Early-life gut microbiota colonisation in UK neonates/infants
Longitudinal cohort study of 1679 gut microbiome samples from neonates and infants (708 from the United Kingdom), mostly healthy controls, examining early microbe exposure and immune development. machine-written summary
2,387 samples · 2,387 runs · GB · Infant / toddler · 2019 · 2.46 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 3,517 sample values (country, family id, family role, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 2,752 sample values (collection date, country, preterm status) · PMC10827747, PMC10904392, PMC11322291, PMC11445081, PMC11733223, PMC11758915, PMC11929092, PMC12122369, PMC12172464, PMC12769767, PMC13236588, PMC13288982, PMC6894937, PMC7211887, PMC8115609, PMC8827105, PMC9248880, PMC9437082, PMC9715557 |
| ✓ Supplementary tables | 19,917 sample values (age, antibiotic exposure, birth weight grams, country, delivery mode, diet, feeding mode, maternal antibiotics) |
| ✓ External resources | 3,394 sample values (age, antibiotic exposure, health condition, health condition detail) · from curatedMetagenomicData 3 (cMD 3) |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
age: supplementary table and curatedMetagenomicData disagree for 149 samples (e.g. 0 vs 11688.0) — withheld; antibiotic exposure: supplementary table and curatedMetagenomicData disagree for 153 samples (e.g. no vs yes) — withheld; sex: two supplementary tables disagree for 86 samples (e.g. female vs male) — withheld.
The sources disagree on 304 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 388)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMEA5616674 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616677 | age | 0 (supplementary table) | 17532.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616681 | age | 0 (supplementary table) | 13879.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616683 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616698 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616706 | age | 0 (supplementary table) | 15340.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616712 | age | 0 (supplementary table) | 10227.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616718 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616719 | age | 0 (supplementary table) | 15340.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616721 | age | 0 (supplementary table) | 13879.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616732 | age | 0 (supplementary table) | 13879.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616735 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616749 | age | 0 (supplementary table) | 10227.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616807 | age | 0 (supplementary table) | 10227.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616812 | age | 0 (supplementary table) | 10227.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616873 | age | 0 (supplementary table) | 13879.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616878 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616879 | age | 0 (supplementary table) | 13879.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616884 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616910 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616919 | age | 0 (supplementary table) | 15340.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616931 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616935 | age | 0 (supplementary table) | 13879.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616946 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616951 | age | 0 (supplementary table) | 13879.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616966 | age | 0 (supplementary table) | 13879.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616978 | age | 0 (supplementary table) | 10227.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616980 | age | 0 (supplementary table) | 13879.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616983 | age | 0 (supplementary table) | 13879.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616989 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5616998 | age | 0 (supplementary table) | 15340.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5617555 | age | 0 (supplementary table) | 8035.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5617579 | age | 0 (supplementary table) | 13879.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5617603 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5617642 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5617654 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5617678 | age | 0 (supplementary table) | 15340.5 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5617680 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5617699 | age | 0 (supplementary table) | 10227.0 (curatedMetagenomicData) | withheld: neither value published |
| SAMEA5617704 | age | 0 (supplementary table) | 11688.0 (curatedMetagenomicData) | withheld: neither value published |
longitudinalmother–infant
4 of 2,381 people sampled more than once (9 samples; median 2, up to 3 per person) · follow-up median 6 d (max 14 d) · median interval between samples 3 d (time from age at collection). Schedule stated by the source: “Neonatal samples at day 4, 7, and/or 21 (<1 month), with a subset re-sampled in infancy (8.75±1.98 months); mothers sampled once (matched).” (time origin: birth); stated follow-up 12 mo.
Each row is one person (4 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).
161 mother–baby families marked (161 mother samples, 366 baby samples) via TITLE _M suffix; 175 mothers/178 babies per paper · 161 families with 527 sampled people (161 with a parent and a child).
motherchild · 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 161 families (one per family structure, then more). 2,381 people in the project overall.
