Infant gut microbiome development, Denmark, longitudinal cohort
400 samples from healthy infants and neonates in Denmark, studying gut microbiome dynamics and stabilization during the first year of life in a longitudinal cohort design. machine-written summary
400 samples · 400 runs · Infant / toddler · 2015 · 3.98 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ○ Sequence archive | records read; no usable sample values |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10092070, PMC10175488, PMC10187079, PMC10230729, PMC10234599, PMC10769871, PMC10827747, PMC10904392, PMC10989911, PMC11170968, PMC11322291, PMC11445081, PMC11497992, PMC11733223, PMC11929092, PMC12769767, PMC13288982, PMC13388695, PMC6158511, PMC6195700, PMC7790408, PMC8020746, PMC8115609, PMC8518733, PMC8827105, PMC9248880, PMC9381805, PMC9437082, PMC9622858, PMC9910082, PMC9980514 |
| ✓ Supplementary tables | 3,114 sample values (age, antibiotic exposure, delivery mode, feeding mode, gestational age weeks, maternal antibiotics, nec status, preterm status) |
| ✓ External resources | 802 sample values (health condition, health condition detail, sex) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
antibiotic exposure: supplementary table and curatedMetagenomicData disagree for 29 samples (e.g. no vs yes) — withheld; country: supplementary table and sequence archive disagree for 400 samples (e.g. SE vs DK) — withheld; sex: supplementary table and curatedMetagenomicData disagree for 3 samples (e.g. female vs male) — withheld.
The sources disagree on 400 samples. Where two incompatible values exist for one sample (or one person's samples disagree on sex), neither value is published: the field is left empty here, in the sample sheet and in the downloads. Both sides, with their sources, are in gut_metadata_contradictions.parquet of the data package (what counts as a contradiction).
Contradicted values (40 of 432)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA2579938 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2579940 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2579941 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2579948 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2579949 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2579982 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2579994 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580006 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580034 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580038 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580050 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580066 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580086 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580099 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580102 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580116 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580117 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580122 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580138 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580163 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580166 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580178 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580210 | antibiotic exposure | yes (supplementary table) | no (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580238 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580254 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580279 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580282 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580288 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2580302 | antibiotic exposure | no (supplementary table) | yes (curatedMetagenomicData) | withheld: neither value published |
| SAMEA2579905 | country | SE (supplementary table) | DK (sequence archive) | withheld: neither value published |
| SAMEA2579906 | country | SE (supplementary table) | DK (sequence archive) | withheld: neither value published |
| SAMEA2579907 | country | SE (supplementary table) | DK (sequence archive) | withheld: neither value published |
| SAMEA2579908 | country | SE (supplementary table) | DK (sequence archive) | withheld: neither value published |
| SAMEA2579909 | country | SE (supplementary table) | DK (sequence archive) | withheld: neither value published |
| SAMEA2579910 | country | SE (supplementary table) | DK (sequence archive) | withheld: neither value published |
| SAMEA2579911 | country | SE (supplementary table) | DK (sequence archive) | withheld: neither value published |
| SAMEA2579912 | country | SE (supplementary table) | DK (sequence archive) | withheld: neither value published |
| SAMEA2579913 | country | SE (supplementary table) | DK (sequence archive) | withheld: neither value published |
| SAMEA2579914 | country | SE (supplementary table) | DK (sequence archive) | withheld: neither value published |
| SAMEA2579915 | country | SE (supplementary table) | DK (sequence archive) | withheld: neither value published |
longitudinal
47 of 353 people sampled more than once (94 samples; median 2, up to 2 per person) · follow-up median 8 mo (max 9 mo) · median interval between samples 8 mo (time from age at collection).
