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三沙湾大黄鱼野生和养殖群体的幽门盲囊微生物群落结构比较分析

张钰霆 张瑞瑞 潘非斐 潘友浩 李聪 林华 陈仕玺 穆景利

张钰霆,张瑞瑞,潘非斐,等. 三沙湾大黄鱼野生和养殖群体的幽门盲囊微生物群落结构比较分析[J]. 海洋学报,2024,46(1):77–87 doi: 10.12284/hyxb2024012
引用本文: 张钰霆,张瑞瑞,潘非斐,等. 三沙湾大黄鱼野生和养殖群体的幽门盲囊微生物群落结构比较分析[J]. 海洋学报,2024,46(1):77–87 doi: 10.12284/hyxb2024012
Zhang Yuting,Zhang Ruirui,Pan Feifei, et al. Comparison of the pyloric caecum microbiota community structure between the wild and farmed Larimichthys crocea in Sansha Bay[J]. Haiyang Xuebao,2024, 46(1):77–87 doi: 10.12284/hyxb2024012
Citation: Zhang Yuting,Zhang Ruirui,Pan Feifei, et al. Comparison of the pyloric caecum microbiota community structure between the wild and farmed Larimichthys crocea in Sansha Bay[J]. Haiyang Xuebao,2024, 46(1):77–87 doi: 10.12284/hyxb2024012

三沙湾大黄鱼野生和养殖群体的幽门盲囊微生物群落结构比较分析

doi: 10.12284/hyxb2024012
基金项目: 2022年福建省海洋服务与高质量发展专项;福建省高校产学研联合创新项目(2021N5005)。
详细信息
    作者简介:

    张钰霆(1990—),男,福建省三明市人,副教授,主要从事海洋生物的生理生态学研究。E-mail:ytzhang@mju.edu.cn

    通讯作者:

    潘非斐(1987—),女,工程师,主要从事渔业资源评估研究。E-mail: panffpan@sina.com

    穆景利(1979—),男,教授,主要从事海洋生态毒理学等研究。E-mail:jlmu@mju.edu.cn

  • 中图分类号: P714+.5;S932.4

Comparison of the pyloric caecum microbiota community structure between the wild and farmed Larimichthys crocea in Sansha Bay

  • 摘要: 大黄鱼(Larimichthys crocea)幽门盲囊呈半封闭结构,保留了部分早期孵化阶段的微生物特征,是用于野生和养殖群体溯源的理想部位。本研究采用高通量测序技术,对三沙湾大黄鱼野生和养殖群体的幽门盲囊微生物的α多样性、核心菌群相对丰度、网络关系等进行分析,构建随机森林模型进行群体溯源分析。结果显示,养殖群体的幽门盲囊微生物有着更多特有操作分类单元(Operational Taxonomic Unit, OTU),其α多样性显著高于野生群体。幽门盲囊微生物的优势菌群有变形菌门(Proteobacteria)、厚壁菌门(Firmicutes)、拟杆菌门(Bacteroidota)、放线菌门(Actinobacteria)及酸杆菌门(Acidobacteria),且各菌群在野生和养殖群体中的相对丰度差异显著。微生物网络分析结果显示,野生和养殖群体的幽门盲囊微生物群落结构差异明显,野生群体拥有更高的负边缘/正边缘比率和模块性以及更少的节点数和连接数。基于此,我们构建了随机森林分类群体溯源预测模型,其准确率(Accuracy, ACC)达92.31%,Kappa系数为0.845 2,ROC曲线下面积为0.952 4,利用此模型识别三沙湾大黄鱼野生和养殖群体的准确率分别可达91.67%和92.86%。综上所述,三沙湾大黄鱼野生和养殖群体的幽门盲囊微生物群落结构差异显著,利用幽门盲囊微生物追踪鱼类来源的方法是可行且有效的,研究结果为区分三沙湾大黄鱼野生和养殖群体提供了新思路。
  • 图  1  三沙湾大黄鱼野生群体(YS)和养殖群体(YZ)幽门盲囊微生物的Venn图

    不同颜色代表不同组样本,图中数字表示OTU数量

    Fig.  1  Venn diagram of the pyloric caecum microbiota of the wild population (YS) and farmed population (YZ) of Larimichthys crocea in Sansha Bay

    Different colors indicate different groups, and the numbers within cycles indicate the number of OTU

