High Throughput Sequencing and Network Analysis Disentangle the Microbial Communities of Ticks and Hosts Within and Between Ecosystems.
High Throughput Sequencing and Network Analysis Disentangle the Microbial Communities of Ticks and Hosts Within and Between Ecosystems.
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DOI：
10.3389/fcimb.2018.00236
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发表时间：
2018
影响因子：
5.7
通讯作者：
Cosson JF
中科院分区：
文献类型：
--
作者：
Estrada-Peña A;Cabezas-Cruz A;Pollet T;Vayssier-Taussat M;Cosson JF
我们的目标是开发一个基于图论的框架，以捕获微生物组数据的纯对比较背后的生态意义。作为概念的证明，我们应用该框架来分析细菌在蓖麻硬蜱蜱或其主要宿主之一的脾脏中的共存，田鼠Myodes glareolus。作为次级淋巴器官，脾脏充当血液的过滤器，并且很好地代表了对血液中循环的微生物的暴露;包括在进食期间由蜱获得和传播的微生物。使用16 S rRNA的下一代测序（NGS）分别分析了301个和269个蜱虫和田鼠样本的微生物组。为了评估栖息地对蜱和田鼠相关细菌生态群落的影响，研究中包括两个不同的生境，森林和生态交错区。采用结合网络分析和细菌共生的遗传学的NGS数据分析方法研究单个样品中细菌之间的关联。在蜱和田鼠中发现的126个细菌属中，62%为两种物种所共有。蜱虫中共生细菌的群落比田鼠中的群落在遗传学上更具有多样性。有趣的是，在约20%的蜱中发现了约80%的细菌系统发育多样性。在田鼠相关细菌中没有观察到这种模式。结果表明，I. ricinus与M. Glareolus的，而生物群落在塑造蜱或田鼠的细菌群落中起着最重要的作用。对16S rRNA衍生的细菌树中网络指数的系统发育信号的分析表明，蜱和田鼠的微生物组具有较高的系统发育多样性，并且最接近的细菌属不会共存。这项研究表明，网络分析是一个很有前途的工具，以解开复杂的微生物群落与节肢动物载体和脊椎动物宿主。
We aimed to develop a framework, based on graph theory, to capture the ecological meaning behind pure pair comparisons of microbiome-derived data. As a proof of concept, we applied the framework to analyze the co-occurrence of bacteria in either Ixodes ricinus ticks or the spleen of one of their main hosts, the vole Myodes glareolus. As a secondary lymphoid organ, the spleen acts as a filter of blood and represents well the exposure to microorganisms circulating in the blood; including those acquired and transmitted by ticks during feeding. The microbiome of 301 and 269 individual tick and vole samples, respectively, were analyzed using next generation sequencing (NGS) of 16S rRNA. To assess the effect of habitat on ecological communities of bacteria associated to ticks and voles, two different biotopes were included in the study, forest, and ecotone. An innovative approach of NGS data analysis combining network analysis and phylogenies of co-occuring of bacteria was used to study associations between bacteria in individual samples. Of the 126 bacterial genera found in ticks and voles, 62% were shared by both species. Communities of co-occurring bacteria were always more phylogenetically diverse in ticks than in voles. Interestingly, ~80% of bacterial phylogenetic diversity was found in ~20% of ticks. This pattern was not observed in vole-associated bacteria. Results revealed that the microbiome of I. ricinus is only slightly related to that of M. glareolus and that the biotope plays the most important role in shaping the bacterial communities of either ticks or voles. The analysis of the phylogenetic signal of the network indexes across the 16S rRNA-derived tree of bacteria suggests that the microbiome of both ticks and voles has high phylogenetic diversity and that closest bacterial genera do not co-occur. This study shows that network analysis is a promising tool to unravel complex microbial communities associated to arthropod vectors and vertebrate hosts.