Understanding the rules that govern the successions of gut microbiota is prerequisite for testing general ecological theories and sustaining a desirable microbiota. However, the ignorance of microeukaryotes raises the question of whether gut microeukaryotes are assembled according to the same rules as bacteria. We tracked the shrimp gut bacterial and microeukaryotic communities by a longitudinal dense sampling. The successions of both domains were significantly correlated with host age, with relatively stable microeukaryotic communities in adult shrimp. Gut microeukaryotes exhibited significantly higher turnover rate, but fewer transient species, lower proportion of temporal generalists, and narrower habitat niche breadth than bacteria. The γ-diversity partitioning analysis revealed that the successions of gut microbiotas were primarily ascribed to the high dissimilarity as shrimp aged (\( \overline{\beta} \)_IntraTimes), whereas the relative importance of \( \overline{\beta} \)_IntraTimes was significantly higher for microeukaryotes than that for bacteria. Compared with contrasting ecological processes in governing free-living bacteria and microeukaryotes, the ecological patterns were comparable between host-associated gut counterparts. However, the gut microeukaryotes were governed more strongly by deterministic selection relative to nestedness compared with the gut bacteria, which supports the “size-plasticity” hypothesis. Our results highlight the importance of independently interpreting free-living and host-associated meta-communities for a comprehensive understanding of the processes that govern microbial successions.

了解检验肠道菌群演替的规则是检验一般生态学理论和维持理想菌群的前提。然而，微真核生物的无知提出了肠道微真核生物是否按照与细菌相同的规则组装的问题。我们通过纵向密集采样跟踪了虾肠道细菌和微真核生物群落。这两个域的演替与寄主年龄显着相关，成年虾的微真核群落相对稳定。肠道微真核生物显示出比细菌高得多的周转率，但瞬时菌种较少，临时通才的比例较低，栖息地的生态位宽度较细菌小。该γ多样性分区分析显示，肠道菌群的演替主要归因于虾龄（\（\ overline {\ beta} \）_IntraTimes）的高度差异，而\（\ overline {\ beta} \）的相对重要性_内部时间微真核生物明显高于细菌。与控制自由活动细菌和微真核生物的生态过程相比，宿主相关肠道对应物的生态模式具有可比性。然而，与肠道细菌相比，肠道微真核生物受嵌套性确定性选择的支配力更强，这支持“大小可塑性”假说。我们的研究结果突出了独立解释自由生活和与宿主相关的元社区对于全面了解控制微生物演替过程的重要性。