001_infant (child): day 112 ENA_fam_0001_infant (child): day 142 ENA_fam_0002_inf ENA_fam_0002_infant (child): day 0 ENA_fam_0002_infant (child): day 18 ENA_fam_0002_infant (child): day 46 ENA_fam_0002_infant (child): day 112 ENA_fam_0003_inf ENA_fam_0003_infant (child): day 0 ENA_fam_0003_infant (child): day 18 ENA_fam_0003_infant (child): day 46 ENA_fam_0003_infant (child): day 112 ENA_fam_0003_infant (child): day 142 ENA_fam_0004_inf ENA_fam_0004_infant (child): day 0 ENA_fam_0004_infant (child): day 18 ENA_fam_0004_infant (child): day 46 ENA_fam_0004_infant (child): day 142 ENA_fam_0005_inf ENA_fam_0005_infant (child): day 0 ENA_fam_0005_infant (child): day 18 ENA_fam_0006_inf ENA_fam_0006_infant (child): day 0 ENA_fam_0006_infant (child): day 18 ENA_fam_0006_infant (child): day 46 ENA_fam_0006_infant (child): day 112 ENA_fam_0006_infant (child): day 142 ENA_fam_0006_infant (child): day 173 ENA_fam_0006_infant (child): day 264 ENA_fam_0007_inf ENA_fam_0007_infant (child): day 0 ENA_fam_0007_infant (child): day 18 ENA_fam_0007_infant (child): day 46 ENA_fam_0007_infant (child): day 112 ENA_fam_0007_infant (child): day 142 ENA_fam_0007_infant (child): day 173 ENA_fam_0007_infant (child): day 264 ENA_fam_0007_infant (child): day 325 ENA_fam_0007_infant (child): day 416 ENA_fam_0008_inf ENA_fam_0008_infant (child): day 0 ENA_fam_0008_infant (child): day 18 ENA_fam_0008_infant (child): day 46 ENA_fam_0008_infant (child): day 112 ENA_fam_0008_infant (child): day 142 ENA_fam_0009_inf ENA_fam_0009_infant (child): day 0 ENA_fam_0009_infant (child): day 28 ENA_fam_0009_infant (child): day 94 ENA_fam_0009_infant (child): day 124 ENA_fam_0009_infant (child): day 155 ENA_fam_0009_infant (child): day 246 ENA_fam_0009_infant (child): day 307 ENA_fam_0009_infant (child): day 398 ENA_fam_0010_inf ENA_fam_0010_infant (child): day 0 ENA_fam_0010_infant (child): day 18 ENA_fam_0010_infant (child): day 46 ENA_fam_0010_infant (child): day 112 ENA_fam_0010_infant (child): day 173 ENA_fam_0010_infant (child): day 264 ENA_fam_0010_infant (child): day 325 ENA_fam_0010_infant (child): day 416 ENA_fam_0011_inf ENA_fam_0011_infant (child): day 0 ENA_fam_0011_infant (child): day 66 ENA_fam_0011_infant (child): day 96 ENA_fam_0011_infant (child): day 127 ENA_fam_0011_infant (child): day 218 ENA_fam_0011_infant (child): day 279 ENA_fam_0011_infant (child): day 370 ENA_fam_0012_inf ENA_fam_0012_infant (child): day 0 ENA_fam_0012_infant (child): day 18 ENA_fam_0012_infant (child): day 46 ENA_fam_0013_inf ENA_fam_0013_infant (child): day 0 ENA_fam_0013_infant (child): day 28 ENA_fam_0014_inf ENA_fam_0014_infant (child): day 0 ENA_fam_0014_infant (child): day 30 ENA_fam_0014_infant (child): day 61 ENA_fam_0014_infant (child): day 152 ENA_fam_0014_infant (child): day 213 ENA_fam_0014_infant (child): day 304 ENA_fam_0015_inf ENA_fam_0015_infant (child): day 0 ENA_fam_0015_infant (child): day 18 ENA_fam_0015_infant (child): day 46 ENA_fam_0015_infant (child): day 112 ENA_fam_0015_infant (child): day 142 ENA_fam_0015_infant (child): day 173 ENA_fam_0015_infant (child): day 264 ENA_fam_0016_inf ENA_fam_0016_infant (child): day 0 ENA_fam_0016_infant (child): day 18 ENA_fam_0016_infant (child): day 46 ENA_fam_0016_infant (child): day 112 ENA_fam_0016_infant (child): day 142 ENA_fam_0016_infant (child): day 173 ENA_fam_0016_infant (child): day 264 ENA_fam_0017_inf ENA_fam_0017_infant (child): day 0 ENA_fam_0017_infant (child): day 18 ENA_fam_0017_infant (child): day 46 ENA_fam_0017_infant (child): day 112 ENA_fam_0017_infant (child): day 142 ENA_fam_0017_infant (child): day 325 ENA_fam_0017_infant (child): day 416 ENA_fam_0018_inf