A network analysis of methane and feed conversion genes in the rumen microbial community
A network analysis of methane and feed conversion genes in the rumen microbial community
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DOI：
10.1109/bibm.2016.7822741
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发表时间：
2016-12
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影响因子：
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通讯作者：
Fiona Browne;Haiying Wang;Huiru Zheng;R. Roehe;R. Dewhurst;P. Walsh
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作者：
Fiona Browne;Haiying Wang;Huiru Zheng;R. Roehe;R. Dewhurst;P. Walsh
宏基因组学涉及从环境样品中的群落提取的微生物DNA的遗传分析。下一代测序技术的出现和成本的下降加速了宏基因组学的研究，提供了对微生物群落的更好理解。在这项研究中，我们调查的性状，甲烷生产和饲料转化率在瘤胃微生物群落重叠的顶部基因排列的拓扑度量在一个共同丰度网络。一个共同的丰度网络构建了1570个微生物基因的丰度值在瘤胃样品中的8头牛在宏基因组学研究中确定在牛肉和绵羊研究中心的苏格兰农村学院。我们使用了4种不同的拓扑度量：度中心性，介数中心性，Bonacich幂中心性和PageRank。使用排列测试，我们发现，甲烷产生性状基因与使用PageRank和Bonacich Power Centrality指标获得的排名靠前的基因显著重叠。利用Bonacich Power Centrality和Betweenness分析饲料转化性状基因与排名靠前的基因重叠。此外，我们观察到来自PageRank和Bonacich Power Centrality的排名最高的基因与参与KEGG甲烷代谢途径的基因显著重叠，并对关键的甲烷生成基因如mcrA和fmdB进行了高度排名。还根据与来自拓扑度量的排名靠前的基因的重叠来分析含有大多数甲烷和饲料转化基因的鉴定的功能簇。
Metagenomics involves the genetic analysis of microbial DNA extracted from communities in an environment sample. Advent and falling costs of next-generation sequencing technologies has accelerated metagenomics research providing an improved understanding of microbial communities. In this study we investigate if the traits methane production and feed conversion rates in the rumen microbial community overlap with top genes ranked by topological metrics in a co-abundance network. A co-abundance network was constructed from abundance values of 1570 microbial genes in rumen samples of 8 cattle identified in a metagenomics study at the Beef and Sheep Research Centre of Scotland's Rural College. We used 4 different topological measures: Degree Centrality, Betweenness Centrality, Bonacich Power Centrality and PageRank to the network. Using permutation testing, we discovered, methane production trait genes significantly overlapped with top ranked genes obtained using the metrics PageRank and Bonacich Power Centrality. Feed conversion trait genes overlapped with top ranked genes using Bonacich Power Centrality and Betweenness. Furthermore, we observed the top ranked genes from PageRank and Bonacich Power Centrality significantly overlapped with genes involved in the KEGG methane metabolism pathway and ranked highly key methanogenesis genes such as mcrA and fmdB. Identified functional clusters containing most methane and feed conversion genes were also analyzed in terms of overlap with top ranked genes from topological metrics.