Ruminants are dependent on their rumen microbiota to obtain energy from plants. The composition of the microbiome was well-known to be associated with health status, and production traits, but published results are difficult to reproduce due to large sources of variation. The objectives of this study were to evaluate the associations of ruminal microbiota and its association with genetic lines selected by somatic cell score (SCS) or milk persistency (PERS), as well as milk production, somatic cell score, fat and protein contents, and fatty acids and proteins of milk, using the principles of compositional data. A large sample of 700 Lacaune dairy ewes from INRAE La Fage feeding the same diet and belonging to two divergent genetic lines selected for SCS or PERS was used. The ruminal bacterial metagenome was sequenced using the 16S rRNA gene, resulting in 2,059 operational taxonomic units affiliated with 112 genera. The abundance data were centred log-transformed after the replacement of zeros with the geometric Bayesian method. Discriminant analysis of the SCS showed differences between SCS+ and SCS- ewes, while for PERS no difference was obtained. Milk traits as fat content, protein content, saturated fatty acids and caseins of milk were negatively associated with Prevotella (R = [-0.08;-0.16]), Suttonella (R = [-0.09;-0.16]) and Ruminococcus (R = [-0.08;-0.16]), and positively associated with Lachnospiraceae (R = [0.09;0.16]) and Christensenellaceae (R = [0.09;0.16]). Our findings provide an understanding of the application of compositional data to microbiome analysis, and the potential association of Prevotella, Suttonella, Ruminococcaceae and Lachnospiraceae with milk production traits such as milk fatty acids and proteins in dairy sheep.

中文翻译：

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针对体细胞评分和牛奶持久性选择的母羊瘤胃细菌的组成分析。

反刍动物依靠其瘤胃微生物群从植物中获取能量。众所周知，微生物组的组成与健康状况和生产性状有关，但由于变异来源很大，已发表的结果难以重现。本研究的目的是评估瘤胃微生物群及其与通过体细胞评分 (SCS) 或牛奶持久性 (PERS) 选择的遗传系的关联，以及产奶量、体细胞评分、脂肪和蛋白质含量，以及牛奶的脂肪酸和蛋白质，使用成分数据的原则。使用了来自 INRAE La Fage 的 700 头 Lacaune 奶母羊的大样本，它们饲喂相同的饮食并且属于为 SCS 或 PERS 选择的两个不同的遗传系。使用 16S rRNA 基因对瘤胃细菌宏基因组进行测序，由此产生了 2,059 个操作分类单位，隶属于 112 个属。丰度数据在用几何贝叶斯方法替换零后进行中心对数变换。SCS 的判别分析显示 SCS+ 和 SCS- 母羊之间存在差异，而 PERS 没有获得差异。牛奶的脂肪含量、蛋白质含量、饱和脂肪酸和酪蛋白等牛奶特性与普氏菌 (R = [-0.08;-0.16])、Suttonella (R = [-0.09;-0.16]) 和瘤胃球菌 (R = [-0.08;-0.16])，并且与毛螺菌科 (R = [0.09;0.16]) 和克里斯滕菌科 (R = [0.09;0.16]) 呈正相关。我们的研究结果提供了对组成数据在微生物组分析中的应用的理解，以及普雷沃氏菌、萨通氏菌、