Families (25 of 161)
Genera, mean relative abundance over 1,518 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 | 2,387 | 100% | ||||
| country | 2,387 | 100% | 708 | 1,537 | 142 | |
| health_condition | 1,644 | 69% | 1,644 | |||
| subject_id | 2,386 | 100% | 1,679 | 707 | ||
| collection_date | 2,387 | 100% | 2,387 | |||
| timepoint_label | 2,387 | 100% | 76 | 2,311 | ||
| age_at_collection_days | 2,232 | 94% | 2,232 | |||
| sex | 2,166 | 91% | 2,166 | |||
| antibiotic_exposure | 1,955 | 82% | 1,955 | |||
| delivery_mode | 1,679 | 70% | 1,679 | |||
| maternal_antibiotics | 1,679 | 70% | 1,679 | |||
| preterm_status | 1,679 | 70% | 1,456 | 223 | ||
| health_condition_detail | 1,644 | 69% | 1,644 | |||
| birth_weight_grams | 1,589 | 67% | 1,589 | |||
| diet | 1,356 | 57% | 1,356 | |||
| feeding_mode | 1,356 | 57% | 1,356 | |||
| family_id | 527 | 22% | 527 | |||
| family_role | 527 | 22% | 527 |
- Strong pathogen competition in neonatal gut colonisation. 2022 PMID 36456554 PMC9715557 cites_accession
- Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. PMID 31534227 PMC6894937 curated
- An individualized mosaic of maternal microbial strains is transmitted to the infant gut microbial community. PMID 32431894 PMC7211887 curated
- Metagenomic analysis of mother-infant gut microbiome reveals global distinct and shared microbial signatures. PMID 33960282 PMC8115609 curated
- Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load. PMID 34677583 PMC8827105 curated
19 more
- Rapid evolution and strain turnover in the infant gut microbiome. PMID 35545448 PMC9248880
- A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID 36050292 PMC9437082
- Strong pathogen competition in neonatal gut colonisation. PMID 36456554 PMC9715557
- 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
- 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
- Early life microbial succession in the gut follows common patterns in humans across the globe. PMID 39809768 PMC11733223
- Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome. PMID 39866568 PMC11758915
- Dynamics of gut resistome and mobilome in early life: a meta-analysis. PMID 40048849 PMC11929092
- Longitudinal profiling of low-abundance strains in microbiomes with ChronoStrain. PMID 40328944 PMC12122369
- parafac4microbiome: exploratory analysis of longitudinal microbiome data using parallel factor analysis. PMID 40396737 PMC12172464
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
- Strain-level transmission inference across multi-kingdom metagenomic data using TRACS. PMID 42032281 PMC13236588
- Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis. PMID 42171373 PMC13288982
- MxSure: a mixture model for inferring within-host substitution rates and transmission SNP thresholds
- Enhanced metagenomics-enabled transmission inference with TRACS
- Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth. 2019 PMID 31534227 PMC6894937
- Primary succession of Bifidobacteria drives pathogen resistance in neonatal microbiota assembly. 2024 PMID 39242817 PMC11445081
Archive description
Study to investigate how early microbe exposure and the developing immune system influence subsequent health and developmental outcomes. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
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)”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA115771184 | age_at_collection_days | 7.0 | R2 | 0.85 | paper.supp.41564_2024_1804_MOESM2_ESM.xlsx[neonatal_sample!Age_day] | A00908_7 Age_day 7 |
| SAMEA5616855 | age_at_collection_days | 0.0 | R2 | 0.75 | external.cmd source | age: 0; age_unit: Day; age_group: Newborn |
| SAMEA115771185 | antibiotic_exposure | no | R2 | 0.75 | paper.supp.41564_2024_1804_MOESM2_ESM.xlsx[neonatal_subject!baby_postnatal_antibiotics] | B03908 baby_postnatal_antibiotics No |
| SAMEA5616554 | antibiotic_exposure | no | R2 | 0.75 | external.cmd source | antibiotics_current_use: No |
| SAMEA5616554 | birth_weight_grams | 3400 | R2 | 0.85 | paper.supp.table | Birth weight in 100 grams=3400 |
| SAMEA115771184 | collection_date | 2014-05/2017-12 | R3 | 0.70 | paper.fulltext.methods | from May 2014 to December 2017 |
