Conteville Liliane Costa, da Silva Juliana Virginio, Andrade Bruno Gabriel Nascimento, Cardoso Tainã Figueiredo, Bruscadin Jennifer Jessica, de Oliveira Priscila Silva Neubern, Mourão Gerson Barreto, Coutinho Luiz Lehmann, Palhares Julio Cesar Pascale, Berndt Alexandre, de Medeiros Sergio Raposo, Regitano Luciana Correia de Almeida
Embrapa Southeast Livestock, São Carlos, Brazil.
Department of Genetics and Evolution, Federal University of São Carlos (UFSCar), São Carlos, Brazil.
Front Microbiol. 2023 Dec 15;14:1282851. doi: 10.3389/fmicb.2023.1282851. eCollection 2023.
Ruminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission.
The ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes' archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di-/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate.
Our findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.
反刍动物的胃肠道内栖息着复杂的微生物群落，该群落对其健康和生理机能起着重要作用。巴西是世界上最大的牛肉生产国之一，超过90%的肉牛群由纯种和杂交的内洛尔牛组成。尽管内洛尔牛对巴西经济和人类饮食很重要，但很少有研究对内洛尔牛的微生物组进行特征描述。因此，我们采用鸟枪法宏基因组学技术，研究了日粮对内洛尔牛微生物组组成和功能的影响，并探讨了特定微生物分类群及其功能与饲料效率和甲烷排放之间的关联。
与粪便微生物组相比，瘤胃微生物组表现出显著更高的微生物多样性、独特的分类特征和微生物功能差异，突出了这些环境中微生物组的不同贡献。接受不同日粮处理的动物，其微生物组的古菌多样性、89个属的丰度以及与每种日粮成分代谢相关的功能均存在显著差异。此外，根据日粮不同，饲料效率高的动物和低甲烷排放动物的粪便微生物组表现出更高的微生物多样性。多个属与表型的增加或减少相关。在分析这些分类群的功能时，我们观察到与饲料效率高和低的牛相关的瘤胃分类群存在显著差异。表征饲料效率高的牛的瘤胃分类群的突出特点是具有更多与碳水化合物代谢相关的功能，如单糖、二糖/寡糖和氨基酸。与甲烷排放相关的分类群具有与甲烷生成以及可能影响甲烷产生的底物（如氢气和甲酸盐）生成相关的功能。
我们的研究结果突出了日粮在塑造内洛尔牛微生物组方面的重要作用，以及其组成和功能如何影响饲料效率和甲烷排放等生产性状。这些见解为实施新型饲养和生物技术策略提供了有价值的支持。
