Phage enrichment protocol in Finnish infant gut virome
1,366 faecal samples from Finnish infants (collected at 1, 6, and 12 months of age) in a longitudinal cohort study comparing PEG-based phage enrichment versus standard protocols for gut virome profiling. machine-written summary
1,366 samples · 1,366 runs · FI · Infant / toddler · 2026 · 0.39 Gbp / sample
One study deposited as 2 BioProjects (2,734 catalog samples together): PRJEB84376 · PRJEB89462 · show together
Checked this project's papers and archive records yourself? Mark it human-verified.
what each source gave
| ✓ Sequence archive | 6,830 sample values (age, country, delivery mode, subject id, timepoint) |
| ○ Abstract / description | read; no usable statement |
| ○ Full text | read; no usable statement or table · PMC13141913 |
| – Supplementary tables | no supplementary tables available (or none open access) |
| – 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 — not resolved
55 of 55 people sampled more than once (1,366 samples; median 26, up to 30 per person). Schedule stated by the source: “Faecal samples collected from infants at 1, 6, and 12 months of age.” (time origin: birth).
No Sandpiper profile for this project's samples yet.
| field | samples | coverage | R1 | R2 | R3 | R4 |
|---|---|---|---|---|---|---|
| age_category | 1,366 | 100% | ||||
| country | 1,366 | 100% | 1,366 | |||
| health_condition | 0 | 0% | ||||
| subject_id | 1,366 | 100% | 1,366 | |||
| age_at_collection_days | 1,366 | 100% | 1,366 | |||
| delivery_mode | 1,366 | 100% | 1,366 | |||
| timepoint_label | 1,366 | 100% | 1,366 |
- Impact of phage enrichment on the observed infant gut phageome. PMID 41873970 PMC13141913 curated
Archive description
The human gut microbiota, particularly during infancy, plays a pivotal role in shaping long-term health outcomes. While research on the bacterial microbiota has advanced rapidly, the infant gut virome—dominated by bacteriophages—remains underexplored due to technical challenges in viral DNA detection and recovery. To address this, we optimized a polyethylene glycol (PEG)-based protocol for phage DNA enrichment tailored to the constraints of infant faecal samples, focusing on maximizing viral yield from minimal input material. We validated the optimized protocol on faecal samples from 41 infants at 1, 6, and 12 months of age, and assessed the impact of phage enrichment on the observed gut phageome. The results demonstrate that the optimized protocol improves viral DNA recovery and significantly alters the observed virome composition, especially in older infants. Without appropriate enrichment, key features of the gut virome may be underrepresented or missed entirely. These findings underscore the importance of protocol optimization in virome studies and provide a scalable, cost-effective method for robust infant gut virome profiling.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by sonnet_x2 with confidence 0.75. Assay shotgun_dna.
- host study.title · “infant gut phageome”
- body site study.description · “infant faecal samples”
- life stage study.description · “faecal samples from 41 infants at 1, 6, and 12 months”
Evidence examples (one per field × route)
| sample | field | value | route | conf. | source | quote |
|---|---|---|---|---|---|---|
| SAMEA118275755 | age_at_collection_days | 183 | R1 | 0.90 | biosample_attr | 6_months |
| SAMEA118275755 | country | FI | R1 | 0.90 | biosample_attr | Finland |
| SAMEA118275755 | delivery_mode | vaginal | R1 | 0.90 | biosample_attr | Vaginal |
| SAMEA118275755 | subject_id | S1_6_months | R1 | 0.85 | biosample.attribute:babyid | S1_6_months |
| SAMEA118275755 | timepoint_label | 1 | R1 | 0.80 | biosample_attr | 1 |
Sequencing
1,366 runs over 1,366 samples · mean 0.46 Gbp per run (median 0.39 Gbp, total 627.07 Gbp; 1,366 runs with a base count) · layout SINGLE 1,366 · platform ILLUMINA 1,366 · models Illumina NovaSeq 6000 (1,366) · 0% of runs with a Sandpiper profile · first public 2026-03-04
Authors (8)
Valenzuela-Diaz S first · Dikareva E · Hickman B · Kiljunen S · Kolho K-L · de Vos W · Salonen A · Korpela K last
Downloads
PRJEB89462.csv.gz (33.9 KB) · parquet (119.6 KB) — all 1,366 samples, every field with route and confidence · PRJEB89462_determinations.csv.gz (34.5 KB) — 6,830 evidence rows