The gut microbiota of aquaculture species contributes to their food metabolism and regulates their health, which has been shown to vary during aquaculture progression of their hosts. However, limited research has examined the outcomes and mechanisms of these changes in the gut microbiota of hosts. Here, Kuruma shrimps from the beginning, middle, and late stages of aquaculture progression (about a time duration of 2 months between each stage) were collected and variations in the gut microbiota of Kuruma shrimp during the whole aquaculture process were examined. High-throughput sequencing demonstrated increases in the diversity and richness of the shrimp gut microbiota with aquaculture progression. In addition, the gut microbiota composition differed among cultural stages, with enrichment of Firmicutes, RF39, and Megamonas and a reduction in Proteobacteria in the mid-stage. Notably, only very few taxa were persistent in the shrimp gut microbiota during the whole aquaculture progression, while the number of taxa that specific to the end of aquaculture was high. Network analysis revealed increasing complexity of the shrimp gut microbiota during aquaculture progression. Moreover, the shrimp gut microbiota became significantly more stable towards the end of aquaculture. According to the results of neutral community model, contribution of stochastic processes for shaping the shrimp gut microbiota was elevated along the aquaculture progression. This study showed substantial variations in shrimp gut microbiota during aquaculture progression and explored the underlying mechanisms regulating these changes.

水产养殖物种的肠道微生物群有助于其食物代谢并调节其健康，这已被证明在其宿主的水产养殖进程中会发生变化。然而，有限的研究探讨了宿主肠道微生物群这些变化的结果和机制。在这里，收集了养殖过程的开始、中期和后期（每个阶段之间大约持续2个月）的车厘虾，并检查了整个养殖过程中车厘虾肠道微生物群的变化。高通量测序表明，随着水产养殖的进展，虾肠道微生物群的多样性和丰富度有所增加。此外，不同培养阶段的肠道微生物群组成也不同，在中期，厚壁菌门、 RF39和巨胞菌门富集，变形菌门减少。值得注意的是，在整个水产养殖过程中，只有很少的类群持续存在于虾肠道微生物群中，而水产养殖结束时特有的类群数量很高。网络分析显示，在水产养殖过程中，虾肠道微生物群的复杂性不断增加。此外，虾肠道微生物群在水产养殖结束时变得更加稳定。根据中性群落模型的结果，随机过程对塑造虾肠道微生物群的贡献随着水产养殖的进展而增加。这项研究显示了水产养殖过程中虾肠道微生物群的巨大变化，并探讨了调节这些变化的潜在机制。