The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge
The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge
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DOI：
10.1186/s40168-020-00840-x
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发表时间：
2020-06-13
期刊：
影响因子：
15.5
通讯作者：
Dinsdale, Elizabeth A.
中科院分区：
文献类型：
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作者：
Doane, Michael P.;Morris, Megan M.;Dinsdale, Elizabeth A.
背景 脊椎动物分支分化为软骨鱼类（鲨鱼、鳐鱼和嵌合体）和硬骨鱼类（硬骨鱼），数量约为 420 米亚，每个群体都积累了巨大的解剖学和生理学差异，包括皮肤特性。软骨鱼类的皮肤覆盖有真皮小齿，而骨鱼鱼类的皮肤覆盖有鳞片并且富含粘液。假设这两个鱼群之间的分歧时间导致了共生体之间可预测的变化。在这里，我们使用鸟枪法宏基因组学来测试这两个鱼类进化枝的皮肤表面微生物组的多样性模式是否符合系统共生理论的预测。我们假设（1）皮肤微生物组将是宿主和分支特异性的，（2）软骨鱼和硬骨鱼的进化差异将与宿主-微生物组差异的伴随增加相对应，（3）这两个群体的皮肤结构将影响微生物组的分类和功能组成。结果我们表明微生物组的分类和功能组成是宿主特异性的。与进化枝之间的比较相比，进化枝内的硬骨鱼的平均微生物组相似性较低，但在基于零的模型中，进化枝之间的组成没有差异。板鱼类的平均相似性在进化枝内与在进化枝之间没有不同，并且在基于空的比较模型中也没有不同。在宿主距离与微生物组距离的比较中，我们发现，对于软骨鱼类来说，微生物组的分类组成与宿主距离有关，但与硬骨鱼无关。相比之下，软骨鱼类的基因功能组成与宿主-生物距离无关，但硬骨鱼的基因功能组成与宿主距离负相关。结论 我们的结果表明，两个鱼类进化枝的系统共生模式并不一致，软骨鱼表现出系统共生，而硬骨鱼则不然。这种差异可能与支撑微生物组组合的替代过程有关，包括软骨鱼类可能的历史宿主微生物组进化和过滤特定微生物群的硬骨鱼的趋同进化。我们对鱼类微生物组的比较代表了对现存脊椎动物宿主最古老分歧的微生物关系的调查，并揭示了微生物关系在整个进化时间尺度上并不一致。
Background The vertebrate clade diverged into Chondrichthyes (sharks, rays, and chimeras) and Osteichthyes fishes (bony fishes) approximately 420 mya, with each group accumulating vast anatomical and physiological differences, including skin properties. The skin of Chondrichthyes fishes is covered in dermal denticles, whereas Osteichthyes fishes are covered in scales and are mucous rich. The divergence time among these two fish groups is hypothesized to result in predictable variation among symbionts. Here, using shotgun metagenomics, we test if patterns of diversity in the skin surface microbiome across the two fish clades match predictions made by phylosymbiosis theory. We hypothesize (1) the skin microbiome will be host and clade-specific, (2) evolutionary difference in elasmobranch and teleost will correspond with a concomitant increase in host-microbiome dissimilarity, and (3) the skin structure of the two groups will affect the taxonomic and functional composition of the microbiomes. Results We show that the taxonomic and functional composition of the microbiomes is host-specific. Teleost fish had lower average microbiome within clade similarity compared to among clade comparison, but their composition is not different among clade in a null based model. Elasmobranch's average similarity within clade was not different than across clade and not different in a null based model of comparison. In the comparison of host distance with microbiome distance, we found that the taxonomic composition of the microbiome was related to host distance for the elasmobranchs, but not the teleost fishes. In comparison, the gene function composition was not related to the host-organism distance for elasmobranchs but was negatively correlated with host distance for teleost fishes. Conclusion Our results show the patterns of phylosymbiosis are not consistent across both fish clades, with the elasmobranchs showing phylosymbiosis, while the teleost fish are not. The discrepancy may be linked to alternative processes underpinning microbiome assemblage, including possible historical host-microbiome evolution of the elasmobranchs and convergent evolution in the teleost which filter specific microbial groups. Our comparison of the microbiomes among fishes represents an investigation into the microbial relationships of the oldest divergence of extant vertebrate hosts and reveals that microbial relationships are not consistent across evolutionary timescales.