Infant Gut Microbiome Development in St Louis Twins
402 samples from twin infants (0-8 months) in Saint Louis, Missouri, most healthy with some having GI infection or diarrhoea; a longitudinal cohort study of gut microbiome functional maturation. machine-written summary
402 samples · 447 runs · US · Infant / toddler · 2018 · 1.03 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 5,694 sample values (age, antibiotic exposure, birth weight grams, collection date, country, diet, family id, family role) |
| ✓ Abstract / description | 515 sample values (health condition, location region) |
| ✓ Full text | 804 sample values (location locality, location site) · PMC10092070, PMC10175488, PMC10230729, PMC10269646, PMC10769871, PMC10904392, PMC11019788, PMC11170968, PMC11322291, PMC11494892, PMC11929092, PMC12549143, PMC12677589, PMC12769767, PMC6294307, PMC8151561, PMC8284144, PMC8383385, PMC8518733, PMC8827105, PMC9437082, PMC9512645, PMC9622858 |
| ✓ Supplementary tables | 474 sample values (delivery mode, maternal antibiotics, nec status, timepoint) |
| ✓ External resources | 442 sample values (health condition, health condition detail) · from GMrepo v3 |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
antibiotic exposure: two sequence archives disagree for 39 samples (e.g. no vs yes) — withheld; health condition: sequence archive and GMrepo disagree for 45 samples (e.g. gi_infection_or_diarrhoea vs healthy_control) — withheld.
The sources disagree on 82 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 84)
| sample | field | value | other value | handling |
|---|---|---|---|---|
| SAMN09259873 | antibiotic exposure | no (sequence archive) | yes (GMrepo) | withheld: neither value published |
| SAMN09259874 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09259875 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09259880 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09259881 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09259904 | antibiotic exposure | no (sequence archive) | yes (GMrepo) | withheld: neither value published |
| SAMN09259909 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09259910 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09259911 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09259912 | antibiotic exposure | no (sequence archive) | yes (GMrepo) | withheld: neither value published |
| SAMN09259957 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09259958 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09259975 | antibiotic exposure | no (supplementary table) | yes (sequence archive) | withheld: neither value published |
| SAMN09259979 | antibiotic exposure | no (supplementary table) | yes (sequence archive) | withheld: neither value published |
| SAMN09259980 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09259981 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09259986 | antibiotic exposure | no (sequence archive) | yes (GMrepo) | withheld: neither value published |
| SAMN09259987 | antibiotic exposure | no (sequence archive) | yes (GMrepo) | withheld: neither value published |
| SAMN09259988 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09259994 | antibiotic exposure | no (sequence archive) | yes (GMrepo) | withheld: neither value published |
| SAMN09260010 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09260012 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09260039 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09260045 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09260046 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09260050 | antibiotic exposure | no (sequence archive) | yes (GMrepo) | withheld: neither value published |
| SAMN09260051 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09260052 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09260053 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09260054 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09260088 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09260101 | antibiotic exposure | no (supplementary table) | yes (sequence archive) | withheld: neither value published |
| SAMN09260105 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09260106 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09260107 | antibiotic exposure | no (sequence archive) | yes (GMrepo) | withheld: neither value published |
| SAMN09260113 | antibiotic exposure | no (sequence archive) | yes (GMrepo) | withheld: neither value published |
| SAMN09260115 | antibiotic exposure | no (sequence archive) | yes (GMrepo) | withheld: neither value published |
| SAMN09260221 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09260222 | antibiotic exposure | no (sequence archive) | yes (sequence archive) | withheld: neither value published |
| SAMN09259865 | health condition | gi_infection_or_diarrhoea (sequence archive) | healthy_control (GMrepo) | withheld: neither value published |
longitudinaltwins
60 of 60 people sampled more than once (402 samples; median 7, up to 9 per person) · follow-up median 7 mo (max 8 mo) · median interval between samples 32 d (time from age at collection). Schedule stated by the source: “Monthly stool sampling from 0 to 8 months of age per infant” (time origin: birth).
Each row is one person (36 shown of 60); 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).
60 twin infants from 31 families (twin pairs); host_family_relationship confirms twin sibling dyads · 27 families with 54 sampled people, 56 twin sets.
twin · 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 29 linked groups from explicit relations. 60 people in the project overall.
