A metagenomic analysis of the camel rumen's microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation.
A metagenomic analysis of the camel rumen's microbiome identifies the major microbes responsible for lignocellulose degradation and fermentation.
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DOI：
10.1186/s13068-018-1214-9
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发表时间：
2018
影响因子：
6.3
通讯作者：
Salekdeh GH
中科院分区：
文献类型：
--
作者：
Gharechahi J;Salekdeh GH
反刍动物瘤胃中存在的多种微生物群有利于植物纤维的消化。本研究对骆驼瘤胃植物纤维粘附微生物进行了散弹枪宏基因组分析，以确定参与木质纤维素降解和短链挥发性脂肪酸（VFA）发酵的关键物种。宏基因组中编码糖苷水解酶的基因密度估计为每Mbp组装DNA 25个，这明显高于其他来源的宏基因组，包括牛瘤胃。也有大量的序列编码支架蛋白，dockerins和黏结蛋白，表明潜在的纤维素介导的木质纤维素降解。对组装好的宏基因组进行分类，确定了65个高质量的基因组箱，这些基因组箱显示了木质纤维素降解酶的高度多样性。拟杆菌门相关的物种具有高比例的脱支酶和低聚糖降解酶基因，而厚壁菌门和纤维杆菌门相关的物种具有丰富的纤维素酶和半纤维素酶基因，因此这些谱系可能是确保木质纤维素降解的关键。拟杆菌门基因组中存在许多“多糖利用位点”（PULs），表明它们具有广泛的底物特异性和高潜在的碳水化合物降解能力。对VFA生物合成途径的分析表明，合成乙酸所需的基因存在于除Elusimicrobiota和Euryarchaeota外的一系列物种中。丙酸盐的生产完全通过琥珀酸途径进行，属于拟杆菌门，厚壁菌门，螺旋体和纤维杆菌门的物种。Bacteroidetes和Lentisphaerae通过butyylcoa: acetate CoA-transferase途径产生丁酸盐，但厚壁菌门通常通过丁酸激酶途径产生丁酸盐。分析证实，骆驼瘤胃的微生物群是一个密集的、但在很大程度上尚未开发的酶来源，具有在生物燃料、精细化学品和食品加工业等一系列生物技术过程中使用的潜力。本文的在线版本（10.1186/s13068-018-1214-9）包含补充内容，仅供授权用户使用。
The diverse microbiome present in the rumen of ruminant animals facilitates the digestion of plant-based fiber. In this study, a shotgun metagenomic analysis of the microbes adhering to plant fiber in the camel rumen was undertaken to identify the key species contributing to lignocellulose degradation and short chain volatile fatty acids (VFA) fermentation. The density of genes in the metagenome encoding glycoside hydrolases was estimated to be 25 per Mbp of assembled DNA, which is significantly greater than what has been reported in other sourced metagenomes, including cow rumen. There was also a substantial representation of sequences encoding scaffoldins, dockerins and cohesins, indicating the potential for cellulosome-mediated lignocellulose degradation. Binning of the assembled metagenome has enabled the definition of 65 high-quality genome bins which showed high diversity for lignocellulose degrading enzymes. Species associated to Bacteroidetes showed a high proportion of genes for debranching and oligosaccharide degrading enzymes, while those belonging to Firmicutes and Fibrobacteres were rich in cellulases and hemicellulases and thus these lineages were probably the key for ensuring the degradation of lignocellulose. The presence of many “polysaccharide utilization loci” (PULs) in Bacteroidetes genomes indicates their broad substrate specificity and high potential carbohydrate degradation ability. An analysis of VFA biosynthesis pathways showed that genes required for the synthesis of acetate were present in a range of species, except for Elusimicrobiota and Euryarchaeota. The production of propionate, exclusively via the succinate pathway, was carried out by species belonging to the phyla Bacteroidetes, Firmicutes, Spirochaetes and Fibrobacteres. Butyrate was generated via the butyrylCoA: acetate CoA-transferase pathway by Bacteroidetes and Lentisphaerae species, but generally via the butyrate kinase pathway by Firmicutes species. The analysis confirmed the camel rumen’s microbiome as a dense and yet largely untapped source of enzymes with the potential to be used in a range of biotechnological processes including biofuel, fine chemicals and food processing industries. The online version of this article (10.1186/s13068-018-1214-9) contains supplementary material, which is available to authorized users.
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牛瘤胃微生物组中纤维体成分的宽大系统发育和功能。
影响因子：
5.1
作者：
Bensoussan L;Moraïs S;Dassa B;Friedman N;Henrissat B;Lombard V;Bayer EA;Mizrahi I
通讯作者：
Mizrahi I
影响因子：
3.7
作者：
Bose T;Haque MM;Reddy C;Mande SS
通讯作者：
Mande SS
影响因子：
4.3
作者：
Huson DH;Beier S;Flade I;Górska A;El-Hadidi M;Mitra S;Ruscheweyh HJ;Tappu R
通讯作者：
Tappu R
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
DOI：
10.1073/pnas.0806191105
发表时间：
2009-02-10
影响因子：
11.1
作者：
Brulc, Jennifer M.;Antonopoulos, Dionysios A.;White, Bryan A.
通讯作者：
White, Bryan A.