Targeted viromes and total metagenomes capture distinct components of bee gut phage communities.

IF 13.8 1区 生物学 Q1 MICROBIOLOGY
Dino Lorenzo Sbardellati, Rachel Lee Vannette
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Abstract

Background: 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.

Results: 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.

Conclusions: 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.

靶向病毒组和总元基因组捕获了蜜蜂肠道噬菌体群落的不同组成部分。
背景:尽管噬菌体是地球上最丰富的生物实体之一,但它仍然是宿主相关系统中未被充分研究的组成部分。研究宿主相关噬菌体的一个限制因素是对噬菌体群落的取样方法缺乏共识。在这里,我们比较了成对的总元基因组和病毒大小分数元基因组(病毒组),将其作为研究与两种蜜蜂(欧洲蜜蜂Apis mellifera和东方大黄蜂Bombus impatiens)消化道相关的dsDNA病毒群落的方法:结果:我们发现,病毒群成功地富集了噬菌体,从而提高了噬菌体的回收率,但这仅限于蜜蜂。与此相反,在熊蜂中,总元基因组恢复了更大的噬菌体多样性。在这两种蜜蜂中,病毒组能更好地采样低占位噬菌体,而总元基因组则偏向于采样温带噬菌体。此外,总元基因组捕获的许多噬菌体在病毒组中完全不存在。通过对不同蜜蜂进行比较,我们发现与蜜蜂相比,商业饲养的大黄蜂中噬菌体群落的多样性明显降低,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,这些结果突出了总元基因组和目标病毒组的互补性,尤其是在应用于与宿主相关的环境时:总之,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使用这两种方法。不过,考虑到病毒组取样的限制,总元基因组可用于对噬菌体群落进行取样,但它们将优先对优势噬菌体和温带噬菌体进行取样。视频摘要。
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来源期刊
Microbiome
Microbiome MICROBIOLOGY-
CiteScore
21.90
自引率
2.60%
发文量
198
审稿时长
4 weeks
期刊介绍: Microbiome is a journal that focuses on studies of microbiomes in humans, animals, plants, and the environment. It covers both natural and manipulated microbiomes, such as those in agriculture. The journal is interested in research that uses meta-omics approaches or novel bioinformatics tools and emphasizes the community/host interaction and structure-function relationship within the microbiome. Studies that go beyond descriptive omics surveys and include experimental or theoretical approaches will be considered for publication. The journal also encourages research that establishes cause and effect relationships and supports proposed microbiome functions. However, studies of individual microbial isolates/species without exploring their impact on the host or the complex microbiome structures and functions will not be considered for publication. Microbiome is indexed in BIOSIS, Current Contents, DOAJ, Embase, MEDLINE, PubMed, PubMed Central, and Science Citations Index Expanded.
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