Laboratorio de Fisiología y Genética de Bacterias Lácticas, Instituto de Biología Molecular y Celular de Rosario (IBR), Concejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad Nacional de Rosario (UNR), Suipacha 531, 2000, Rosario, Argentina.
Centro de Estudios Fotosintéticos y Bioquímicos (CEFOBI), Concejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) - UNR, Rosario, Argentina.
World J Microbiol Biotechnol. 2023 Jul 13;39(9):250. doi: 10.1007/s11274-023-03694-1.
Ruminants enable the conversion of indigestible plant material into animal consumables, including dairy products, meat, and valuable fibers. Microbiome research is gaining popularity in livestock species because it aids in the knowledge of illnesses and efficiency processes in animals. In this study, we use WGS metagenomic data to thoroughly characterize the ruminal ecosystem of cows to infer positive and negative livestock traits determined by the microbiome. The rumen of cows from Argentina were described by combining different gene biomarkers, pathways composition and taxonomic information. Taxonomic characterization indicated that the two major phyla were Bacteroidetes and Firmicutes; in third place, Proteobacteria was highly represented followed by Actinobacteria; Prevotella, and Bacteroides were the most abundant genera. Functional profiling of carbohydrate-active enzymes indicated that members of the Glycoside Hydrolase (GH) class accounted for 52.2 to 55.6% of the total CAZymes detected, among them the most abundant were the oligosaccharide degrading enzymes. The diversity of GH families found suggested efficient hydrolysis of complex biomass. Genes of multidrug, macrolides, polymyxins, beta-lactams, rifamycins, tetracyclines, and bacitracin resistance were found below 0.12% of relative abundance. Furthermore, the clustering analysis of genera and genes that correlated to methane emissions or feed efficiency, suggested that the cows analysed could be regarded as low methane emitters and clustered with high feed efficiency reference animals. Finally, the combination of bioinformatic analyses used in this study can be applied to assess cattle traits difficult to measure and guide enhanced nutrition and breeding methods.
反刍动物能够将难以消化的植物物质转化为动物可食用的物质，包括乳制品、肉类和有价值的纤维。微生物组研究在畜牧物种中越来越受欢迎，因为它有助于了解动物的疾病和效率过程。在这项研究中，我们使用 WGS 宏基因组数据来全面描述奶牛的瘤胃生态系统，以推断由微生物组决定的积极和消极的家畜特征。通过结合不同的基因生物标志物、途径组成和分类学信息，描述了来自阿根廷的奶牛的瘤胃。分类特征表明，两个主要的门是拟杆菌门和厚壁菌门；第三大的是变形菌门，紧随其后的是放线菌门；普雷沃氏菌属和拟杆菌属是最丰富的属。碳水化合物活性酶的功能分析表明，糖苷水解酶（GH）类的成员占检测到的总 CAZymes 的 52.2%到 55.6%，其中最丰富的是寡糖降解酶。发现的 GH 家族的多样性表明，它们能够有效地水解复杂的生物质。发现的多药、大环内酯类、多粘菌素类、β-内酰胺类、利福霉素类、四环素类和杆菌肽类耐药基因的相对丰度低于 0.12%。此外，与甲烷排放或饲料效率相关的属和基因的聚类分析表明，所分析的奶牛可以被认为是低甲烷排放者，并与高饲料效率的参考动物聚类。最后，本研究中使用的生物信息学分析的组合可以用于评估难以衡量的牛的特征，并指导增强的营养和繁殖方法。
