The rabbit cecum hosts and interacts with a complex microbial ecosystem that contributes to the variation of traits of economic interest. Although the influence of host genetics on microbial diversity and specific microbial taxa has been studied in several species (e.g., humans, pigs, or cattle), it has not been investigated in rabbits. Using a Bayes factor approach, the aim of this study was to dissect the effects of host genetics, litter and cage on 984 microbial traits that are representative of the rabbit microbiota. Analysis of 16S rDNA sequences of cecal microbiota from 425 rabbits resulted in the relative abundances of 29 genera, 951 operational taxonomic units (OTU), and four microbial alpha-diversity indices. Each of these microbial traits was adjusted with mixed linear and zero-inflated Poisson (ZIP) models, which all included additive genetic, litter and cage effects, and body weight at weaning and batch as systematic factors. The marginal posterior distributions of the model parameters were estimated using MCMC Bayesian procedures. The deviance information criterion (DIC) was used for model comparison regarding the statistical distribution of the data (normal or ZIP), and the Bayes factor was computed as a measure of the strength of evidence in favor of the host genetics, litter, and cage effects on microbial traits. According to DIC, all microbial traits were better adjusted with the linear model except for the OTU present in less than 10% of the animals, and for 25 of the 43 OTU with a frequency between 10 and 25%. On a global scale, the Bayes factor revealed substantial evidence in favor of the genetic control of the number of observed OTU and Shannon indices. At the taxon-specific level, significant proportions of the OTU and relative abundances of genera were influenced by additive genetic, litter, and cage effects. Several members of the genera Bacteroides and Parabacteroides were strongly influenced by the host genetics and nursing environment, whereas the family S24-7 and the genus Ruminococcus were strongly influenced by cage effects. This study demonstrates that host genetics shapes the overall rabbit cecal microbial diversity and that a significant proportion of the taxa is influenced either by host genetics or environmental factors, such as litter and/or cage.

中文翻译：

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使用贝叶斯因子评估宿主遗传学、垫料和笼子对兔盲肠微生物群的影响

兔盲肠宿主复杂的微生物生态系统并与之相互作用，这有助于经济利益特征的变化。尽管宿主遗传学对微生物多样性和特定微生物分类群的影响已经在几个物种（例如，人类、猪或牛）中进行了研究，但尚未在兔子中进行过研究。使用贝叶斯因子方法，本研究的目的是剖析宿主遗传学、垫料和笼子对代表兔子微生物群的 984 种微生物特性的影响。对来自 425 只兔子的盲肠微生物群的 16S rDNA 序列的分析得出了 29 个属、951 个操作分类单元 (OTU) 和四个微生物 alpha 多样性指数的相对丰度。这些微生物特征中的每一个都用混合线性和零膨胀泊松 (ZIP) 模型进行了调整，其中包括加性遗传、窝和笼子效应，以及断奶和分批体重作为系统因素。使用 MCMC 贝叶斯程序估计模型参数的边际后验分布。偏差信息标准 (DIC) 用于关于数据统计分布（正常或 ZIP）的模型比较，并计算贝叶斯因子作为有利于宿主遗传学、垃圾和笼子的证据强度的度量对微生物性状的影响。根据 DIC，除了 OTU 存在于不到 10% 的动物中，以及 43 个 OTU 中有 25 个频率在 10% 到 25% 之间，所有微生物特征都用线性模型进行了更好的调整。在全球范围内，贝叶斯因子揭示了大量证据支持观察到的 OTU 和香农指数数量的遗传控制。在分类单元特定水平上，OTU 的显着比例和属的相对丰度受到加性遗传、凋落物和笼效应的影响。拟杆菌属和副杆菌属的几个成员受到宿主遗传学和护理环境的强烈影响，而 S24-7 家族和瘤胃球菌属则受到笼效应的强烈影响。这项研究表明，宿主遗传学决定了整个兔子盲肠微生物的多样性，并且很大一部分分类群受到宿主遗传学或环境因素（例如垫料和/或笼子）的影响。显着比例的 OTU 和属的相对丰度受到加性遗传、凋落物和笼效应的影响。拟杆菌属和副杆菌属的几个成员受到宿主遗传学和护理环境的强烈影响，而 S24-7 家族和瘤胃球菌属则受到笼效应的强烈影响。这项研究表明，宿主遗传学决定了整个兔子盲肠微生物的多样性，并且很大一部分分类群受到宿主遗传学或环境因素（例如垫料和/或笼子）的影响。显着比例的 OTU 和属的相对丰度受到加性遗传、凋落物和笼效应的影响。拟杆菌属和副杆菌属的几个成员受到宿主遗传学和护理环境的强烈影响，而 S24-7 家族和瘤胃球菌属则受到笼效应的强烈影响。这项研究表明，宿主遗传学决定了整个兔子盲肠微生物的多样性，并且很大一部分分类群受到宿主遗传学或环境因素（例如垫料和/或笼子）的影响。而 S24-7 家族和瘤胃球菌属则受到笼效应的强烈影响。这项研究表明，宿主遗传学决定了整个兔子盲肠微生物的多样性，并且很大一部分分类群受到宿主遗传学或环境因素（例如垫料和/或笼子）的影响。而 S24-7 家族和瘤胃球菌属则受到笼效应的强烈影响。这项研究表明，宿主遗传学决定了整个兔子盲肠微生物的多样性，并且很大一部分分类群受到宿主遗传学或环境因素（例如垫料和/或笼子）的影响。