Department of Entomology and Nematology, University of California Davis, Davis, CA, USA.
Microbiome. 2024 Aug 23;12(1):155. doi: 10.1186/s40168-024-01875-0.
Despite being among the most abundant biological entities on earth, bacteriophage (phage) remain an understudied component of host-associated systems. One limitation to studying host-associated phage is the lack of consensus on methods for sampling phage communities. Here, we compare paired total metagenomes and viral size fraction metagenomes (viromes) as methods for investigating the dsDNA viral communities associated with the GI tract of two bee species: the European honey bee Apis mellifera and the eastern bumble bee Bombus impatiens.
We find that viromes successfully enriched for phage, thereby increasing phage recovery, but only in honey bees. In contrast, for bumble bees, total metagenomes recovered greater phage diversity. Across both bee species, viromes better sampled low occupancy phage, while total metagenomes were biased towards sampling temperate phage. Additionally, many of the phage captured by total metagenomes were absent altogether from viromes. Comparing between bees, we show that phage communities in commercially reared bumble bees are significantly reduced in diversity compared to honey bees, likely reflecting differences in bacterial titer and diversity. In a broader context, these results highlight the complementary nature of total metagenomes and targeted viromes, especially when applied to host-associated environments.
Overall, we suggest that studies interested in assessing total communities of host-associated phage should consider using both approaches. However, given the constraints of virome sampling, total metagenomes may serve to sample phage communities with the understanding that they will preferentially sample dominant and temperate phage. Video Abstract.
尽管噬菌体（phage）是地球上最丰富的生物实体之一，但它们仍然是宿主相关系统中研究不足的组成部分。研究宿主相关噬菌体的一个限制因素是缺乏对噬菌体群落采样方法的共识。在这里，我们比较了配对的总宏基因组和病毒大小分数宏基因组（病毒组），作为研究两种蜜蜂物种（欧洲蜜蜂 Apis mellifera 和东部大黄蜂 Bombus impatiens）胃肠道相关双链 DNA 病毒群落的方法。
我们发现病毒组成功地富集了噬菌体，从而增加了噬菌体的回收，这仅在蜜蜂中如此。相比之下，对于大黄蜂来说，总宏基因组回收了更多的噬菌体多样性。在这两个蜜蜂物种中，病毒组更好地采样了低占有率的噬菌体，而总宏基因组偏向于采样温带噬菌体。此外，许多被总宏基因组捕获的噬菌体根本不存在于病毒组中。在比较蜜蜂时，我们表明，商业养殖的大黄蜂中的噬菌体群落多样性明显低于蜜蜂，这可能反映了细菌滴度和多样性的差异。从更广泛的角度来看，这些结果强调了总宏基因组和靶向病毒组的互补性，特别是在应用于宿主相关环境时。
总的来说，我们建议有兴趣评估宿主相关噬菌体总群落的研究应考虑同时使用这两种方法。然而，鉴于病毒组采样的限制，总宏基因组可能有助于采样噬菌体群落，同时要理解它们将优先采样优势和温带噬菌体。视频摘要。
