Phage enrichment methods in Finnish infant gut virome
Impact of phage enrichment on the observed infant gut virome
1368 fecal samples from Finnish infants (1, 6, and 12 months old) in a longitudinal cohort study comparing five phage enrichment protocols for viral DNA extraction and their effect on observed gut phageome composition. machine-written summary
Sequencing depth per sample · this project all projects
Sampling design and relatedness
longitudinal
41 of 41 people sampled more than once (1,366 samples; median 29, up to 72 per person) · follow-up median 6 mo (max 11 mo) · median interval between samples 6 mo(time from age at collection).
Schedule stated by the source: “fecal samples at 1, 6 and 12 months of age (daily sampling for 20-30 days during months 6 and 12)” (time origin: birth).
Each row is one person (13 shown of 41); dots are samples at days since that person's first sample.
Clostridium 79.0%Thomasclavelia 3.2%Sarcina 3.0%Finegoldia 0.8%Rothia 0.5%Lachnospira 0.2%Faecalibacterium 0.2%Streptococcus 0.0%Intestinibacter 0.0%not assigned to a genus 13.1%
Genera, mean relative abundance over 55 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Impact of phage enrichment on the observed infant gut phageome. 2026PMID 41873970PMC13141913own_data
Details
Archive description
The human gut microbiota, especially in infants, plays a crucial role in long-term health. While research on the bacterial microbiota has advanced rapidly, our understanding of the virome, which includes a diverse range of bacteriophages, is still limited due to challenges in detection, quantification and analysis. To address these gaps, we evaluated the efficacy of five phage enrichment (PE) protocols for extracting viral DNA from 41 infant fecal samples at 1, 6 and 12 months of age. We additionally assessed their impact on the observed gut phageome of infants at 6 and 12 months of age. The results showed that PEG-based phage enrichment yields higher viral DNA concentrations than the DTT-based method in 12-month-old infants. Importantly, the observed phageome associations with age and birth mode depend on phage DNA enrichment without enrichment, studies risk misrepresenting the phageome composition. These findings demonstrate that phage enrichment in combination with whole metagenomics can boost and improve the captured profile in phageome analysis.
How this project entered the registry
Classified as human gut / stool shotgun DNA metagenome of infant / toddler by sonnet_x2 with confidence 0.60. Assay shotgun_dna.
hoststudy.description · “The human gut microbiota, especially in infants”
body sitestudy.title · “infant gut virome”
life stagestudy.description · “41 infant fecal samples at 1, 6 and 12 months”
Evidence examples (one per field × route)
sample
field
value
route
conf.
source
quote
SAMEA117637787
age_at_collection_days
183
R1
0.90
biosample_attr
6_months
SAMEA117637787
country
FI
R1
0.90
biosample_attr
Finland
SAMEA117637787
delivery_mode
vaginal
R1
0.90
biosample_attr
Vaginal
SAMEA118246715
subject_id
B1
R1
0.70
sample.name_rule:sample_alias
B1__1
SAMEA117637787
timepoint_label
10
R1
0.80
biosample_attr
10
Sequencing
1,368 runs over 1,368 samples · mean 0.46 Gbp per run (median 0.39 Gbp, total 627.12 Gbp; 1,368 runs with a base count) · layout SINGLE 1,368 · platform ILLUMINA 1,368 · models Illumina NovaSeq 6000 (1,368) · 4% of runs with a Sandpiper profile · first public 2025-02-07 – 2025-05-06