Institute of Agrifood Research and Technology (IRTA)-Animal Breeding and Genetics, Caldes de Montbui, Barcelona, Spain.
Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Barcelona, Spain.
Genet Sel Evol. 2022 Jun 27;54(1):46. doi: 10.1186/s12711-022-00738-2.
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.
兔盲肠中栖息着复杂的微生物生态系统，该系统有助于经济性状的变异。尽管宿主遗传学对微生物多样性和特定微生物类群的影响已在多种物种（例如人类、猪或牛）中进行了研究，但在兔中尚未进行研究。本研究采用贝叶斯因子方法，旨在剖析宿主遗传学、窝和笼对 984 个代表兔微生物群的微生物特征的影响。
对 425 只兔子盲肠微生物 16S rDNA 序列的分析得到了 29 个属、951 个操作分类单位（OTU）和 4 个微生物α多样性指数的相对丰度。这些微生物特征中的每一个都使用混合线性和零膨胀泊松（ZIP）模型进行了调整，这些模型均包括加性遗传、窝和笼效应以及断奶和批次的体重作为系统因素。使用 MCMC 贝叶斯程序估计模型参数的边缘后验分布。使用偏差信息准则（DIC）比较了关于数据（正态或 ZIP）统计分布的模型，贝叶斯因子被计算为支持宿主遗传学、窝和笼效应对微生物特征的证据强度的度量。根据 DIC，除了在 10%以下动物中存在的 OTU 以及在 10%至 25%之间的 25 个 OTU 外，所有微生物特征均通过线性模型进行了更好的调整。在全局范围内，贝叶斯因子揭示了支持遗传控制观察到的 OTU 数量和 Shannon 指数的有力证据。在分类群特异性水平上，OTU 和属相对丰度的显著比例受加性遗传、窝和笼效应的影响。属 Bacteroides 和 Parabacteroides 的多个成员强烈受宿主遗传学和饲养环境的影响，而科 S24-7 和属 Ruminococcus 强烈受笼效应的影响。
本研究表明，宿主遗传学塑造了兔盲肠微生物多样性的整体情况，而且很大一部分类群受宿主遗传学或环境因素（如窝和/或笼）的影响。
