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Harnessing the strategy of metagenomics for exploring the intestinal microecology of sable (Martes zibellina), the national first-level protected animal.
AMB Express ( IF 3.5 ) Pub Date : 2020-09-18 , DOI: 10.1186/s13568-020-01103-6
Jiakuo Yan 1 , Xiaoyang Wu 1 , Jun Chen 2 , Yao Chen 2 , Honghai Zhang 1
Affiliation  

Sable (Martes zibellina), a member of family Mustelidae, order Carnivora, is primarily distributed in the cold northern zone of Eurasia. The purpose of this study was to explore the intestinal flora of the sable by metagenomic library-based techniques. Libraries were sequenced on an Illumina HiSeq 4000 instrument. The effective sequencing data of each sample was above 6000 M, and the ratio of clean reads to raw reads was over 98%. The total ORF length was approximately 603,031, equivalent to 347.36 Mbp. We investigated gene functions with the KEGG database and identified 7140 KEGG ortholog (KO) groups comprising 129,788 genes across all of the samples. We selected a subset of genes with the highest abundances to construct cluster heat maps. From the results of the KEGG metabolic pathway annotations, we acquired information on gene functions, as represented by the categories of metabolism, environmental information processing, genetic information processing, cellular processes and organismal systems. We then investigated gene function with the CAZy database and identified functional carbohydrate hydrolases corresponding to genes in the intestinal microorganisms of sable. This finding is consistent with the fact that the sable is adapted to cold environments and requires a large amount of energy to maintain its metabolic activity. We also investigated gene functions with the eggNOG database; the main functions of genes included gene duplication, recombination and repair, transport and metabolism of amino acids, and transport and metabolism of carbohydrates. In this study, we attempted to identify the complex structure of the microbial population of sable based on metagenomic sequencing methods, which use whole metagenomic data, and to map the obtained sequences to known genes or pathways in existing databases, such as CAZy, KEGG, and eggNOG. We then explored the genetic composition and functional diversity of the microbial community based on the mapped functional categories.



中文翻译:

利用宏基因组学策略探索国家一级保护动物紫貂肠道微生态。

Sable ( Martes zibellina ),科的成员,目食肉目,主要分布在欧亚大陆寒冷的北部地区。本研究的目的是通过基于宏基因组文库的技术探索紫貂的肠道菌群。文库在 Illumina HiSeq 4000 仪器上测序。每个样本的有效测序数据均在6000M以上,cleanreads与rawreads的比例超过98%。ORF 的总长度约为 603,031,相当于 347.36 Mbp。我们使用 KEGG 数据库研究了基因功能,并确定了 7140 个 KEGG 直系同源 (KO) 组,包括所有样本中的 129,788 个基因。我们选择了丰度最高的基因子集来构建集群热图。从 KEGG 代谢途径注释的结果中,我们获得了基因功能的信息,以代谢类别为代表,环境信息处理、遗传信息处理、细胞过程和有机体系统。然后,我们使用 CAZy 数据库研究了基因功能,并确定了与紫貂肠道微生物中基因相对应的功能性碳水化合物水解酶。这一发现与紫貂适应寒冷环境并需要大量能量来维持其代谢活动的事实一致。我们还使用eggNOG 数据库研究了基因功能;基因的主要功能包括基因复制、重组和修复、氨基酸的转运和代谢、碳水化合物的转运和代谢。在这项研究中,我们试图基于宏基因组测序方法识别紫貂微生物种群的复杂结构,该方法使用整个宏基因组数据,并将获得的序列映射到现有数据库中的已知基因或通路,例如 CAZy、KEGG 和 eggNOG。然后,我们基于映射的功能类别探索了微生物群落的遗传组成和功能多样性。

更新日期:2020-09-20
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