    图  2  三沙湾大黄鱼野生群体(YS)和养殖群体(YZ)幽门盲囊微生物的Alpha多样性分析

    Fig.  2  Alpha diversity of the pyloric caecum microbiota of the wild population (YS) and farmed population (YZ) of Larimichthys crocea in Sansha Bay

    图  3  三沙湾大黄鱼野生群体(YS)和养殖群体(YZ)幽门盲囊微生物的PCoA分析

    图中每个点代表一个样本,点的颜色代表样本的分组

    Fig.  3  PCoA analysis of the pyloric caecum microbiota of the wild population (YS) and farmed population (YZ) of Larimichthys crocea in Sansha Bay

    Each point represents a sample, and different colors indicate different groups

    图  4  三沙湾大黄鱼野生群体(YS)和养殖群体(YZ)幽门盲囊微生物在门水平的相对丰度分布

    *代表显著性差异(p < 0.05)

    Fig.  4  Relative abundance of the dominant bacterial phyla of the pyloric caecum microbiota in the wild population (YS) and farmed population (YZ) of Larimichthys crocea in Sansha Bay

    * Indicates significant difference (p < 0.05)

    图  5  三沙湾大黄鱼野生群体(YS)和养殖群体(YZ)幽门盲囊微生物在属水平的相对丰度分布

    *代表显著性差异(p < 0.05)

    Fig.  5  Relative abundance of dominant bacterial genera in the wild (YS) and farmed (YZ) of Larimichthys crocea in Sansha Bay

    * Indicates significant difference (p < 0.05)

    图  6  三沙湾大黄鱼野生群体(YS)和养殖群体(YZ)幽门盲囊微生物的LEfSe分析

    Fig.  6  LEfSe analysis of the pyloric caecum microbiota of the wild population (YS) and farmed population (YZ) of Larimichthys crocea in Sansha Bay

    图  7  三沙湾大黄鱼野生群体(YS)和养殖群体(YZ)幽门盲囊微生物的网络关系

    图中点的不同颜色代表不同门,点的大小表示连接到该节点边缘数的多少;各点之间相互连线的粗细表示相关性系数绝对值的大小(p < 0.05, r > 0.6)

    Fig.  7  The co-occurrence networks of the pyloric caecum microbiota of the wild population (YS) and farmed population (YZ) of Larimichthys crocea in Sansha Bay

    Different colors of nodes indicate different bacterial phyla, and the size of nodes indicates the number of connected edges; the thickness of the connecting line between each point indicates the absolute value of correlation coefficient (p < 0.05, r > 0.6)

    图  8  随机森林规模与误差率的关系

    图中黑线、红线和绿线分别代表所有个体、养殖群体和野生群体的误差率

    Fig.  8  The relationship between random forest size and error rate

    Black line, red line and green line indicate the error rate of all individuals, farmed population and wild population, respectively

    表  1  三沙湾大黄鱼野生群体(YS)和养殖群体(YZ)幽门盲囊微生物的网络图特征参数

    Tab.  1  Characteristic parameters of network diagram of the pyloric caecum microbiota of the wild population (YS) and farmed population (YZ) of Larimichthys crocea in Sansha Bay

    网络图特征参数YSYZ
    节点数163306
    连接数1 56112 309
    正连接数1 52512 125
    负连接数36184
    负/正连接数比0.0230.015
    平均度5.42352.118
    平均聚集系数0.4610.631
    模块性0.6950.292
    下载: 导出CSV

    表  2  随机森林模型参数

    Tab.  2  The parameters of the random forest model

    模型参数数值
    准确率92.31%
    Kappa系数0.8452
    敏感性92.86%
    特异性91.67%
    正预测值92.86%
    负预测值91.67%
    平衡精度92.26%
    ROC 曲线下面积0.952 4
    下载: 导出CSV

    表  3  测试集中随机森林预测模型分类结果

    Tab.  3  Classification results of the test set using the random forest prediction model

    预测分类 实际分类 准确率/%
    YS YZ
    YS 11 1 91.67
    YZ 1 13 92.86
    下载: 导出CSV
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出版历程
  • 收稿日期:  2023-07-12
  • 修回日期:  2023-10-09
  • 网络出版日期:  2023-12-20
  • 刊出日期:  2024-01-01

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