Zhu Haojun, Qiang Jun, Li Quanjie, Nie Zhijuan, Gao Jiancao, Sun Yi, Xu Gangchun
Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.
Front Physiol. 2022 Sep 12;13:974398. doi: 10.3389/fphys.2022.974398. eCollection 2022.
Genetically improved farmed tilapia (GIFT, ) are intensively farmed in China, where most of the yield derives from the pond culture system (PCS). The in-pond raceway system (IPRS) is a new type of highly efficient aquaculture mode, and has been recommended as a novel system for GIFT farming. To determine the effects of these culture modes on the gut microbiome of GIFT, we conducted a 90-days experiment in IPRS and PCS units. A 16S rRNA gene profile analysis showed that the composition of gut microbiota in GIFT under IPRS and PCS conditions gradually separated as rearing progressed, with divergent responses by the midgut and hindgut bacteria. The α-diversity in hindgut decreased significantly by day 90, as compared with on day 7 ( < 0.05), with a significantly greater decrease in PCS-reared fish than in IPRS fish ( < 0.05). The α-diversity of microbiota in midgut remained stable ( > 0.05). The overall dominant gut bacteria were Bacteroidetes, Proteobacteria, and Firmicutes. Rearing mode affected the taxonomic profile of the gut bacteria; in midgut, IPRS samples had more Firmicutes and Fusobacteria compared with PCS samples, but less Proteobacteria, Verrucomicrobia, and Actinobacteria. Firmicutes was enriched in IPRS hindgut, and Fusobacteria was enriched in PCS hindgut. Using random-forest models and LEfSe, we also screened core taxa that could discriminate between the gut microbial communities under IPRS and PCS conditions. The genus (of family Fusobacteriaceae) was significantly enriched in midgut in IPRS fish, and enriched in hindgut in PCS fish. The genus sensu stricto (of family Clostridiaceae 1) was significantly enriched in both IPRS midgut and hindgut. Analysis with PICRUSt2 software revealed that the culture modes were similar in their effects on the gut microbial metabolic functions. The predicted pathways were significantly enriched in the metabolism class (level 1). Further, the relative abundance of functions related to amino acid metabolic, carbohydrate metabolic, energy metabolic, and metabolic of cofactors and vitamins were high at hierarchy level 2, as the metabolic activity of intestinal bacteria is especially active. Overall, this study enhances our understanding of the characteristics of gut microbiota in GIFT under IPRS and PCS culture modes. Moreover, our findings provide insights into the microecological balance in IPRS units, and a theoretical reference for further development of this culture system.
遗传改良尼罗罗非鱼（GIFT）在中国被广泛养殖，其产量大多来自池塘养殖系统（PCS）。池塘内循环流水养殖系统（IPRS）是一种新型高效养殖模式，已被推荐用于GIFT养殖。为了确定这些养殖模式对GIFT肠道微生物群的影响，我们在IPRS和PCS养殖单元中进行了为期90天的实验。16S rRNA基因谱分析表明，随着养殖时间的推移，IPRS和PCS条件下GIFT肠道微生物群的组成逐渐分离，中肠和后肠细菌的反应不同。与第7天相比，后肠中的α多样性在第90天显著下降（P<0.05），PCS养殖的鱼下降幅度显著大于IPRS养殖的鱼（P<0.05）。中肠微生物群的α多样性保持稳定（P>0.05）。肠道中总体优势细菌为拟杆菌门、变形菌门和厚壁菌门。养殖模式影响肠道细菌的分类谱；在中肠中，与PCS样本相比，IPRS样本中的厚壁菌门和梭杆菌门更多，但变形菌门、疣微菌门和放线菌门更少。厚壁菌门在IPRS后肠中富集，梭杆菌门在PCS后肠中富集。使用随机森林模型和线性判别分析效应大小（LEfSe），我们还筛选出了能够区分IPRS和PCS条件下肠道微生物群落的核心分类群。梭杆菌科的某属在IPRS养殖的鱼的中肠中显著富集，在PCS养殖的鱼的后肠中富集。狭义的某梭菌属（属于梭菌科1）在IPRS的中肠和后肠中均显著富集。使用PICRUSt2软件分析表明，养殖模式对肠道微生物代谢功能的影响相似。预测的途径在代谢类别（一级）中显著富集。此外，在二级层次上，与氨基酸代谢、碳水化合物代谢、能量代谢以及辅因子和维生素代谢相关的功能相对丰度较高，因为肠道细菌的代谢活性特别活跃。总体而言，本研究增进了我们对IPRS和PCS养殖模式下GIFT肠道微生物群特征的理解。此外，我们的研究结果为IPRS养殖单元的微生态平衡提供了见解，并为该养殖系统的进一步发展提供了理论参考。
