Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland.
Proc Natl Acad Sci U S A. 2020 Mar 31;117(13):7355-7362. doi: 10.1073/pnas.2000228117. Epub 2020 Mar 16.
The honey bee gut microbiota influences bee health and has become an important model to study the ecology and evolution of microbiota-host interactions. Yet, little is known about the phage community associated with the bee gut, despite its potential to modulate bacterial diversity or to govern important symbiotic functions. Here we analyzed two metagenomes derived from virus-like particles, analyzed the prevalence of the identified phages across 73 bacterial metagenomes from individual bees, and tested the host range of isolated phages. Our results show that the honey bee gut virome is composed of at least 118 distinct clusters corresponding to both temperate and lytic phages and representing novel genera with a large repertoire of unknown gene functions. We find that the phage community is prevalent in honey bees across space and time and targets the core members of the bee gut microbiota. The large number and high genetic diversity of the viral clusters seems to mirror the high extent of strain-level diversity in the bee gut microbiota. We isolated eight lytic phages that target the core microbiota member , but that exhibited different host ranges at the strain level, resulting in a nested interaction network of coexisting phages and bacterial strains. Collectively, our results show that the honey bee gut virome consists of a complex and diverse phage community that likely plays an important role in regulating strain-level diversity in the bee gut and that holds promise as an experimental model to study bacteria-phage dynamics in natural microbial communities.
蜜蜂肠道微生物群影响蜜蜂健康，已成为研究微生物群-宿主相互作用的生态学和进化的重要模型。然而，尽管噬菌体有可能调节细菌多样性或控制重要的共生功能，但与蜜蜂肠道相关的噬菌体群落却知之甚少。在这里，我们分析了两个源自病毒样颗粒的宏基因组，分析了在所研究的 73 个来自个体蜜蜂的细菌宏基因组中鉴定出的噬菌体的普遍性，并测试了分离出的噬菌体的宿主范围。我们的研究结果表明，蜜蜂肠道病毒组由至少 118 个不同的聚类组成，这些聚类对应于温和噬菌体和裂解噬菌体，代表了具有大量未知基因功能的新型属。我们发现，噬菌体群落普遍存在于蜜蜂中，且无论在空间上还是时间上都存在这种现象，并以蜜蜂肠道微生物群的核心成员为目标。大量且具有高度遗传多样性的病毒聚类似乎反映了蜜蜂肠道微生物群在菌株水平上的高度多样性。我们分离出了 8 种针对核心微生物群成员的裂解噬菌体，但在菌株水平上表现出不同的宿主范围，导致共存噬菌体和细菌菌株之间存在嵌套的相互作用网络。总的来说，我们的研究结果表明，蜜蜂肠道病毒组由复杂多样的噬菌体群落组成，这些噬菌体很可能在调节蜜蜂肠道的菌株水平多样性方面发挥着重要作用，并且有望成为研究自然微生物群落中细菌-噬菌体动态的实验模型。