Families (25 of 27)
Genera, mean relative abundance over 204 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 | 402 | 100% | ||||
| country | 402 | 100% | 402 | |||
| health_condition | 357 | 89% | 23 | 221 | 113 | |
| subject_id | 402 | 100% | 402 | |||
| age_at_collection_days | 402 | 100% | 402 | |||
| birth_weight_grams | 402 | 100% | 402 | |||
| collection_date | 402 | 100% | 402 | |||
| delivery_mode | 402 | 100% | 402 | |||
| detailed_location | 402 | 100% | ||||
| family_role | 402 | 100% | 402 | |||
| feeding_mode | 402 | 100% | 402 | |||
| gestational_age_weeks | 402 | 100% | 402 | |||
| location_locality | 402 | 100% | 402 | |||
| location_region | 402 | 100% | 402 | |||
| location_site | 402 | 100% | 402 | |||
| preterm_status | 402 | 100% | 402 | |||
| sex | 402 | 100% | 402 | |||
| timepoint_label | 402 | 100% | 401 | 1 | ||
| family_id | 370 | 92% | 370 | |||
| antibiotic_exposure | 363 | 90% | 363 | |||
| maternal_antibiotics | 358 | 89% | 307 | 51 | ||
| health_condition_detail | 289 | 72% | 68 | 221 | ||
| diet | 113 | 28% | 113 | |||
| medication | 29 | 7% | 29 | |||
| nec_status | 20 | 5% | 20 |
- Infant diet and maternal gestational weight gain predict early metabolic maturation of gut microbiomes. PMID 30374198 PMC6294307 curated
- A Machine Learning Approach to Study Glycosidase Activities from Bifidobacterium. PMID 34064844 PMC8151561 curated
- 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 curated
- Antibiotic-driven intestinal dysbiosis in pediatric short bowel syndrome is associated with persistently altered microbiome functions and gut-derived bloodstream infections. PMID 34264786 PMC8284144 curated
- Deterministic transition of enterotypes shapes the infant gut microbiome at an early age. PMID 34429130 PMC8383385 curated
19 more
- Early-life formula feeding is associated with infant gut microbiota alterations and an increased antibiotic resistance load. PMID 34677583 PMC8827105
- 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
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645
- Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium. PMID 36316342 PMC9622858
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488
- Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria. PMID 37191543 PMC10269646
- 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
- A metagenomic catalog of the early-life human gut virome. PMID 38424077 PMC10904392
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788
- Infant age inversely correlates with gut carriage of resistance genes, reflecting modifications in microbial carbohydrate metabolism during early life. PMID 38882494 PMC11170968
- Bifidobacterium and Lactobacillus Probiotics and Gut Dysbiosis in Preterm Infants: The PRIMAL Randomized Clinical Trial. PMID 39102225 PMC12549143
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892
- Dynamics of gut resistome and mobilome in early life: a meta-analysis. PMID 40048849 PMC11929092
- The Gut Resistome Atlas in Preterm Infants Enables Prediction of Necrotizing Enterocolitis Onset. PMID 41025564 PMC12677589
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
- Metagenomic estimation of dietary intake from human stool
Archive description
This is a short-read-sequence based longitudinal analysis of gut microbiome development in healthy twins 0-8 months of age in St Louis, Missouri.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and adult 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 Infant Gut Microbiome”
- body site study.description · “longitudinal analysis of gut microbiome development in”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Infant Diet and Maternal”
- life stage study.title · “Infant Diet and Maternal Gestational Weight Gain”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN09259835 | age_at_collection_days | 50 | R1 | 0.90 | biosample_attr | 49.85 |
| SAMN09259835 | antibiotic_exposure | no | R1 | 0.85 | biosample_attr | False |
| SAMN09259835 | birth_weight_grams | 3060 | R1 | 0.90 | biosample_attr | 3060 |
| SAMN09259835 | collection_date | 2010 | R1 | 0.85 | biosample.attribute:collection_date | 2010 |
| SAMN09259835 | country | US | R1 | 0.90 | biosample_attr | USA:Saint Louis |
| SAMN09259835 | delivery_mode | c_section | R2 | 0.75 | paper.supp.table | Mode of delivery=cesarean |
| SAMN09259846 | diet | formula | R1 | 0.85 | biosample.attribute:host_diet | Exclusively Formula-Fed, Cow's Milk Formula, Galacto-oligosaccharides, Lactose, Maltodextrin, Polydextrose |
| SAMN09259845 | family_id | 3 | R1 | 0.85 | biosample.attribute:host_family | 3 |
