Biases and complementarity in gut viromes obtained from bulk and virus-like particle-enriched metagenomic sequencing

作者：Yun Li, Chuqing Sun, Jiaying Zhu, Mingyan Geng, Min Li, Xing‐Ming Zhao, Wei‐Hua Chen · 发表于：Microbiology Spectrum · 年份：2025 · DOI：10.1128/spectrum.00013-25 · 被引用次数：4 · 研究领域：Bacteriophages and microbial interactions、Genomics and Phylogenetic Studies、Respiratory viral infections research

Due to varying sequencing strategies, current gut virome findings show significant variability. Specifically, bulk- and virus-like particle (VLP)-enriched metagenomic sequencing (termed bulk and VLP, respectively) present unique advantages and limitations, affecting viral genome discovery, taxonomic annotation, and community structure analysis. A comprehensive comparison of these strategies is crucial for thoroughly understanding the gut virome. This study comprehensively compared gut viromes identified from paired bulk and VLP data from 151 adult and 141 infant fecal samples. The VLP method showed superior performance to bulk in viral genome discovery in both data sets by recovering longer and more complete viral genomes, with higher sensitivity for low-abundant ones, resulting in a higher taxonomic annotation rate. However, we observed no correlations in the viral community structure (i.e., Shannon diversities) between bulk- and VLP-derived viromes, implying biases introduced during VLP enrichment. Such biases could be caused by the bacterial host features, such as the structural differences in cell walls and the prevalence and abundance of the viruses. Viruses that are of low prevalence, low abundance, or have Gram-positive bacteria as their hosts were enriched in VLP-derived viromes, in both the adult and infant data sets. Significant complementarity was observed between bulk and VLP viromes, with only about a quarter (26.7% in infants; 29.3% in adults) of VLP-viral genom...