During the evolution of aquatic animals, co-evolution between host and microbes has been overlooked. Previous studies have shown that microbes were present in the fertilized egg of fish, but compared with fish, little information is available for crustaceans. High-throughput Illumina Miseq DNA sequencing of the V3-V4 domain of the 16S rRNA gene was used to assess the microbial community composition during different stages of embryonic development in Macrobrachium rosenbergii: fertilized egg stage (OM1), cleavage stage (OM2), blastula stage (OM3), gastrula stage (OM4), egg nauplius stage (OM5), egg metanauplius stage (OM6), protozoea stage (OM7) and zoea stage (OM8). Water samples (WMZ) were also assessed. The results showed that Proteobacteria (82.92%), Bacteroidetes (9.27%), and Actinobacteria (4.49%) were the predominant phylum in the M. rosenbergii embryo. At the genus level, the microbial composition was constantly changing during embryonic development. We concluded that OM3 and OM4 might be the critical stage for transformation of the microbial composition in the M. rosenbergii embryo. The main factor responsible for microbial colonization in the embryo was primarily selective pressure exerted by the shrimp, while the microbial community in the water environment had a lower impact. This study describes bacterial communities in different stages of embryonic development in M. rosenbergii, and the effects of the surrounding environment on microbial colonization. These findings provide valuable information for further studies examining the formation of early intestinal flora in crustaceans.

在水生动物的进化过程中，宿主与微生物之间的共同进化一直被忽视。先前的研究表明，鱼的受精卵中存在微生物，但与鱼相比，甲壳类动物的信息很少。使用高通量Illumina Miseq DNA测序技术对16S rRNA基因的V3-V4结构域进行评估，以评估罗氏沼虾胚胎发育不同阶段的微生物群落组成：受精卵期（OM1），卵裂期（OM2），囊胚阶段（OM3），腹股沟期（OM4），无节幼体阶段（OM5），变卵无节阶段（OM6），原生动物阶段（OM7）和zoea阶段（OM8）。还评估了水样（WMZ）。结果表明，变形杆菌（82.92％），拟杆菌属（9.27％）和放线菌（4.49％）是罗氏沼虾胚胎的主要门。在属水平上，微生物组成在胚胎发育过程中不断变化。我们得出结论，OM3和OM4可能是罗氏沼虾胚胎中微生物组成转化的关键阶段。导致微生物在胚胎中定居的主要因素主要是虾施加的选择性压力，而水环境中的微生物群落影响较小。这项研究描述了罗氏沼虾胚胎发育不同阶段的细菌群落，以及周围环境对微生物定植的影响。这些发现为进一步研究甲壳类动物早期肠道菌群的形成提供了有价值的信息。