MetaTopics: an integration tool to analyze microbial community profile by topic model. (January 2017)

• Record Type: Journal Article
• Authors: Yan, Jifang; Chuai, Guohui; Qi, Tao; Shao, Fangyang; Zhou, Chi; Zhu, Chenyu; Yang, Jing; Yu, Yifei; Shi, Cong; Kang, Ning; He, Yuan; Liu, Qi
• Is Part Of: BMC genomics. Volume 18:Number 1(2017)
• Page Start: 1
• Page End: 5
• Publication Date: 2017-01
• Subjects: Metagenomics -- R -- Topic model -- Microbial community -- Disease status; Genomes -- Periodicals; Gene mapping -- Periodicals; Genomics -- Periodicals; Base Sequence -- Periodicals; Chromosome Mapping -- Periodicals; Genetic Techniques -- Periodicals; Sequence Analysis, DNA -- Periodicals; 572.8605
• DOI: 10.1186/s12864-016-3257-2
• Languages: English
• ISSNs: 1471-2164

Abstract

Abstract Background Deciphering taxonomical structures based on high dimensional sequencing data is still challenging in metagenomics study. Moreover, the common workflow processed in this field fails to identify microbial communities and their effect on a specific disease status. Even the relationships and interactions between different bacteria in a microbial community keep unknown. Results MetaTopics can efficiently extract the latent microbial communities which reflect the intrinsic relations or interactions among several major microbes. Furthermore, a quantitative measurement, Quetelet Index, is defined to estimate the influence of a latent sub-community on a certain disease status for given samples. An analysis of our in-house oral metagenomics data and public gut microbe data was presented to demonstrate the application and usefulness ofMetaTopics . To preset a user-friendly R package, we have built a dedicated website, https://github.com/bm2-lab/MetaTopics, which includes free downloads, detailed tutorials and illustration examples. Conclusions MetaTopics is the first interactive R package to integrate the state-of-arts topic model derived from statistical learning community to analyze and visualize the metagenomics taxonomy data.