Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen
Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions to utilize high lignocellulosic forages in the cattle rumen
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DOI：
10.1038/s41396-020-00837-2
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发表时间：
2020-12-01
期刊：
影响因子：
11
通讯作者：
Salekdeh, Ghasem Hosseini
中科院分区：
文献类型：
--
作者：
Gharechahi, Javad;Vahidi, Mohammad Farhad;Salekdeh, Ghasem Hosseini
瘤胃微生物群在反刍动物消化和利用植物材料中发挥着关键作用，这对温室气体排放具有重要意义。然而，人们对消化过程中涉及的关键类群和潜在基因功能知之甚少。在这里，我们对瘤胃瘘牛中附着于六种不同木质纤维素生物量的瘤胃微生物群进行了以基因组为中心的分析。我们的宏基因组测序为瘤胃中 523 种未培养的细菌和 15 种大部分未培养的古细菌的功能潜力提供了新的基因组见解。组装的基因组主要属于拟杆菌门、厚壁菌门、疣微菌门和纤维杆菌门，并且富集了与木质纤维素聚合物降解和降解产物发酵成短链挥发性脂肪酸相关的基因。我们还发现在瘤胃发酵过程中从富营养型向寡营养型的转变，这对于在生理化学复杂且变化的瘤胃环境中消化顽固的木质纤维素底物可能很重要。瘤胃微生物群对草料（孵化的木质纤维素材料）的差异定殖表明，分类和代谢多样化是对构成牛饮食主要成分的不同木质纤维素底物的进化适应。我们的数据还为独特的微生物多样性和相关基因功能在瘤胃中顽固木质纤维素材料降解中的关键作用提供了新的见解。
Rumen microbiota play a key role in the digestion and utilization of plant materials by the ruminant species, which have important implications for greenhouse gas emission. Yet, little is known about the key taxa and potential gene functions involved in the digestion process. Here, we performed a genome-centric analysis of rumen microbiota attached to six different lignocellulosic biomasses in rumen-fistulated cattle. Our metagenome sequencing provided novel genomic insights into functional potential of 523 uncultured bacteria and 15 mostly uncultured archaea in the rumen. The assembled genomes belonged mainly to Bacteroidota, Firmicutes, Verrucomicrobiota, and Fibrobacterota and were enriched for genes related to the degradation of lignocellulosic polymers and the fermentation of degraded products into short chain volatile fatty acids. We also found a shift from copiotrophic to oligotrophic taxa during the course of rumen fermentation, potentially important for the digestion of recalcitrant lignocellulosic substrates in the physiochemically complex and varying environment of the rumen. Differential colonization of forages (the incubated lignocellulosic materials) by rumen microbiota suggests that taxonomic and metabolic diversification is an evolutionary adaptation to diverse lignocellulosic substrates constituting a major component of the cattle's diet. Our data also provide novel insights into the key role of unique microbial diversity and associated gene functions in the degradation of recalcitrant lignocellulosic materials in the rumen.