遗传改良养殖罗非鱼(GIFT,尼罗罗非鱼)在中国养殖密集,其中大部分产量来自池塘培养系统(PCS)。池内滚道系统(IPRS)是一种新型的高效养殖模式,并被推荐为GIFT农业的新型系统。为了确定这些培养模式对GIFT肠道微生物组的影响,我们在IPRS和PCS装置中进行了90天的实验。16SrRNA基因谱分析表明,随着饲养的进行,在IPRS和PCS条件下,GIFT中肠道菌群的组成逐渐分离。中肠和后肠细菌的反应不同。与第7天相比,到第90天,后肠的α多样性显着降低(p<0.05),PCS饲养鱼的下降幅度明显大于IPRS鱼(p<0.05)。中肠微生物的α-多样性保持稳定(p>0.05)。总体上优势的肠道细菌是拟杆菌,变形杆菌,和Firmicutes。饲养模式影响肠道细菌的分类学特征;在中肠,与PCS样品相比,IPRS样品具有更多的Firmicutes和Fusobacteria,但变形杆菌较少,Verrucomicrobia,和放线菌.Firmicutes富含IPRS后肠,在PCS后肠中富集了镰刀菌。使用随机森林模型和LEfSe,我们还筛选了在IPRS和PCS条件下可以区分肠道微生物群落的核心分类群。在IPRS鱼的中肠中,Cetobacterium属(Fusobacteriaceae科)显着富集,并富含PCS鱼的后肠。敏感梭菌属(梭菌科1)在IPRS中肠和后肠中均显着富集。PICRUSt2软件分析显示培养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(水平1)中显著富集。Further,与氨基酸代谢相关的功能的相对丰度,碳水化合物代谢,能量代谢,辅因子和维生素的代谢在2级较高,因为肠道细菌的代谢活性特别活跃。总的来说,这项研究增强了我们对IPRS和PCS培养模式下GIFT肠道菌群特征的理解。此外,我们的发现提供了对IPRS单位微生态平衡的见解,为进一步发展这一文化体系提供理论参考。
Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) 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 (p < 0.05), with a significantly greater decrease in PCS-reared fish than in IPRS fish (p < 0.05). The α-diversity of microbiota in midgut remained stable (p > 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 Cetobacterium (of family Fusobacteriaceae) was significantly enriched in midgut in IPRS fish, and enriched in hindgut in PCS fish. The genus Clostridium 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.