Reducing eukaryotic viruses while preserving the phageome to achieve a safer virome for fecal virome transplantation.

The virome plays a significant role in maintaining the gut health of the host. Fecal virome transplantation (FVT), a burgeoning therapeutic strategy, holds promise in regulating intestinal microecology and treating associated diseases. However, the presence of eukaryotic viruses in FVT poses potential risks, which may compromise its safety and efficacy. This study leverages the key distinction between bacteriophages and eukaryotic viruses-namely, the presence or absence of an envelope-to reduce the burden of eukaryotic viruses in samples via solvent/detergent (S/D) treatment, while preserving the biologically active phageome. To this end, fecal samples were collected from healthy AA broilers, and the virome was isolated and subjected to S/D treatment. Subsequent DNA virome sequencing analysis was conducted to evaluate the impact of this treatment. The results indicated that S/D treatment tended to decrease the relative abundance of eukaryotic viral families (e.g., Adenoviridae, Parvoviridae), while bacteriophages remained the dominant viral component. α-diversity analysis revealed no significant differences in overall viral diversity post-treatment. However, β-diversity analysis indicated shifts in viral community composition. Further differential virus analysis revealed a significant increase in the relative abundance of specific bacteriophages following treatment. Finally, functional analysis of the virome revealed a diverse array of genes involved in DNA metabolism and host cell wall remodeling. Notably, the primary functional distinction between FVT0 and FVT1 was the attenuated response to eukaryotic viruses in FVT1. Collectively, this study suggests that S/D treatment may reduce the abundance of eukaryotic viruses in FVT, thereby enhancing clinical safety. These findings provide a theoretical basis and methodological support for the safe application of FVT in the treatment of animal diseases, paving the way for more secure and effective viral therapies.