The impact of aquaculture system on the microbiome and gut metabolome of juvenile Chinese softshell turtle (Pelodiscus sinensis)
The impact of aquaculture system on the microbiome and gut metabolome of juvenile Chinese softshell turtle (Pelodiscus sinensis)
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DOI：
10.1002/imt2.17
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发表时间：
2022-06-01
期刊：
影响因子：
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通讯作者：
Hong, Yijiang
中科院分区：
文献类型：
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作者：
Ding, Xia;Jin, Feng;Hong, Yijiang
在各种水产养殖系统中，商业水生动物微生物组可能显著影响成功宿主的养殖。然而，人们对它知之甚少。本研究通过比较两种不同的养殖系统——稻鱼养殖（RFC）和集约化池塘养殖（IPC）系统，对中华软壳龟幼龟的皮肤、口腔和肠道微生物组以及肠道代谢组进行了解构。RFC中华鲟微生物群落的α -多样性和功能冗余度高于IPC。水产养殖系统对肠道微生物组的影响最大，其次是皮肤微生物组，最后是口腔微生物组。来源跟踪分析显示，在所有身体区域中，RFC的微生物群落来源比IPC的未知来源更多。引人注目的是，RFC的口腔和皮肤微生物组比IPC表现出更高的通才比例和更宽的栖息地生态位宽度，但肠道却没有。零模型分析显示，RFC的口腔和皮肤微生物群落组装受确定性过程的支配比例明显高于IPC，但不受肠道的支配。我们进一步确定了5种显著改变的肠道代谢物的关键基因和微生物贡献，即2-氧戊二酸盐、n -乙酰-d-甘露糖胺、顺式-4-羟基-d-脯氨酸、烟酰胺和l-丙氨酸，这些代谢物与微生物介导的重要过程类别显著相关，包括氨基酸代谢、gaba能突触、ABC转运蛋白、不饱和脂肪酸的生物合成以及柠檬酸循环。此外，不同的养殖制度对中华对虾肝脏脂质代谢和体型有显著影响。我们的研究结果为水产养殖系统对水生动物微生物群落结构特征和组装机制的影响提供了新的见解，也突出了肠道微生物组-代谢组关联中代谢物变化的关键微生物组和基因贡献。
The commercial aquatic animal microbiome may markedly affect the successful host's farming in various aquaculture systems. However, very little was known about it. Here, two different aquaculture systems, the rice-fish culture (RFC) and intensive pond culture (IPC) systems, were compared to deconstruct the skin, oral, and gut microbiome, as well as the gut metabolome of juvenile Chinese softshell turtle (Pelodiscus sinensis). Higher alpha-diversity and functional redundancy of P. sinensis microbial community were found in the RFC than those of the IPC. The aquaculture systems have the strongest influence on the gut microbiome, followed by the skin microbiome, and finally the oral microbiome. Source-tracking analysis showed that the RFC's microbial community originated from more unknown sources than that of the IPC across all body regions. Strikingly, the RFC's oral and skin microbiome exhibited a significantly higher proportion of generalists and broader habitat niche breadth than those of the IPC, but not the gut. Null model analysis revealed that the RFC's oral and skin microbial community assembly was governed by a significantly greater proportion of deterministic processes than that of the IPC, but not the gut. We further identified the key gene and microbial contribution to five significantly changed gut metabolites, 2-oxoglutarate, N-acetyl-d-mannosamine, cis-4-hydroxy-d-proline, nicotinamide, and l-alanine, which were significantly correlated with important categories of microbe-mediated processes, including the amino acid metabolism, GABAergic synapse, ABC transporters, biosynthesis of unsaturated fatty acids, as well as citrate cycle. Moreover, different aquaculture systems have a significant impact on the hepatic lipid metabolism and body shape of P. sinensis. Our results provide new insight into the influence of aquaculture systems on the microbial community structure feature and assembly mechanism in an aquatic animal, also highlighting the key microbiome and gene contributions to the metabolite variation in the gut microbiome-metabolome association.