MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data. Issue 4 (13th March 2021)

• Record Type: Journal Article
• Authors: Kim, Jiwoong; Jiang, Shuang; Wang, Yiqing; Xiao, Guanghua; Xie, Yang; Liu, Dajiang J; Li, Qiwei; Koh, Andrew; Zhan, Xiaowei
• Editors: Sachs, M S
• Is Part Of: G3. Volume 11:Issue 4(2021)
• Publication Date: 2021-03-13
• Subjects: metagenomics sequence analysis -- joint analysis -- microbiome biomarker; Genetics -- Research -- Periodicals; Genomics -- Periodicals; Genetics; Genomics; Genes; Genetics -- Research; Genomics; Electronic journals; Periodical; Periodicals; Fulltext; Internet Resources; Periodicals; 572.8
• DOI: 10.1093/g3journal/jkab046
• Languages: English
• ISSNs: 2160-1836

Abstract

Abstract: In microbiome research, metagenomic sequencing generates enormous amounts of data. These data are typically classified into taxa for taxonomy analysis, or into genes for functional analysis. However, a joint analysis where the reads are classified into taxa-specific genes is often overlooked. To enable the analysis of this biologically meaningful feature, we developed a novel bioinformatic toolkit, MetaPrism, which can analyze sequence reads for a set of joint taxa/gene analyses to: 1) classify sequence reads and estimate the abundances for taxa-specific genes; 2) tabularize and visualize taxa-specific gene abundances; 3) compare the abundances between groups; and 4) build prediction models for clinical outcome. We illustrated these functions using a published microbiome metagenomics dataset from patients treated with immune checkpoint inhibitor therapy and showed the joint features can serve as potential biomarkers to predict therapeutic responses. MetaPrism is a toolkit for joint taxa and gene analysis. It offers biological insights on the taxa-specific genes on top of the taxa-alone or gene-alone analysis. MetaPrism is open-source software and freely available at https://github.com/jiwoongbio/MetaPrism . The example script to reproduce the manuscript is also provided in the above code repository.