Impact of phage enrichment on the observed infant gut virome

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.