CDEMI: Characterizing differences in microbial composition and function in microbiome data

作者全名："Wang, Lidan; Liang, Xiao; Chen, Hao; Cao, Lijie; Liu, Lan; Zhu, Feng; Ding, Yubin; Tang, Jing; Xie, Youlong"

作者地址："[Wang, Lidan; Liang, Xiao; Chen, Hao; Cao, Lijie; Liu, Lan; Tang, Jing] Chongqing Med Univ, Sch Basic Med, Chongqing 400016, Peoples R China; [Wang, Lidan; Ding, Yubin] Chongqing Med Univ, Dept Obstet & Gynecol, Women & Childrens Hosp, Chongqing 401147, Peoples R China; [Tang, Jing; Xie, Youlong] Chongqing Med Univ, Sch Publ Hlth, Dept Reprod Biol, Joint Int Res Lab Reprod & Dev, Chongqing 400016, Peoples R China; [Zhu, Feng] Zhejiang Univ, Coll Pharmaceut Sci, Hangzhou 310058, Peoples R China"

通信作者："Tang, J (通讯作者)，Chongqing Med Univ, Sch Basic Med, Chongqing 400016, Peoples R China.; Ding, YB (通讯作者)，Chongqing Med Univ, Dept Obstet & Gynecol, Women & Childrens Hosp, Chongqing 401147, Peoples R China.; Tang, J; Xie, YL (通讯作者)，Chongqing Med Univ, Sch Publ Hlth, Dept Reprod Biol, Joint Int Res Lab Reprod & Dev, Chongqing 400016, Peoples R China."

来源：COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL

ESI学科分类：BIOLOGY & BIOCHEMISTRY

WOS号：WOS:000976483900001

JCR分区：Q2

影响因子：4.4

年份：2023

卷号：21

期号：　

开始页：2502

结束页：2513

文献类型：Article

关键词：Microbiome; Microbial composition; Functional characterization; Microbial association; Metabolic pathway

摘要："Microbial communities influence host phenotypes through microbiota-derived metabolites and interactions between exogenous active substances (EASs) and the microbiota. Owing to the high dynamics of microbial community composition and difficulty in microbial functional analysis, the identification of mechanistic links between individual microbes and host phenotypes is complex. Thus, it is important to characterize variations in microbial composition across various conditions (for example, topographical locations, times, physiological and pathological conditions, and populations of different ethnicities) in microbiome studies. However, no web server is currently available to facilitate such characterization. Moreover, accurately annotating the functions of microbes and investigating the possible factors that shape microbial function are critical for discovering links between microbes and host phenotypes. Herein, an online tool, CDEMI, is introduced to discover microbial composition variations across different conditions, and five types of microbe libraries are provided to comprehensively characterize the functionality of microbes from different perspectives. These collective microbe libraries include (1) microbial functional pathways, (2) disease associations with microbes, (3) EASs associations with microbes, (4) bioactive microbial metabolites, and (5) human body habitats. In summary, CDEMI is unique in that it can reveal microbial patterns in distributions/compositions across different conditions and facilitate biological interpretations based on diverse microbe libraries. CDEMI is accessible at http://rdblab.cn/cdemi/ (c) 2023 The Authors. Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)."

基金机构："National Key Research and Development Program of China [2018YFC1004401]; Science and Technology Research Program of Chongqing Municipal Education Commission [KJQN202100421]; Basic Research and Frontiers Exploration Project of the Science and Technology Committee of Yuzhong District, Chongqing [20210119]; Chongqing Science and Technology Commission [cstc2021jcyj-bshX0105]"

基金资助正文："This work was supported by the National Key Research and Development Program of China (2018YFC1004401), the Science and Technology Research Program of Chongqing Municipal Education Commission (KJQN202100421), the Basic Research and Frontiers Exploration Project of the Science and Technology Committee of Yuzhong District, Chongqing (20210119), and the Chongqing Science and Technology Commission (cstc2021jcyj-bshX0105)."