Ortiz-Chura Abimael, Corral-Jara Karla Fabiola, Tournayre Jeremy, Cantalapiedra-Hijar Gonzalo, Popova Milka, Morgavi Diego P
Université Clermont Auvergne, INRAE, VetAgro Sup, UMR 1213 Herbivores Unit, Saint-Gènes-Champanelle, France.
Anim Nutr. 2025 Mar 15;21:378-389. doi: 10.1016/j.aninu.2024.11.027. eCollection 2025 Jun.
Given the role of the rumen microbiome in providing nutrients to the host ruminant, it is expected that rumen microbes contribute to inter-animal variations in feed efficiency. However, the link between microbial structure and an "efficient" host phenotype is unclear. We hypothesized that extreme residual feed intake (RFI) phenotypes would display distinctive microbiome features regardless of the diet. In this study, we selected the 32 most extreme RFI Charolais bulls from a cohort of 100 animals fed corn-silage (CS; = 50) or grass-silage (GS; = 50) based diets. Rumen samples were obtained 3 h after feeding, at slaughter, for fermentation and metataxonomic and metatranscriptomic microbial analysis. Volatile fatty acid profiles showed no differences between diets and between extreme RFI phenotypes ( > 0.05). Total bacteria and methanogen populations did not differ between extreme RFI phenotypes ( > 0.05), although methanogens expressed per liquid rumen digesta weight tended to decrease in the most efficient bulls compared to the least efficient ones ( = 0.10). The rumen microbial community structure differed between diets ( < 0.001), and between extreme RFI phenotypes in the GS diet. In the whole dataset, we identified , , and CAG-238 as bacteria discriminant between extreme RFI phenotypes ( < 0.10). Within diets, these four genera were also discriminant in the GS diet and were all associated with the least efficient bulls. In contrast, in bulls fed the CS diet, only and were discriminant but they were positively associated with the most efficient bulls. Rumen microbial functional features did not differ between extreme RFI phenotypes but did differ between diets. In conclusion, the rumen microbiome was mainly influenced by diet, with the RFI phenotype being a marginal effector. , , , and CAG-238 were discriminant between extreme RFI phenotypes regardless of diet. However, the direction of the association with RFI was diet dependent, indicating a diet-RFI interaction and suggesting that these discriminating microbes may be suitable microbial indicator species for RFI only when considered in conjunction with the diet information.
鉴于瘤胃微生物群在为反刍动物宿主提供营养方面的作用，可以预期瘤胃微生物会导致动物间饲料效率的差异。然而，微生物结构与“高效”宿主表型之间的联系尚不清楚。我们假设，无论饮食如何，极端剩余采食量（RFI）表型都会表现出独特的微生物群特征。在本研究中，我们从100头饲喂玉米青贮（CS；n = 50）或青草青贮（GS；n = 50）日粮的夏洛来公牛群体中挑选出32头最极端RFI的公牛。在饲喂后3小时、屠宰时采集瘤胃样本，用于发酵、宏分类学和宏转录组学微生物分析。挥发性脂肪酸谱在日粮之间以及极端RFI表型之间没有差异（P > 0.05）。极端RFI表型之间的总细菌和产甲烷菌数量没有差异（P > 0.05），尽管与效率最低的公牛相比，效率最高的公牛每液体瘤胃消化物重量中产甲烷菌的表达量有下降趋势（P = 0.10）。瘤胃微生物群落结构在日粮之间（P < 0.001）以及GS日粮的极端RFI表型之间存在差异。在整个数据集中，我们将Ruminococcus、Succiniclasticum、Prevotella和CAG - 238鉴定为极端RFI表型之间有差异的细菌（P < 0.10）。在日粮中，这四个属在GS日粮中也有差异，并且都与效率最低的公牛相关。相反，在饲喂CS日粮的公牛中，只有Ruminococcus和Prevotella有差异，但它们与效率最高的公牛呈正相关。瘤胃微生物功能特征在极端RFI表型之间没有差异，但在日粮之间存在差异。总之，瘤胃微生物群主要受日粮影响，RFI表型是一个次要影响因素。无论日粮如何，Ruminococcus、Succiniclasticum、Prevotella和CAG - 238在极端RFI表型之间有差异。然而，与RFI的关联方向取决于日粮，表明日粮与RFI之间存在相互作用，这表明只有在结合日粮信息考虑时，这些有差异的微生物才可能是RFI合适的微生物指示物种。