ENA_fam_0018_infant (child): day 0 ENA_fam_0018_infant (child): day 28 ENA_fam_0018_infant (child): day 94 ENA_fam_0018_infant (child): day 124 ENA_fam_0018_infant (child): day 155 ENA_fam_0018_infant (child): day 246 ENA_fam_0018_infant (child): day 307 ENA_fam_0018_infant (child): day 398 ENA_fam_0019_inf ENA_fam_0019_infant (child): day 0 ENA_fam_0019_infant (child): day 46 ENA_fam_0019_infant (child): day 112 ENA_fam_0019_infant (child): day 142 ENA_fam_0019_infant (child): day 173 ENA_fam_0019_infant (child): day 264 ENA_fam_0019_infant (child): day 325 ENA_fam_0019_infant (child): day 416 ENA_fam_0020_inf ENA_fam_0020_infant (child): day 0 ENA_fam_0020_infant (child): day 112 ENA_fam_0020_infant (child): day 142 ENA_fam_0020_infant (child): day 173 ENA_fam_0020_infant (child): day 264 ENA_fam_0021_inf ENA_fam_0021_infant (child): day 0 ENA_fam_0021_infant (child): day 96 ENA_fam_0021_infant (child): day 218 ENA_fam_0021_infant (child): day 279 ENA_fam_0021_infant (child): day 370 ENA_fam_0022_inf ENA_fam_0022_infant (child): day 0 ENA_fam_0022_infant (child): day 18 ENA_fam_0022_infant (child): day 46 ENA_fam_0022_infant (child): day 142 ENA_fam_0022_infant (child): day 173 ENA_fam_0022_infant (child): day 264 ENA_fam_0022_infant (child): day 325 ENA_fam_0022_infant (child): day 416 ENA_fam_0023_inf ENA_fam_0023_infant (child): day 0 ENA_fam_0023_infant (child): day 91 ENA_fam_0023_infant (child): day 152 ENA_fam_0023_infant (child): day 243 ENA_fam_0024_inf ENA_fam_0024_infant (child): day 0 ENA_fam_0024_infant (child): day 18 ENA_fam_0024_infant (child): day 46 ENA_fam_0024_infant (child): day 112 ENA_fam_0024_infant (child): day 142 ENA_fam_0024_infant (child): day 173 ENA_fam_0024_infant (child): day 264 ENA_fam_0024_infant (child): day 325 ENA_fam_0024_infant (child): day 416 ENA_fam_0025_inf ENA_fam_0025_infant (child): day 0 ENA_fam_0025_infant (child): day 18 ENA_fam_0025_infant (child): day 46 ENA_fam_0025_infant (child): day 112 ENA_fam_0025_infant (child): day 142 ENA_fam_0025_infant (child): day 264 ENA_fam_0025_infant (child): day 325 ENA_fam_0025_infant (child): day 416 ENA_fam_0026_inf ENA_fam_0026_infant (child): day 0 ENA_fam_0026_infant (child): day 18 ENA_fam_0026_infant (child): day 46 ENA_fam_0026_infant (child): day 142 ENA_fam_0026_infant (child): day 173 ENA_fam_0026_infant (child): day 264 ENA_fam_0026_infant (child): day 325 ENA_fam_0026_infant (child): day 416 ENA_fam_0027_inf ENA_fam_0027_infant (child): day 0 ENA_fam_0027_infant (child): day 30 ENA_fam_0027_infant (child): day 61 ENA_fam_0027_infant (child): day 152 ENA_fam_0027_infant (child): day 213 ENA_fam_0027_infant (child): day 304 ENA_fam_0028_inf ENA_fam_0028_infant (child): day 0 ENA_fam_0028_infant (child): day 18 ENA_fam_0028_infant (child): day 46 ENA_fam_0028_infant (child): day 142 ENA_fam_0028_infant (child): day 173 ENA_fam_0028_infant (child): day 264 ENA_fam_0028_infant (child): day 325 ENA_fam_0028_infant (child): day 416 ENA_fam_0029_inf ENA_fam_0029_infant (child): day 0 ENA_fam_0029_infant (child): day 46 ENA_fam_0029_infant (child): day 142 ENA_fam_0029_infant (child): day 173 ENA_fam_0029_infant (child): day 264 ENA_fam_0029_infant (child): day 325 ENA_fam_0029_infant (child): day 416 ENA_fam_0030_inf ENA_fam_0030_infant (child): day 0 ENA_fam_0030_infant (child): day 18 ENA_fam_0030_infant (child): day 46 ENA_fam_0030_infant (child): day 112 ENA_fam_0030_infant (child): day 173 ENA_fam_0030_infant (child): day 264 ENA_fam_0030_infant (child): day 325 ENA_fam_0030_infant (child): day 416 ENA_fam_0031_inf ENA_fam_0031_infant (child): day 0 ENA_fam_0031_infant (child): day 18 ENA_fam_0031_infant (child): day 46 ENA_fam_0031_infant (child): day 173 ENA_fam_0031_infant (child): day 264 ENA_fam_0031_infant (child): day 325 ENA_fam_0032_inf ENA_fam_0032_infant (child): day 0 ENA_fam_0032_infant (child): day 46 ENA_fam_0032_infant (child): day 112 ENA_fam_0032_infant (child): day 142 ENA_fam_0032_infant (child): day 173 ENA_fam_0032_infant (child): day 264 ENA_fam_0032_infant (child): day 325 ENA_fam_0032_infant (child): day 416 ENA_fam_0033_inf ENA_fam_0033_infant (child): day 0 ENA_fam_0033_infant (child): day 28 ENA_fam_0033_infant (child): day 124 ENA_fam_0033_infant (child): day 246 ENA_fam_0033_infant (child): day 307 ENA_fam_0033_infant (child): day 398 ENA_fam_0034_inf ENA_fam_0034_infant (child): day 0 ENA_fam_0034_infant (child): day 28 ENA_fam_0034_infant (child): day 94 ENA_fam_0034_infant (child): day 124 ENA_fam_0034_infant (child): day 155 ENA_fam_0034_infant (child): day 398 ENA_fam_0036_inf ENA_fam_0036_infant (child): day 0 ENA_fam_0036_infant (child): day 28 ENA_fam_0036_infant (child): day 94 ENA_fam_0036_infant (child): day 155 ENA_fam_0036_infant (child): day 246 ENA_fam_0036_infant (child): day 307 ENA_fam_0036_infant (child): day 398 ENA_fam_0037_inf ENA_fam_0037_infant (child): day 0 ENA_fam_0037_infant (child): day 66 ENA_fam_0037_infant (child): day 96 ENA_fam_0037_infant (child): day 127 ENA_fam_0037_infant (child): day 218 ENA_fam_0037_infant (child): day 279 0 d 3 mo 7 mo 10 mo 14 mo
Each row is one person (36 shown of 134); 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 ).
139 families: 139 infants (longitudinal), 115 mothers and 6 fathers sampled once postpartum (host family id) · 115 families with 236 sampled people (115 with a parent and a child).
mother M child C 109 × mother + child
mother M father F child C 6 × mother + father + child
family ENA_fam_0006 ENA_fam_0006_infant — child · 7 samples C infant ENA_fam_0006_mother — mother · 1 sample M mother ENA_fam_0006… family ENA_fam_0001 ENA_fam_0001_infant — child · 5 samples C infant ENA_fam_0001_father — father · 1 sample F father ENA_fam_0001_mother — mother · 1 sample M mother ENA_fam_0001… family ENA_fam_0008 ENA_fam_0008_infant — child · 5 samples C infant ENA_fam_0008_mother — mother · 1 sample M mother ENA_fam_0008… family ENA_fam_0002 ENA_fam_0002_infant — child · 4 samples C infant ENA_fam_0002_father — father · 1 sample F father ENA_fam_0002_mother — mother · 1 sample M mother ENA_fam_0002… family ENA_fam_0009 ENA_fam_0009_infant — child · 8 samples C infant ENA_fam_0009_mother — mother · 1 sample M mother ENA_fam_0009… family ENA_fam_0003 ENA_fam_0003_infant — child · 5 samples C infant ENA_fam_0003_father — father · 1 sample F father ENA_fam_0003_mother — mother · 1 sample M mother ENA_fam_0003… family ENA_fam_0010 ENA_fam_0010_infant — child · 8 samples C infant ENA_fam_0010_mother — mother · 1 sample M mother ENA_fam_0010… family ENA_fam_0004 ENA_fam_0004_infant — child · 4 samples C infant ENA_fam_0004_father — father · 1 sample F father ENA_fam_0004_mother — mother · 1 sample M mother ENA_fam_0004… family ENA_fam_0011 ENA_fam_0011_infant — child · 7 samples C infant ENA_fam_0011_mother — mother · 1 sample M mother ENA_fam_0011… family ENA_fam_0005 ENA_fam_0005_infant — child · 2 samples C infant ENA_fam_0005_father — father · 1 sample F father ENA_fam_0005_mother — mother · 1 sample M mother ENA_fam_0005… family ENA_fam_0012 ENA_fam_0012_infant — child · 3 samples C infant ENA_fam_0012_mother — mother · 1 sample M mother ENA_fam_0012… family ENA_fam_0007 ENA_fam_0007_infant — child · 9 samples C infant ENA_fam_0007_father — father · 1 sample F father ENA_fam_0007_mother — mother · 1 