Human infant gut virome in early life (USA:PA)
249 gut virome samples from infants/neonates (ages: 187 infant, 20 neonate, 42 unknown) collected in USA:PA, studying gut virome dynamics during very early life; no health conditions or interventions specified. machine-written summary
249 samples · 465 runs · US · Infant / toddler · 2020 · 2.10 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 1,488 sample values (collection date, country, delivery mode, diet, feeding mode, sex, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC10092070, PMC10175488, PMC10904392, PMC11322291, PMC11494892, PMC12227732, PMC12323601, PMC12769767, PMC13434738, PMC8518733, PMC9512645, PMC9622858, PMC9851330 |
| ✓ Supplementary tables | 327 sample values (age, timepoint) |
| – External resources | not covered by the external resources we ingest |
| – User contribution | nothing uploaded yet |
| – Human verified | not yet checked by a person · I checked this project — verify it |
longitudinal
24 of 204 people sampled more than once (69 samples; median 3, up to 4 per person) · follow-up median 4 mo (max 18 mo) · median interval between samples 3 mo (time from age at collection).
Each row is one person (24 shown); dots are samples at days since that person's first sample.
Genera, mean relative abundance over 136 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 | 207 | 83% | ||||
| country | 249 | 100% | 249 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 249 | 100% | 249 | |||
| collection_date | 248 | 100% | 248 | |||
| timepoint_label | 209 | 84% | 89 | 120 | ||
| age_at_collection_days | 207 | 83% | 207 | |||
| delivery_mode | 185 | 74% | 185 | |||
| sex | 185 | 74% | 185 | |||
| feeding_mode | 165 | 66% | 165 | |||
| diet | 118 | 47% | 118 |
- 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
- Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach. PMID 36123315 PMC10092070 curated
- Gut microbe metabolism of small molecules supports human development across the early stages of life. PMID 36177457 PMC9512645 curated
- Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium. PMID 36316342 PMC9622858 curated
- PhaTYP: predicting the lifestyle for bacteriophages using BERT. PMID 36659812 PMC9851330 curated
8 more
- Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota. PMID 37169786 PMC10175488
- 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
- Exploring the vitamin biosynthesis landscape of the human gut microbiota. PMID 39287373 PMC11494892
- Biases and complementarity in gut viromes obtained from bulk and virus-like particle-enriched metagenomic sequencing. PMID 40600714 PMC12323601
- Negativeome characterization and decontamination in early-life virome studies. PMID 40615392 PMC12227732
- Compiling an early life human gut microbiome atlas and identification of key microbial drivers. PMID 41350579 PMC12769767
- A meta-analysis of infant gut viromes reveals global patterns in bacteriophage community assembly and functional capacity over the first three years of life. PMID 42315844 PMC13434738
Archive description
This is a study to analyze the dynamic of human gut virome during very early life of the infants.
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 infant gut virome”
- body site study.description · “dynamic of human gut virome during very”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “Human infant gut virome”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMN11031277 | age_at_collection_days | 1 | R2 | 0.75 | paper.supp.table | Age (days)=1 |
| SAMN11031277 | collection_date | 2015-10-26 | R1 | 0.85 | biosample.attribute:collection_date | collection_date: 2015-10-26 |
| SAMN11031277 | country | US | R1 | 0.90 | biosample_attr | USA:PA |
| SAMN11031277 | delivery_mode | c_section_emergency | R1 | 0.90 | biosample_attr | C-Section with labor |
| SAMN11031278 | diet | formula | R1 | 0.85 | biosample.attribute:Infant_feeding_type | Formula |
| SAMN11031278 | feeding_mode | formula | R1 | 0.85 | biosample_attr | Formula |
| SAMN11031277 | sex | female | R1 | 0.90 | biosample_attr | Female |
| SAMN11031277 | subject_id | 333 | R1 | 0.85 | biosample_attr | 333 |
| SAMN11031368 | timepoint_label | D100 | R1 | 0.70 | run.library_name | D100 |
| SAMN11281196 | timepoint_label | Year 2~5 | R1 | 0.85 | biosample.attribute:study_group | Year 2~5 |
| SAMN11031277 | timepoint_label | Neonatal | R2 | 0.75 | paper.supp.table | Time Group=Neonatal |
Sequencing
465 runs over 249 samples · mean 1.00 Gbp per run (median 0.85 Gbp, total 465.36 Gbp; 465 runs with a base count) · layout PAIRED 465 · platform ILLUMINA 465 · models Illumina HiSeq 2500 (400), Illumina MiSeq (65) · 47% of runs with a Sandpiper profile · first public 2020-01-06
Authors (63)
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 · Tarracchini C · Bianchi MG · Rizzo SM · Argentini C · Vergna LM · Taurino G · Chiu M · Bussolati O · van Sinderen D · Shang J first · Tang X · Sun Y last · Zeng S first · Almeida A · Li S · Ying J · Wang H · Qu Y · Paul Ross R · Stanton C · Zhou Z · Niu X · Mu D · Wang S last · He W first · Russel J · Klincke F · Nesme J · Sørensen SJ last · Li Y first · Sun C · Zhu J · Geng M · Li M · Zhao X-M · Chen W-H last · Kuzub N first · Kurilshikov A · Zhernakova A · Garmaeva S last · Gennaioli E · Muscò A · Vitale SG · Angioni S · Shamash M first · Maurice CF last
Downloads
PRJNA524703.csv.gz (9.7 KB) · parquet (84.0 KB) — all 249 samples, every field with route and confidence · PRJNA524703_determinations.csv.gz (14.9 KB) — 1,815 evidence rows