Faecal virome in Danish infants, longitudinal cohort
655 faecal virome samples from healthy Danish infants (age 1 year) in a longitudinal cohort study, characterizing DNA viruses (mostly temperate bacteriophages, plus human viruses) in the gut. machine-written summary
655 samples · 1,310 runs · DK · Infant / toddler · 2022 · 0.47 Gbp / sample
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 655 sample values (country) |
| ○ Abstract / description | read; no usable statement |
| ✓ Full text | 1,310 sample values (age, location locality) · PMC10159846, PMC11923282, PMC12227732, PMC13434738 |
| ○ Supplementary tables | files read; no table could be matched to the samples |
| – 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 2 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 | 655 | 100% | ||||
| country | 655 | 100% | 655 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 0 | 0% | ||||
| age_at_collection_days | 655 | 100% | 655 | |||
| detailed_location | 655 | 100% | ||||
| location_locality | 655 | 100% | 655 |
- (no title) curated
- Expanding known viral diversity in the healthy infant gut. PMID 37037943 PMC10159846 curated
- Prophages in the infant gut are pervasively induced and may modulate the functionality of their hosts. PMID 40108202 PMC11923282 curated
- (no title) curated
- Negativeome characterization and decontamination in early-life virome studies. PMID 40615392 PMC12227732 curated
3 more
- (no title)
- 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
- (no title)
Archive description
The COPSAC2010 cohort of Danish children is a population-based cohort where viromes were extracted and deeply sequenced for age 1 year faecal samples. The children in the cohort were all born around 2010, but their mothers were recruited for the study already during pregnancy. The aim was to study the causes and mechanisms that lead to chronic inflammatory diseases. To this end the children have been sampled extensively since birth for multi-omics analyses, along with records of early-life exposures and clinical assessments. Such clinical data is associated with the omics data with the goal of uncovering unknown disease mechanisms for common childhood diseases. The age 1 year faecal virome study made available here is part of that effort, and was performed as part of the EarlyVir project (http://copsac.com/EarlyVir) funded by JPI-HDHL. The reads have been assembled and an exhaustive taxonomy for all known and novel DNA viruses in the samples has been made available here: http://copsac.com/earlyvir/f1y/fig1.svg . Most DNA viruses in the samples were bacteriophages, although human viruses also made up a substantial portion. Most bacteriophages belonged to novel families and were temperate rather than virulent.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler and child 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 · “Deep sequencing of faecal DNA viromes from”
- body site study.description · “age 1 year faecal samples. The children”
- life stage external_curation.infant_catalog · “infant triage verdict include (0-3 y scope)”
- life stage study.title · “647 healthy Danish infants”
- life stage study.description · “cohort of Danish children is a population-based”
- life stage study.description · “2010, but their mothers were recruited for”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA12335878 | age_at_collection_days | 365 | R3 | 0.55 | paper.fulltext.methods | collected from all infants at age 1 year |
| SAMEA12335878 | country | DK | R1 | 0.90 | biosample_attr | Denmark |
| SAMEA12335878 | location_locality | Copenhagen area | R3 | 0.60 | paper.fulltext.results | around the greater Copenhagen area |
Sequencing
1,310 runs over 655 samples · mean 0.27 Gbp per run (median 0.21 Gbp, total 348.12 Gbp; 1,310 runs with a base count) · layout PAIRED 655, SINGLE 655 · platform ILLUMINA 1,310 · models Illumina HiSeq 2000 (1,310) · 0% of runs with a Sandpiper profile · first public 2022-02-01
Authors (45)
Johansen J first · Plichta DR · Nissen JN · Jespersen ML · Shah SA · Deng L · Stokholm J · Bisgaard H · Nielsen DS · Sørensen SJ · Rasmussen S last · Thorsen J · Pedersen AG · Dion MB · Castro-Mejía JL · Silins R · Romme FO · Sausset R · Jessen LE · Ndela EO · Hjelmsø M · Rasmussen MA · Redgwell TA · Leal Rodríguez C · Vestergaard G · Zhang Y · Chawes B · Bønnelykke K · Enault F · Moineau S · Petit MA · Russel J · Sørensen S · Kuzub N first · Kurilshikov A · Zhernakova A · Garmaeva S last · Boulund U first · Larsen F · Poulsen CS · Widdowson M · Jiang J · Tranæs K · Shamash M first · Maurice CF last
Help complete this project
2 of the 4 core fields are below 50% coverage: health_condition, subject_id. Share metadata
Downloads
PRJEB46943.csv.gz (16.4 KB) · parquet (96.7 KB) — all 655 samples, every field with route and confidence · PRJEB46943_determinations.csv.gz (6.4 KB) — 1,965 evidence rows