sample M mother ENA_fam_0007… family ENA_fam_0013 ENA_fam_0013_infant — child · 2 samples C infant ENA_fam_0013_mother — mother · 1 sample M mother ENA_fam_0013… family ENA_fam_0014 ENA_fam_0014_infant — child · 6 samples C infant ENA_fam_0014_mother — mother · 1 sample M mother ENA_fam_0014… family ENA_fam_0015 ENA_fam_0015_infant — child · 7 samples C infant ENA_fam_0015_mother — mother · 1 sample M mother ENA_fam_0015… family ENA_fam_0016 ENA_fam_0016_infant — child · 7 samples C infant ENA_fam_0016_mother — mother · 1 sample M mother ENA_fam_0016… family ENA_fam_0017 ENA_fam_0017_infant — child · 7 samples C infant ENA_fam_0017_mother — mother · 1 sample M mother ENA_fam_0017… family ENA_fam_0018 ENA_fam_0018_infant — child · 8 samples C infant ENA_fam_0018_mother — mother · 1 sample M mother ENA_fam_0018… family ENA_fam_0019 ENA_fam_0019_infant — child · 8 samples C infant ENA_fam_0019_mother — mother · 1 sample M mother ENA_fam_0019… family ENA_fam_0022 ENA_fam_0022_infant — child · 8 samples C infant ENA_fam_0022_mother — mother · 1 sample M mother ENA_fam_0022… family ENA_fam_0024 ENA_fam_0024_infant — child · 9 samples C infant ENA_fam_0024_mother — mother · 1 sample M mother ENA_fam_0024… family ENA_fam_0025 ENA_fam_0025_infant — child · 8 samples C infant ENA_fam_0025_mother — mother · 1 sample M mother ENA_fam_0025… family ENA_fam_0026 ENA_fam_0026_infant — child · 8 samples C infant ENA_fam_0026_mother — mother · 1 sample M mother ENA_fam_0026… family ENA_fam_0027 ENA_fam_0027_infant — child · 6 samples C infant ENA_fam_0027_mother — mother · 1 sample M mother ENA_fam_0027…
Families (25 of 115) How longitudinal and relatedness information is derived
Details
Archive description The fecal microbiota of 139 infants and their parents. The infant fecal samples were collected at ages 1 -2 weeks, and 1, 2, 4, 5, 6, 9, 11 and 14 months. Parental samples were collected around 1-2 week postpartum. Paired-end shotgun metagenome sequencing with BGISEQ 500.
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.title · “LucKi Gut - Longitudinal metagenomic”body site study.description · “The fecal microbiota of 139”life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”life stage study.title · “metagenomic sequencing of infant gut microbiota”Evidence examples (one per field × route)
sample field value route conf. source quote
SAMEA118322587 age_at_collection_days 10 R1 0.70 biosample_attr 1-2 weeks SAMEA118322587 collection_date 2021 R1 0.85 biosample.attribute:collection date 2021 SAMEA118322587 country NL R1 0.90 biosample_attr Netherlands SAMEA118322587 family_id ENA_fam_0001 R1 0.85 biosample.attribute:host family id ENA_fam_0001 SAMEA118322587 family_role child R1 0.85 biosample.attribute:host family relationship infant SAMEA118322587 sex female R1 0.90 biosample_attr female SAMEA118322587 subject_id ENA_fam_0001_infant R1 0.85 biosample_attr ENA_fam_0001_infant SAMEA118322587 timepoint_label 1-2 weeks R1 0.85 biosample.attribute:Age_group_at_sample 1-2 weeks SAMEA118322659 timepoint_label 5 months R2 0.85 paper.supp.table Age group1=5 months
Sequencing 929 runs over 929 samples · mean 16.01 Gbp per run (median 15.73 Gbp, total 14,875.84 Gbp; 929 runs with a base count) · layout PAIRED 929 · platform BGISEQ 929 · models BGISEQ-500 (929) · 0% of runs with a Sandpiper profile · first public 2025-05-19
Authors (8) Dikareva E first · van Best N · Bervoets L · West CE · Rossel C · Driessen C · Mommers M · Penders J last
Downloads PRJEB89491.csv.gz (33.3 KB) · parquet (114.1 KB) — all 929 samples, every field with route and confidence · PRJEB89491_determinations.csv.gz (52.1 KB) — 7,191 evidence rows