Each row is one person (36 shown of 47); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 357 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 | 398 | 100% | ||||
| country | 0 | 0% | ||||
| health_condition | 400 | 100% | 400 | |||
| subject_id | 400 | 100% | 400 | |||
| health_condition_detail | 400 | 100% | 400 | |||
| age_at_collection_days | 397 | 99% | 397 | |||
| delivery_mode | 392 | 98% | 392 | |||
| preterm_status | 392 | 98% | 392 | |||
| sex | 391 | 98% | 391 | |||
| timepoint_label | 388 | 97% | 388 | |||
| feeding_mode | 284 | 71% | 284 | |||
| antibiotic_exposure | 265 | 66% | 265 | |||
| gestational_age_weeks | 69 | 17% | 69 | |||
| maternal_antibiotics | 69 | 17% | 69 | |||
| nec_status | 69 | 17% | 69 |
- Bifidobacterial Dominance of the Gut in Early Life and Acquisition of Antimicrobial Resistance. PMID 30258040 PMC6158511 curated
- Competitive lottery-based assembly of selected clades in the human gut microbiome. PMID 30340536 PMC6195700 curated
- Predicting drug-metagenome interactions: Variation in the microbial β-glucuronidase level in the human gut metagenomes. PMID 33411719 PMC7790408 curated
- CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention. PMID 33753486 PMC8020746 curated
- Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures. PMID 33960282 PMC8115609 curated
27 more
- 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
- Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load. PMID 34677583 PMC8827105
- Rapid evolution and strain turnover in the infant gut microbiome. PMID 35545448 PMC9248880
- Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides. PMID 35768643 PMC9381805
- 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
- Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium. PMID 36316342 PMC9622858
- Microbial characterization based on multifractal analysis of metagenomes. PMID 36779183 PMC9910082
- Gut microbiome function and composition in infants from rural Kenya and association with human milk oligosaccharides. PMID 36794816 PMC9980514
- 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
- Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides. PMID 37188713 PMC10187079
- Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut. PMID 37259063 PMC10230729
- 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
- StrainPanDA: Linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data. PMID 38868710 PMC10989911
- 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
- Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly. PMID 39242817 PMC11445081
- Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy. PMID 39428758 PMC11497992
- Early life microbial succession in the gut follows common patterns in humans across the globe. PMID 39809768 PMC11733223
- 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
- Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis. PMID 42171373 PMC13288982
- Dual human milk oligosaccharide-fibre utilisation is a selection cue for the weaning gut microbiome. PMID 42203770 PMC13388695
- Longitudinal Variability of Bifidobacterium Species in the Infant Gut is Independent of Maternal Milk HMO Composition
Archive description
The gastrointestinal tracts of mammalians are sterile in utero and colonized by microorganisms immediately after delivery. The subsequent development of the infant gut microbiota involves a complex succession of microbes, driven by factors such as gestational age, mode of delivery, antibiotic use, hygiene, geographical zone and type of feeding.
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 · “of the Human Gut Microbiome during the”
- body site study.description · “The gastrointestinal tracts of mammalians”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Microbiome during the First Year of Life”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA2579905 | age_at_collection_days | 380 | R2 | 0.85 | paper.supp.table | Sampling, day=380 |
| SAMEA2579905 | antibiotic_exposure | no | R2 | 0.85 | paper.supp.table | Postnatal antibiotic intervention in infants=NO |
| SAMEA2579905 | delivery_mode | vaginal | R2 | 0.85 | paper.supp.table | Mode of delivery=vaginal |
