Belanche Alejandro, Kingston-Smith Alison H, Griffith Gareth W, Newbold Charles J
Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom.
Estación Experimental del Zaidín (CSIC), Granada, Spain.
Front Microbiol. 2019 Feb 11;10:122. doi: 10.3389/fmicb.2019.00122. eCollection 2019.
Increasing feed efficiency is a key target in ruminant science which requires a better understanding of rumen microbiota. This study investigated the effect of a shift from a non-grazing to a grazing diet on the rumen bacterial, methanogenic archaea, fungal, and protozoal communities. A systems biology approach based on a description of the community structure, core microbiota, network analysis, and taxon abundance linked to the rumen fermentation was used to explore the benefits of increasing depth of the community analysis. A total of 24 sheep were fed ryegrass hay supplemented with concentrate (CON) and subsequently ryegrass pasture (PAS) following a straight through experimental design. Results showed that concentrate supplementation in CON-fed animals (mainly starch) promoted a simplified rumen microbiota in terms of network density and bacterial, methanogen and fungal species richness which favored the proliferation of amylolytic microbes and VFA production (+48%), but led to a lower (ca. 4-fold) ammonia concentration making the N availability a limiting factor certain microbes. The adaptation process from the CON to the PAS diet consisted on an increase in the microbial concentration (biomass of bacteria, methanogens, and protozoa), diversity (+221, +3, and +21 OTUs for bacteria, methanogens, and fungi, respectively), microbial network complexity (+18 nodes and +86 edges) and in the abundance of key microbes involved in cellulolysis (, and ), proteolysis ( and Entodiniinae), lactate production ( and ), as well as methylotrophic archaea (Methanomassiliicoccaceae). This microbial adaptation indicated that pasture degradation is a complex process which requires a diverse consortium of microbes working together. The correlations between the abundance of microbial taxa and rumen fermentation parameters were not consistent across diets suggesting a metabolic plasticity which allowed microbes to adapt to different substrates and to shift their fermentation products. The core microbiota was composed of 34, 9, and 13 genera for bacteria, methanogens, and fungi, respectively, which were shared by all sheep, independent of diet. This systems biology approach adds a new dimension to our understanding of the rumen microbial interactions and may provide new clues to describe the mode of action of future nutritional interventions.
提高饲料效率是反刍动物科学的一个关键目标，这需要更好地了解瘤胃微生物群。本研究调查了从非放牧日粮转变为放牧日粮对瘤胃细菌、产甲烷古菌、真菌和原生动物群落的影响。采用基于群落结构描述、核心微生物群、网络分析以及与瘤胃发酵相关的分类群丰度的系统生物学方法，以探索增加群落分析深度的益处。按照直接实验设计，对24只绵羊先饲喂补充精料的黑麦草干草（CON），随后饲喂黑麦草牧场牧草（PAS）。结果表明，在CON组动物中补充精料（主要是淀粉），就网络密度以及细菌、产甲烷菌和真菌物种丰富度而言，促进了瘤胃微生物群的简化，这有利于淀粉分解微生物的增殖和挥发性脂肪酸的产生（增加48%），但导致氨浓度降低（约4倍），使氮的可利用性成为某些微生物的限制因素。从CON日粮到PAS日粮的适应过程包括微生物浓度（细菌、产甲烷菌和原生动物的生物量）增加、多样性增加（细菌、产甲烷菌和真菌分别增加221、3和21个操作分类单元）、微生物网络复杂性增加（增加18个节点和86条边）以及参与纤维素分解（、和）、蛋白质水解（和内毛虫科）、乳酸产生（和）以及甲基营养型古菌（甲烷鬃菌科）的关键微生物丰度增加。这种微生物适应表明，牧草降解是一个复杂的过程，需要多种微生物协同作用。不同日粮中微生物分类群丰度与瘤胃发酵参数之间的相关性不一致，这表明微生物具有代谢可塑性，能够适应不同底物并改变其发酵产物。核心微生物群分别由34个、9个和13个细菌、产甲烷菌和真菌属组成，所有绵羊都有这些属，与日粮无关。这种系统生物学方法为我们理解瘤胃微生物相互作用增添了新的维度，并可能为描述未来营养干预的作用方式提供新线索。
