Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients

作     者：Lianshuo Li Zicheng Wang Peng He Shining Ma Jie Du Rui Jiang 

作者机构：MOE Key Laboratory of Bioinformatics and Bioinformatics DivisionTNLIST/Department of Automation Tsinghua University Beijing Anzhen HospitalCapital Medical UniversityBeijing Institute of HeartLungand Blood Vessel Diseases 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2016年第14卷第5期

页      面：314-324页

核心收录：

学科分类：0710[理学-生物学] 1002[医学-临床医学] 1001[医学-基础医学(可授医学、理学学位)] 100201[医学-内科学(含：心血管病、血液病、呼吸系病、消化系病、内分泌与代谢病、肾病、风湿病、传染病)] 0714[理学-统计学（可授理学、经济学学位）] 0703[理学-化学] 0701[理学-数学] 0812[工学-计算机科学与技术（可授工学、理学学位）] 10[医学] 

基　　金：project was partially supported by the National Basic Research Program of China (973 Program Grant No.2012CB316504) the National High-tech R&D Program of China (863 Program Grant No.2012AA020401) the National Natural Science Foundation of China (Grant Nos.61175002 and 61573207) 

主　　题：Functional networkMicrobiome Type 2 diabetes Metagenomics Network motif 

摘      要：Although networks of microbial species have been widely used in the analysis of 16S rRNA sequencing data of a microbiome, the construction and analysis of a complete microbial gene network are in general problematic because of the large number of microbial genes in metagenomics studies. To overcome this limitation, we propose to map microbial genes to functional units, including KEGG orthologous groups and the evolutionary genealogy of genes： Non-supervised Orthologous Groups （eggNOG） orthologous groups, to enable the construction and analysis of a microbial functional network. We devised two statistical methods to infer pairwise relationships between microbial functional units based on a deep sequencing dataset of gut microbiome from type 2 diabetes （T2D） patients as well as healthy controls. Networks containing such functional units and their significant interactions were constructed subsequently. We conducted a variety of analyses of global properties, local properties, and functional modules in the resulting functional networks. Our data indicate that besides the observations consistent with the current knowledge, this study provides novel biological insights into the gut microbiome associated with T2D.