Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome
Strain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome
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DOI：
10.1128/msphere.00694-20
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发表时间：
2020-07-01
期刊：
影响因子：
4.8
通讯作者：
Raymann, Kasie
中科院分区：
文献类型：
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作者：
Bobay, Louis-Marie;Wissel, Emily F.;Raymann, Kasie
宿主相关微生物组对动植物的健康和正常发育至关重要。关于微生物群落的获取模式和微进化的许多基本问题的答案仍有待建立。破译菌株水平动力学对于充分理解微生物群落如何进化至关重要，但塑造微生物群落菌株水平动力学的力量在很大程度上仍未被探索，主要是因为方法问题和成本。在这里，我们使用靶向菌株水平深度测序，以蜜蜂肠道微生物组作为模型系统，揭示宿主相关微生物群落中的菌株动态。我们的研究结果表明，使用物种特异性引物对保守的蛋白质编码基因区域进行扩增子测序是一种经济有效且准确的探索菌株水平多样性的方法。事实上，使用这种方法，我们能够确认菌株水平的结果，这些结果已经从蜜蜂肠道微生物组的全基因组鸟枪测序中获得，但分辨率要高得多。重要的是，我们的深度测序方法使我们能够探索低频菌株（即隐菌）对微生物组动力学的影响。结果表明，隐菌多样性不是蜜蜂微生物组组成变化的原因。总之，这些发现揭示了关于宿主相关微生物群落的菌株动力学的新的基本见解。驱动肠道微生物群落精细组成和动态的因素尚不清楚。在这项研究中，我们使用宏基因组扩增子深度测序来破译蜜蜂肠道微生物组的两个关键成员的菌株动态。利用这种高通量和高成本效益的方法，我们能够确认以前大规模全基因组霰弹枪（WGS）元基因组测序研究的结果，同时也获得了蜜蜂肠道微生物组两个核心成员的群落动态的额外见解。此外，我们能够证明，隐菌株不负责在蜜蜂中观察到的微生物组组成的变化。
Host-associated microbiomes can be critical for the health and proper development of animals and plants. The answers to many fundamental questions regarding the modes of acquisition and microevolution of microbiome communities remain to be established. Deciphering strain-level dynamics is essential to fully understand how microbial communities evolve, but the forces shaping the strain-level dynamics of microbial communities remain largely unexplored, mostly because of methodological issues and cost. Here, we used targeted strain-level deep sequencing to uncover the strain dynamics within a host-associated microbial community using the honey bee gut microbiome as a model system. Our results revealed that amplicon sequencing of conserved protein-coding gene regions using species-specific primers is a cost-effective and accurate method for exploring strain-level diversity. In fact, using this method we were able to confirm strain-level results that have been obtained from whole-genome shotgun sequencing of the honey bee gut microbiome but with a much higher resolution. Importantly, our deep sequencing approach allowed us to explore the impact of low-frequency strains (i.e., cryptic strains) on microbiome dynamics. Results show that cryptic strain diversity is not responsible for the observed variations in microbiome composition across bees. Altogether, the findings revealed new fundamental insights regarding strain dynamics of host-associated microbiomes.IMPORTANCE The factors driving fine-scale composition and dynamics of gut microbial communities are poorly understood. In this study, we used metagenomic amplicon deep sequencing to decipher the strain dynamics of two key members of the honey bee gut microbiome. Using this high-throughput and cost-effective approach, we were able to confirm results from previous large-scale whole-genome shotgun (WGS) metagenomic sequencing studies while also gaining additional insights into the community dynamics of two core members of the honey bee gut microbiome. Moreover, we were able to show that cryptic strains are not responsible for the observed variations in microbiome composition across bees.