| SAMEA2579905 | feeding_mode | weaned | R2 | 0.75 | paper.supp.table | feeding_practice=only solids |
| SAMEA2579908 | gestational_age_weeks | 32.0 | R2 | 0.75 | paper.supp.table | Gest_age=32 |
| SAMEA2579905 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA2579905 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA2579908 | maternal_antibiotics | no | R2 | 0.75 | paper.supp.table | Mat_AB=False |
| SAMEA2579908 | nec_status | no | R2 | 0.75 | paper.supp.table | NEC=False |
| SAMEA2579905 | preterm_status | term | R2 | 0.85 | paper.supp.table | Gestational age=full-term |
| SAMEA2579905 | sex | male | R2 | 0.85 | paper.supp.table | Gender=male |
| SAMEA2580060 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
| SAMEA2579905 | subject_id | 10 | R2 | 0.85 | paper.supp.table | 591=10 |
| SAMEA2579905 | timepoint_label | post-weaning | R2 | 0.75 | paper.supp.table | Time Group=post-weaning |
Sequencing
400 runs over 400 samples · mean 3.97 Gbp per run (median 3.98 Gbp, total 1,586.93 Gbp; 400 runs with a base count) · layout PAIRED 400 · platform ILLUMINA 400 · models Illumina HiSeq 2000 (400) · 89% of runs with a Sandpiper profile · first public 2015-06-01
Authors (273)
Taft DH first · Liu J · Maldonado-Gomez MX · Akre S · Huda MN · Ahmad SM · Stephensen CB · Mills DA last · Verster AJ first · Borenstein E last · Elmassry MM first · Kim S · Busby B last · Geng J first · Ji B · Li G · López-Isunza F · Nielsen J 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 · Tisza MJ first · Buck CB last · Fontana F first · Mancabelli L · Lugli GA · Taracchini C · Alessandri G · Longhi G · Anzalone R · Viappiani A · Famo R · Brognan M · Micondo KH · Turroni F · Ventura M · D'Alfonso R · Milani C last · Pärnänen KMM first · Hultman J · Markkanen M · Satokari R · Rautava S · Lamendella R · Wright J · McLimans CJ · Kelleher SL · Virta MP last · Chen DW first · Garud NR last · Ojima MN first · Jiang L · Arzamasov AA · Yoshida K · Odamaki T · Xiao J · Nakajima A · Kitaoka M · Hirose J · Urashima T · Katoh T · Gotoh A · van Sinderen D · Rodionov DA · Osterman AL · Sakanaka M · Katayama T 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 · Xie XH first · Huang YJ · Han GS · Yu ZG · Ma YL last · Derrien M first · Mikulic N · Uyoga MA · Chenoll E · Climent E · Howard-Varona A · Nyilima S · Stoffel NU · Karanja S · Kottler R · Stahl B · Zimmermann MB · Bourdet-Sicard R last · Manara S first · Selma-Royo M · Huang KD · Asnicar F · Armanini F · 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 · Pasolli E · Collado MC · Segata N last · Orihara K first · Yahagi K · Saito Y · Watanabe Y · Sasai T · Hara T · Tsukuda N · Oki K · Fujimoto J · Matsuki T last · Ormaasen I first · Rudi K · Diep DB · Snipen L last · 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 · Yassour M last · Li S · Ying J · Wang H · Qu Y · Niu X · Hu H first · Tan Y · Li C · Chen J · Kou Y · Xu ZZ · Liu YY · Dai L last · Xu X first · Feng Q · Zhang T · Gao Y · Cheng Q · Zhang W · Wu Q · Xu K · Li Y · Nguyen N · Lemay DG · Zhu W · Mao S · Zhang A · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Shao Y first · Garcia-Mauriño C · Clare S · Dawson NJR · Mu A · Adoum A · Harcourt K · Browne HP · Stares MD · Rodger A · Brocklehurst P · Field N · Lawley TD last · Minot SS first · Mayer-Blackwell K · Fiore-Gartland A · Johnson A · Self S · Bhatti P · Yao L · Liu L · Sun X · Jinfa Y · Kublin J last · Fahur Bottino G first · Bonham KS · Patel F · McCann S · Zieff M · Naspolini N · Ho D · Portlock T · Joos R · Midani FS · Schüroff P · Das A · Shennon I · Wilson BC · O'Sullivan JM · Britton RA · Murray DM · Kiely ME · Taddei CR · Beltrão-Braga PCB · Campos AC · Polanczyk GV · Huttenhower C · Donald KA · Klepac-Ceraj V 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 · Schroer HW first · Beghini F · Raygoza Garay JA · Christakis NA · Bosch DE last · So Y first · Pichler MJ · Kappel SS · Jin C · Eriksen C · Chatzigiannidou I · Andersen MHB · Tsiamis V · Lukassen MV · Skytthe LE · Teneberg S · Kristiansen K · Brix S · Aunsholt L · Abou Hachem M last
Downloads
PRJEB6456.csv.gz (13.9 KB) · parquet (90.8 KB) — all 400 samples, every field with route and confidence · PRJEB6456_determinations.csv.gz (42.3 KB) — 3,916 evidence rows