Offspring Microbiomes Differ Across Breeding Sites in a Panmictic Species
Offspring Microbiomes Differ Across Breeding Sites in a Panmictic Species
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DOI：
10.3389/fmicb.2019.00035
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发表时间：
2019-02-06
影响因子：
5.2
通讯作者：
Sommer, Simone
中科院分区：
文献类型：
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作者：
Gillingham, Mark Alan Frank;Bechet, Arnaud;Sommer, Simone
众所周知，高传播率会使宿主种群遗传结构均匀化，并破坏宿主对当地环境的适应。长距离传播也可能使微生物在大的地理区域传播。然而，到目前为止，形成宿主群体遗传学的选择机制在多大程度上反映在肠道微生物群的群体结构中仍不清楚。高扩散率和水平亲本转移可能使繁殖地点之间的细菌群落均质化（均质假说）。另外，来自当地环境的强选择可能会在不同的繁殖地点区分细菌群落（异质假说）。此外，来自特定年龄的环境或生理因素的选择可能会区分幼鱼和成鱼之间的微生物组。本研究分析了地中海西部9个繁殖地、4个繁殖期（731只）初生大火烈鸟（Phoenicopterus roseus）和同一繁殖地（27只）成年大火烈鸟（731只）的阴囊细菌16S rRNA基因。我们发现，尽管成虫的扩散率很高，但通过α多样性、β多样性、归属于门和门内属组成的指定序列变异（asv）的相对丰度来测量，雏鸟的肠道微生物组在不同的采样地点和不同的时间内都存在显著差异。时空效应对个体ASV缺失/存在的影响大于对ASV丰度（即核心微生物组组成）的影响。空间效应强于时间效应，尤其是对ASV丰度的影响。我们的研究支持异质假说，即当地环境条件选择和分化细菌群落，从而对抗高分散宿主物种的均质效应。此外，成虫和雏鸟样本之间核心微生物组的差异表明，年龄特异性环境和/或生理因素的差异导致不同年龄群体之间核心肠道微生物组的选择压力不同，即使在相同的环境中也是如此。特别是棒状杆菌属，在以前的研究中与季节性脂肪摄取和迁移有关，在高分散的雏鸟中比在更多的成年鸟中丰富得多。综上所述，塑造宿主遗传结构的选择机制不能扩展到肠道微生物群的遗传结构，这对我们理解宿主局部适应机制和肠道微生物群群体遗传学具有重要意义。
High dispersal rates are known to homogenize host's population genetic structure in panmictic species and to disrupt host local adaptation to the environment. Long-distance dispersal might also spread micro-organisms across large geographical areas. However, so far, to which extent selection mechanisms that shape host's population genetics are mirrored in the population structure of the enteric microbiome remains unclear. High dispersal rates and horizontal parental transfer may homogenize bacterial communities between breeding sites (homogeneous hypothesis). Alternatively, strong selection from the local environment may differentiate bacterial communities between breeding sites (heterogeneous hypothesis). Furthermore, selection from age-specific environmental or physiological factors may differentiate the microbiome between juveniles and adults. Here, we analyzed the cloacal bacterial 16S rRNA gene of fledgling greater flamingos, Phoenicopterus roseus, across nine western Mediterranean breeding sites and four breeding seasons (n = 731) and adult birds (n = 27) from a single site. We found that fledgling cloacal microbiome, as measured by alpha diversity, beta diversity, the relative abundance of assigned sequence variants (ASVs) belonging to a phylum and genus composition within phylum, varied significantly between sampling sites and across time within site despite high adult dispersal rates. The spatio-temporal effects were stronger on individual ASV absence/presence than on ASV abundance (i.e., than on core microbiome composition). Spatial effects had a stronger effect than temporal effects, particularly on ASV abundance. Our study supports the heterogeneous hypothesis whereby local environmental conditions select and differentiate bacterial communities, thus countering the homogenizing effects of high-dispersing host species. In addition, differences in core microbiome between adult vs. fledgling samples suggests that differences in age-specific environmental and/or physiological factors result in differential selection pressure of core enteric microbiome between age classes, even within the same environment. In particular, the genus Corynebacterium, associated with both seasonal fat uptake and migration in previous studies, was much more abundant in high-dispersing fledglings than in more resident adults. To conclude, selection mechanisms that shape the host's genetic structure cannot be extended to the genetic structure of the enteric microbiome, which has important implications regarding our understanding of both host local adaptation mechanisms and enteric microbiome population genetics.