Gut microbiome dysbiosis is associated with host genetics in the Norwegian Lundehund

A group of diseases have been shown to correlate with a phenomenon called microbiome dysbiosis, where the bacterial species composition of the gut becomes abnormal. The gut microbiome of an animal is influenced by many factors including diet, exposures to bacteria during post-gestational growth, lifestyle, and disease status. Studies also show that host genetics can affect microbiome composition. We sought to test whether host genetic background is associated with gut microbiome composition in the Norwegian Lundehund dog, a highly inbred breed with an effective population size of 13 individuals. The Lundehund has a high rate of a protein-losing enteropathy in the small intestine that is often reported as Lundehund syndrome, which negatively affects longevity and life-quality. An outcrossing project with the Buhund, Norrbottenspets and Icelandic sheepdog was recently established to reintroduce genetic diversity to the Lundehund and improve its health. To assess whether there was an assoc..., In April to August 2021, we collected stool samples from Lundehund (P, n = 50), Lundehund x Buhund crosses (F1, n = 8), and F1 x Lundehund crosses (F2, n = 22). The lower number of individuals in the F1 cohort is due to the challenge in finding owners of Buhund females that were willing to let their dog being paired with a Lundehund. Owners were instructed in how to collect and handle fresh naturally deposed samples, avoiding contamination. The stool samples were stored at room temperature in Stool Nucleic Acid Collection and Preservation Tubes (Norgen BioTek Corp, Cat. 45660). In September 2021, the samples were analyzed with the ZymoBIOMICS® Targeted Sequencing Service (Zymo Research, Irvine, CA). The ZymoBIOMICS®-96 MagBead DNA Kit (Zymo Research, Irvine, CA) was used to extract DNA using an automated platform. Bacterial 16S ribosomal RNA gene targeted sequencing was performed using the Quick-16S™ NGS Library Prep Kit (Zymo Research, Irvine, CA). The bacterial 16S rRNA primers amplif..., The data can be analysed with different softwares, we used R version 4.1.3 with RStudio version 2022.07.2 and with the R packages Phyloseq and Microbiome. More details about scripts are in the README.md file.

已有研究表明，一类疾病与肠道菌群失调（microbiome dysbiosis）这一现象相关，此时动物肠道内的细菌物种组成会出现异常。动物的肠道菌群受多种因素影响，包括饮食、产后生长过程中的细菌暴露、生活方式以及疾病状态。另有研究显示，宿主遗传学也会对菌群组成产生影响。
本研究旨在探究挪威伦德猎犬（Norwegian Lundehund）的宿主遗传背景是否与其肠道菌群组成存在关联。伦德猎犬是一种高度近交的犬种，有效种群大小（effective population size）仅为13只个体。该犬种高发一种以小肠蛋白丢失性肠病（protein-losing enteropathy）为特征的病症，常被称为伦德猎犬综合征（Lundehund syndrome），该病症会对犬只的寿命与生活质量产生负面影响。近期一项杂交育种项目已启动，选用布赫德犬（Buhund）、诺博顿斯皮特犬（Norrbottenspets）与冰岛牧羊犬（Icelandic sheepdog）作为杂交亲本，以期为伦德猎犬重新引入遗传多样性并改善其健康状况。
为评估二者是否存在关联……，2021年4月至8月期间，研究团队分别采集了伦德猎犬（P组，n=50）、伦德猎犬与布赫德犬的杂交一代（F1组，n=8）以及F1与伦德猎犬的回交二代（F2组，n=22）的粪便样本。F1组样本量较少的原因在于，难以找到愿意让自家布赫德母犬与伦德猎犬配种的犬主。
研究人员向犬主详细说明了如何采集并处理新鲜自然排出的粪便样本，以避免污染。粪便样本被置于粪便核酸收集保存管（Stool Nucleic Acid Collection and Preservation Tubes，Norgen BioTek公司，货号45660）中，室温保存。2021年9月，研究团队使用ZymoBIOMICS®靶向测序服务（Zymo Research，加州欧文市）对样本进行了分析。
研究采用ZymoBIOMICS®-96磁珠DNA提取试剂盒（Zymo Research，加州欧文市），通过自动化平台完成DNA提取。使用Quick-16S™ NGS文库制备试剂盒（Zymo Research，加州欧文市）进行细菌16S核糖体RNA（16S ribosomal RNA）基因靶向测序。细菌16S rRNA引物扩增……
该数据集可通过多种软件进行分析，本研究使用了R 4.1.3版本搭配RStudio 2022.07.2版本，并辅以Phyloseq与Microbiome这两个R软件包。有关脚本的更多细节可参见README.md文件。