| SAMEA115771184 | country | GB | R1 | 0.90 | sample.attr.geographic_location_country_and_or_sea | United Kingdom |
| SAMEA5616559 | country | GB | R2 | 0.85 | paper.supp.table | Country=UK |
| SAMEA5616554 | country | GB | R3 | 0.40 | paper.fulltext.methods | NHS London - City and East Research Ethics Committee |
| SAMEA5616554 | delivery_mode | c_section | R2 | 0.75 | paper.supp.table | Delivery_mode=Caesarean |
| SAMEA5616609 | diet | other_diet | R2 | 0.85 | paper.supp.EMS84123-supplement-Supplementary_Tables.xlsx[S1 BBS metadata table!Feeding_method] | Mixed |
| SAMEA115771184 | family_id | A00908 | R1 | 0.70 | sample.name_rule:TITLE | TITLE: A00908_7 |
| SAMEA115771184 | family_role | child | R1 | 0.70 | sample.name_rule:TITLE | TITLE: A00908_7 |
| SAMEA5616609 | feeding_mode | mixed | R2 | 0.85 | paper.supp.table | Feeding_method=Mixed |
| SAMEA5616554 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA5616554 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMEA5616554 | maternal_antibiotics | no | R2 | 0.85 | paper.supp.table | Abx_mother_prior_birth=no |
| SAMEA5616559 | preterm_status | term | R2 | 0.85 | paper.supp.table | Gestational age=full-term |
| SAMEA5616554 | preterm_status | term | R3 | 0.80 | paper.fulltext.results | 596 healthy babies from full-term pregnancies |
| SAMEA115771185 | sex | male | R2 | 0.75 | paper.supp.41564_2024_1804_MOESM2_ESM.xlsx[neonatal_subject!Sex] | B03908 Sex Male |
| SAMEA5616554 | subject_id | 5826STDY7976007 | R1 | 0.85 | biosample_attr | 5826STDY7976007 |
| SAMEA115771184 | subject_id | A00908 | R2 | 0.85 | paper.supp.41564_2024_1804_MOESM2_ESM.xlsx[sample_accession!Subject] | A00908_7 A00908 |
| SAMEA5616658 | timepoint_label | T2 | R1 | 0.70 | sample.title | A00021_T2_4 |
| SAMEA115771184 | timepoint_label | day 7 | R2 | 0.85 | paper.supp.41564_2024_1804_MOESM2_ESM.xlsx[sample_accession!Time_point] | A00908_7 7 |
Sequencing
2,387 runs over 2,387 samples · mean 2.52 Gbp per run (median 2.46 Gbp, total 6,005.19 Gbp; 2,387 runs with a base count) · layout PAIRED 2,387 · platform ILLUMINA 2,387 · models Illumina HiSeq 2500 (1,679), Illumina HiSeq 4000 (708) · 91% of runs with a Sandpiper profile · first public 2019-07-01 – 2024-06-27
Authors (160)
Shao Y first · Forster SC · Tsaliki E · Vervier K · Strang A · Simpson N · Kumar N · Stares MD · Rodger A · Brocklehurst P · Field N · Lawley TD last · Koo H first · McFarland BC · Hakim JA · Crossman DK · Crowley MR · Rodriguez JM · Benveniste EN · Morrow CD 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 · 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 · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Mäklin T first · Thorpe HA · Pöntinen AK · Gladstone RA · Pesonen M · McNally A · Johnsen PJ · Samuelsen Ø · Honkela A · Corander J last · Ennis D first · Shmorak S · Jantscher-Krenn E · Yassour M last · Li S · Ying J · Wang H · Qu Y · Niu X · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Garcia-Mauriño C · Clare S · Dawson NJR · Mu A · Adoum A · Harcourt K · Liu J · Browne HP · 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 · Pucci N first · Ujčič-Voortman J · Verhoeff AP · Mende DR last · Bargheet A first · Noordzij HT · Ponsero AJ · Jian C · Korpela K · Valles-Colomer M · Debelius J · Kurilshikov A · Pettersen VK last · Kim Y first · Worby CJ · Acharya S · van Dijk LR · Alfonsetti D · Gromko Z · Azimzadeh PN · Dodson KW · Gerber GK · Hultgren SJ · Earl AM · Berger B · Gibson TE last · van der Ploeg GR first · Westerhuis JA · Heintz-Buschart A · Smilde AK last · Tarracchini C first · Longhi G · Gennaioli E · Muscò A · Rizzo SM · Viappiani A · Vitale SG · Mancabelli L · Lugli GA · Angioni S · Turroni F · van Sinderen D · Milani C · Ventura M last · Tonkin-Hill G first · Zarebski AE · Mallawaarachchi S · Xie O · Davies MR · Bentley SD · Schroer HW first · Beghini F · Raygoza Garay JA · Christakis NA · Bosch DE last
Downloads
PRJEB32631.csv.gz (77.6 KB) · parquet (198.9 KB) — all 2,387 samples, every field with route and confidence · PRJEB32631_determinations.csv.gz (332.5 KB) — 29,580 evidence rows