New Hampshire infant gut microbiome cohort
1063 samples from infants in Lebanon, New Hampshire, USA, studied longitudinally to examine intestinal bacterial colonization in pre- and full-term infants and its link to infection and allergy risk. machine-written summary
1,063 samples · 1,082 runs · US · Infant / toddler · 2019 · 4.52 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 2,125 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,810 sample values (age, location region) · PMC6033232, PMC6105615, PMC7511970, PMC8252198, PMC8400760, PMC9659678 |
| ✓ Supplementary tables | 67 sample values (subject id) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet · share metadata |
| – Human verified | not yet checked by a person · I checked this project — verify it |
Genera, mean relative abundance over 694 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 | 1,063 | 100% | ||||
| country | 1,063 | 100% | 1,063 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 67 | 6% | 67 | |||
| detailed_location | 1,063 | 100% | ||||
| location_region | 1,063 | 100% | 1,063 | |||
| collection_date | 1,062 | 100% | 1,062 | |||
| age_at_collection_days | 747 | 70% | 747 |
- Maternal diet during pregnancy is related with the infant stool microbiome in a delivery mode-dependent manner. PMID 29973274 PMC6033232 curated
- Sex-specific associations of infants' gut microbiome with arsenic exposure in a US population. PMID 30135504 PMC6105615 curated
- Prospective associations of the infant gut microbiome and microbial function with social behaviors related to autism at age 3 years. PMID 32968156 PMC7511970 curated
- The infant gut resistome is associated with E. coli and early-life exposures. PMID 34215179 PMC8252198 curated
- Associations between the gut microbiome and metabolome in early life. PMID 34454437 PMC8400760 curated
12 more
- Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies. PMID 35568730 PMC9659678
- The relationship between the gut microbiome and the risk of respiratory infections among newborns. PMID 35847562 PMC9283516
- Metagenomic analysis reveals associations between salivary microbiota and body composition in early childhood. PMID 35906254 PMC9338228
- A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome. PMID 36050292 PMC9437082
- Umbilical cord blood immune cell profiles in relation to the infant gut microbiome. PMID 36632065 PMC9826880
- Early-life exposure to per- and polyfluoroalkyl substances and infant gut microbial composition. PMID 36777525 PMC9916123
- Human milk-associated bacterial communities associate with the infant gut microbiome over the first year of life. PMID 37138613 PMC10149717
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488
- Machine-learning analysis of cross-study samples according to the gut microbiome in 12 infant cohorts. PMID 37874156 PMC10734493
- A metagenomic catalog of the early-life human gut virome. PMID 38424077 PMC10904392
- Prospective association of the infant gut microbiome with social behaviors in the ECHO consortium. PMID 38760865 PMC11101342
- Insights into the ecology of the infant gut plasmidome. PMID 39138199 PMC11322291
Archive description
Investigation of intestinal bacterial colonization in pre- and full-term infants and its connection to infection and allergy risk
How this project entered the registry
Classified as human gut / stool / oral cavity 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 · “Investigation of intestinal bacterial colonization in”
- body site external_curation.infant_catalog · “infant triage verdict include (gut/stool scope)”
- body site run.scientific_name · “human saliva metagenome”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.description · “pre- and full-term infants and its connection”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN04108636 | age_at_collection_days | 42 | R3 | 0.70 | paper.fulltext.methods | infant stool samples were collected at the 6-week |
| SAMN04108636 | collection_date | 2012 | R1 | 0.85 | biosample.attribute:collection_date | 2012 |
| SAMN04108636 | country | US | R1 | 0.90 | biosample_attr | USA: New Hampshire, Lebanon |
| SAMN04108636 | location_region | New Hampshire | R3 | 0.70 | paper.fulltext.methods | pregnant women obtaining prenatal care in New Hampshire, US clinics |
| SAMN04108639 | subject_id | SRR8692196 | R2 | 0.75 | paper.supp.table | BioSample=SRR8692196 |
Sequencing
1,082 runs over 1,063 samples · mean 5.79 Gbp per run (median 4.47 Gbp, total 6,261.94 Gbp; 1,082 runs with a base count) · layout SINGLE 754, PAIRED 328 · platform ILLUMINA 1,082 · models NextSeq 500 (932), Illumina MiSeq (150) · 92% of runs with a Sandpiper profile · first public 2019-03-07 – 2022-11-03
Authors (89)
Lundgren SN first · Madan JC · Emond JA · Morrison HG · Christensen BC · Karagas MR · Hoen AG last · Li Z · Coker M · Palys T · Jackson BP · Sogin ML · Cottingham KL · Laue HE first · Korrick SA · Baker ER · Lebeaux RM first · Coker MO · Dade EF · Palys TJ · Ross BD · Nguyen QP first · Dade E · Pathmasiri WW · McRitche S · Sumner SJ · Frost HR · Moroishi Y · Pettigrew MM · Gui J · Nadeau KC · Li H · Gilbert-Diamond D · Zeng S first · Patangia D · Almeida A · Zhou Z · Mu D · Paul Ross R · Stanton C · Wang S last · Salas LA · Zhou J · Everson TM · Marsit CJ · Madan J · Criswell RL · Peterson LA · Huset CA · Romano ME last · Lugli GA first · Mancabelli L · Milani C · Fontana F · Tarracchini C · Alessandri G · van Sinderen D · Turroni F · Ventura M last · Vänni P first · Tejesvi MV · Paalanne N · Aagaard K · Ackermann G · Camargo CA · Eggesbø M · Hasegawa K · Kolho K-L · Laursen MF · Ludvigsson J · Ownby D · Stokholm J · Tapiainen T last · Li S · Ying J · Wang H · Qu Y · Niu X · Bonham KS · Pathmasiri W · McRitchie S · Sumner S · Klepac-Ceraj V · program collaborators for Environmental influences on Child Health Outcomes last · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJNA296814.csv.gz (29.4 KB) · parquet (113.7 KB) — all 1,063 samples, every field with route and confidence · PRJNA296814_determinations.csv.gz (20.9 KB) — 4,002 evidence rows