| SAMN09259835 | family_role | twin | R1 | 0.85 | biosample.attribute:host_family_relationship | Twin sibling to subject T0132B |
| SAMN09259835 | feeding_mode | mixed | R1 | 0.85 | biosample_attr | Mostly Breastfed, Cow's Milk Formula, Galacto-oligosaccharides, Lactose, Polydextrose |
| SAMN09259835 | gestational_age_weeks | 37.29 | R1 | 0.90 | biosample_attr | 37.28571429 |
| SAMN09259845 | health_condition | gi_infection_or_diarrhoea | R1 | 0.60 | biosample.attribute:gastrointest_disord | gastrointest_disord: Reflux |
| SAMN09259835 | health_condition | healthy_control | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN09259843 | health_condition | healthy_control | R4 | 0.45 | study.description | healthy twins 0-8 months of age |
| SAMN09259845 | health_condition_detail | Reflux | R1 | 0.90 | biosample.attribute:gastrointest_disord | gastrointest_disord: Reflux |
| SAMN09259835 | health_condition_detail | Health | R2 | 0.75 | external.gmrepo source | phenotype: Health |
| SAMN09259835 | location_locality | St. Louis | R3 | 0.70 | paper.fulltext.methods | a birth cohort of healthy twins in St. Louis |
| SAMN09259835 | location_region | Missouri | R4 | 0.45 | ena.study_description | St Louis, Missouri |
| SAMN09259835 | location_site | Washington University School of Medicine in St. Louis | R3 | 0.70 | paper.fulltext.methods | Washington University School of Medicine in St. Louis |
| SAMN09259835 | maternal_antibiotics | yes | R1 | 0.85 | biosample_attr | cefazolin |
| SAMN09259891 | maternal_antibiotics | no | R2 | 0.75 | paper.supp.table | maternal_abx=no |
| SAMN09259835 | medication | other_medication | R1 | 0.85 | biosample.attribute:host_other_current_medications | Multivitamin (unknown type) |
| SAMN09259858 | nec_status | no | R2 | 0.75 | paper.supp.table | NEC=False |
| SAMN09259835 | preterm_status | term | R1 | 0.85 | biosample_attr | 37.28571429 |
| SAMN09259835 | sex | male | R1 | 0.90 | biosample_attr | male |
| SAMN09259835 | subject_id | T0132A | R1 | 0.85 | biosample_attr | T0132A |
| SAMN09259835 | timepoint_label | 2 month | R1 | 0.70 | sample.title | Family T0132, Twin A, 2 month timepoint |
| SAMN09260083 | timepoint_label | 0 - 1 month | R2 | 0.75 | paper.supp.table | AGE GROUP G12=0 - 1 month |
Sequencing
447 runs over 402 samples · mean 1.11 Gbp per run (median 1.01 Gbp, total 494.84 Gbp; 447 runs with a base count) · layout PAIRED 447 · platform ILLUMINA 447 · models NextSeq 500 (447) · 48% of runs with a Sandpiper profile · first public 2018-05-26
Authors (195)
Baumann-Dudenhoeffer AM first · D'Souza AW · Tarr PI · Warner BB · Dantas G last · Sabater C first · Ruiz L · Margolles A 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 · Thänert R first · Thänert A · Ou J · Bajinting A · Burnham CD · Engelstad HJ · Tecos ME · Ndao IM · Hall-Moore C · Rouggly-Nickless C · Carl MA · Rubin DC · Davidson NO · Warner BW last · Xiao L first · Wang J · Zheng J · Li X · Zhao F last · Pärnänen KMM first · Hultman J · Markkanen M · Satokari R · Rautava S · Lamendella R · Wright J · McLimans CJ · Kelleher SL · Virta MP last · Zeng S first · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Stanton C · Wang S last · Tarracchini C · Bianchi MG · Rizzo SM · Argentini C · Vergna LM · Taurino G · Chiu M · Bussolati O · van Sinderen D · 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 · Li S · Ying J · Wang H · Qu Y · Niu X · De Biase R · Bocchio F · De Conto F · Nouvenne A · Ticinesi A · Meschi T · Cecchi R · Xu X first · Feng Q · Zhang T · Gao Y · Cheng Q · Zhang W · Wu Q · Xu K · Li Y · Nguyen N · Taft DH · Mills DA · Lemay DG · Zhu W · Mao S · Zhang A · Liu J last · Van Rossum T first · Haiß A · Knoll RL · Marißen J · Podlesny D · Pagel J · Bleskina M · Vens M · Fortmann I · Siller B · Ricklefs I · Klopp J · Hilbert K · Meyer C · Thielemann R · Goedicke-Fritz S · Kuntz M · Wieg C · Teig N · Körner T · Kribs A · Hudalla H · Knuf M · Stein A · Gille C · Bagci S · Dohle F · Proquitté H · Olbertz DM · Schmidt E · Koch L · Pirr S · Rupp J · Spiegler J · Kopp MV · Göpel W · Herting E · Forslund SK · Viemann D · Zemlin M · Bork P · Gehring S · König IR · Henneke P · Härtel C last · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Bargheet A first · Noordzij HT · Ponsero AJ · Jian C · Korpela K · Valles-Colomer M · Debelius J · Kurilshikov A · Pettersen VK last · Zhang L · Yuan Y · Tian M · Zhou M · Hu Y · Huang J · Zou R · Su X · Liu Q · He Y · Feng J · Huang W · Luo Y · Shen W · Gennaioli E · Muscò A · Vitale SG · Angioni S
Downloads
PRJNA473126.csv.gz (16.9 KB) · parquet (93.8 KB) — all 402 samples, every field with route and confidence · PRJNA473126_determinations.csv.gz (66.8 KB) — 7,929 evidence rows