Department of Energy, Joint Genome Institute, Walnut Creek, California, USA.
AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.
Nat Biotechnol. 2018 Apr;36(4):359-367. doi: 10.1038/nbt.4110. Epub 2018 Mar 19.
Productivity of ruminant livestock depends on the rumen microbiota, which ferment indigestible plant polysaccharides into nutrients used for growth. Understanding the functions carried out by the rumen microbiota is important for reducing greenhouse gas production by ruminants and for developing biofuels from lignocellulose. We present 410 cultured bacteria and archaea, together with their reference genomes, representing every cultivated rumen-associated archaeal and bacterial family. We evaluate polysaccharide degradation, short-chain fatty acid production and methanogenesis pathways, and assign specific taxa to functions. A total of 336 organisms were present in available rumen metagenomic data sets, and 134 were present in human gut microbiome data sets. Comparison with the human microbiome revealed rumen-specific enrichment for genes encoding de novo synthesis of vitamin B, ongoing evolution by gene loss and potential vertical inheritance of the rumen microbiome based on underrepresentation of markers of environmental stress. We estimate that our Hungate genome resource represents ∼75% of the genus-level bacterial and archaeal taxa present in the rumen.
反刍动物的生产力取决于瘤胃微生物群，它们将植物不可消化的多糖发酵成用于生长的营养物质。了解瘤胃微生物群执行的功能对于减少反刍动物的温室气体排放以及从木质纤维素中开发生物燃料非常重要。我们展示了 410 株培养的细菌和古菌，以及它们的参考基因组，代表了每个培养的瘤胃相关古菌和细菌家族。我们评估了多糖降解、短链脂肪酸产生和产甲烷途径，并将特定的分类群分配到功能上。共有 336 种生物存在于现有的瘤胃宏基因组数据集，134 种存在于人类肠道微生物组数据集中。与人类微生物组的比较表明，瘤胃中存在丰富的编码从头合成维生素 B 的基因，通过基因缺失进行持续进化，以及基于环境压力标志物的代表性不足，可能存在瘤胃微生物组的垂直遗传。我们估计，我们的亨格特基因组资源代表了瘤胃中属水平细菌和古菌分类群的约 75%。
