Solden Lindsey M, Hoyt David W, Collins William B, Plank Johanna E, Daly Rebecca A, Hildebrand Erik, Beavers Timothy J, Wolfe Richard, Nicora Carrie D, Purvine Sam O, Carstensen Michelle, Lipton Mary S, Spalinger Donald E, Firkins Jeffrey L, Wolfe Barbara A, Wrighton Kelly C
Department of Microbiology, The Ohio State University, Columbus, OH, USA.
Pacific Northwest National Laboratory, Richland, WA, USA.
ISME J. 2017 Mar;11(3):691-703. doi: 10.1038/ismej.2016.150. Epub 2016 Dec 13.
Ruminants have co-evolved with their gastrointestinal microbial communities that digest plant materials to provide energy for the host. Some arctic and boreal ruminants have already shown to be vulnerable to dietary shifts caused by changing climate, yet we know little about the metabolic capacity of the ruminant microbiome in these animals. Here, we use meta-omics approaches to sample rumen fluid microbial communities from Alaskan moose foraging along a seasonal lignocellulose gradient. Winter diets with increased hemicellulose and lignin strongly enriched for BS11, a Bacteroidetes family lacking cultivated or genomically sampled representatives. We show that BS11 are cosmopolitan host-associated bacteria prevalent in gastrointestinal tracts of ruminants and other mammals. Metagenomic reconstruction yielded the first four BS11 genomes; phylogenetically resolving two genera within this previously taxonomically undefined family. Genome-enabled metabolic analyses uncovered multiple pathways for fermenting hemicellulose monomeric sugars to short-chain fatty acids (SCFA), metabolites vital for ruminant energy. Active hemicellulosic sugar fermentation and SCFA production was validated by shotgun proteomics and rumen metabolites, illuminating the role BS11 have in carbon transformations within the rumen. Our results also highlight the currently unknown metabolic potential residing in the rumen that may be vital for sustaining host energy in response to a changing vegetative environment.
反刍动物与其胃肠道微生物群落共同进化，这些微生物群落消化植物材料为宿主提供能量。一些北极和北方的反刍动物已显示出易受气候变化导致的饮食变化影响，但我们对这些动物反刍动物微生物组的代谢能力知之甚少。在这里，我们使用元组学方法从沿着季节性木质纤维素梯度觅食的阿拉斯加驼鹿的瘤胃液中采集微生物群落样本。冬季饮食中半纤维素和木质素含量增加，强烈富集了BS11，这是一个缺乏培养或基因组采样代表的拟杆菌科。我们表明，BS11是在反刍动物和其他哺乳动物胃肠道中普遍存在的与宿主相关的细菌。宏基因组重建产生了前四个BS11基因组；从系统发育上解析了这个以前分类未定义的科中的两个属。基于基因组的代谢分析发现了多种将半纤维素单糖发酵为短链脂肪酸（SCFA）的途径，SCFA是反刍动物能量至关重要的代谢物。通过鸟枪法蛋白质组学和瘤胃代谢物验证了活跃的半纤维素糖发酵和SCFA产生，阐明了BS11在瘤胃内碳转化中的作用。我们的结果还突出了瘤胃中目前未知的代谢潜力，这可能对在不断变化的营养环境中维持宿主能量至关重要。
