Longitudinal Gut Microbiome Cohort in Peru and USA
58 samples from healthy control individuals spanning adult, child, infant, and adolescent age groups in Peru and the USA, studied using a longitudinal cohort design. machine-written summary
58 samples · 116 runs · PE, US · Infant / toddler · 2015 · 4.33 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 116 sample values (collection date, country) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC5088602 |
| ✓ Supplementary tables | 122 sample values (age, sex, subject id, timepoint) |
| ✓ External resources | 229 sample values (age, bmi, 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 |
Genera, mean relative abundance over 56 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 | 56 | 97% | ||||
| country | 58 | 100% | 58 | |||
| health_condition | 58 | 100% | 58 | |||
| subject_id | 35 | 60% | 35 | |||
| collection_date | 58 | 100% | 58 | |||
| health_condition_detail | 58 | 100% | 58 | |||
| age_at_collection_days | 57 | 98% | 57 | |||
| sex | 57 | 98% | 57 | |||
| bmi | 51 | 88% | 51 | |||
| timepoint_label | 35 | 60% | 35 |
- An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. PMID 27803195 PMC5088602 curated
- Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood: the TEDDY study. PMID 35672407 PMC9174155 curated
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
- Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides. PMID 37188713 PMC10187079 curated
- Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut. PMID 37259063 PMC10230729 curated
3 more
- Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation. PMID 38441032 PMC11019788
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
Archive description
Gut microbiome diversity
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 · “Human Gut Microbiome Metagenome”
- body site study.description · “Gut microbiome diversity”
- 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 |
|---|---|---|---|---|---|---|
| SAMN03283237 | age_at_collection_days | 3287.25 | R2 | 0.75 | external.cmd source | age: 9; age_unit: Year; age_group: Child |
| SAMN03283279 | age_at_collection_days | 730 | R2 | 0.75 | paper.supp.table | Age (day)=730 |
| SAMN03283237 | bmi | 14.05 | R2 | 0.75 | external.cmd source | bmi: 14.05 |
| SAMN03283237 | collection_date | 2012 | R1 | 0.85 | biosample.attribute:collection_date | 2012 |
| SAMN03283237 | country | PE | R1 | 0.90 | biosample_attr | Peru |
| SAMN03283237 | health_condition | healthy_control | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN03283237 | health_condition_detail | Healthy | R2 | 0.75 | external.cmd source | disease: Healthy |
| SAMN03283237 | sex | female | R2 | 0.75 | paper.supp.table | Sex=F |
| SAMN03283238 | sex | female | R2 | 0.75 | external.cmd source | sex: Female |
| SAMN03283237 | subject_id | SRR1761664 | R2 | 0.75 | paper.supp.table | Sample=SRR1761664 |
| SAMN03283237 | timepoint_label | 5 yr - 10 yr | R2 | 0.75 | paper.supp.table | AGE GROUP G12=5 yr - 10 yr |
Sequencing
116 runs over 58 samples · mean 1.92 Gbp per run (median 0.63 Gbp, total 222.27 Gbp; 116 runs with a base count) · layout PAIRED 58, SINGLE 58 · platform ILLUMINA 116 · models Illumina HiSeq 2500 (116) · 84% of runs with a Sandpiper profile · first public 2015-02-17
Authors (74)
Pehrsson EC first · Tsukayama P · Patel S · Mejía-Bautista M · Sosa-Soto G · Navarrete KM · Calderon M · Cabrera L · Hoyos-Arango W · Bertoli MT · Berg DE · Gilman RH · Dantas G last · Nayfach S first · Rodriguez-Mueller B · Garud N · Pollard KS last · Tisza MJ first · Buck CB last · Auchtung TA first · Stewart CJ · Smith DP · Triplett EW · Agardh D · Hagopian WA · Ziegler AG · Rewers MJ · She JX · Toppari J · Lernmark Å · Akolkar B · Krischer JP · Vehik K · Auchtung JM · Ajami NJ · Petrosino JF last · Tarracchini C first · Fontana F · Mancabelli L · Lugli GA · Alessandri G · Turroni F · Ventura M · Milani C 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 · De Biase R · Bocchio F · Viappiani A · De Conto F · Nouvenne A · Ticinesi A · Bussolati O · Meschi T · Cecchi R · van Sinderen D · Longhi G · Gennaioli E · Muscò A · Rizzo SM · Vitale SG · Angioni S
Downloads
PRJNA268964.csv.gz (3.2 KB) · parquet (73.4 KB) — all 58 samples, every field with route and confidence · PRJNA268964_determinations.csv.gz (6.3 KB) — 467 evidence rows