MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data

Jiwoong Kim, Shuang Jiang, Wang Yiqing, Guanghua Xiao, Yang Xie, Dajiang J. Liu, Qiwei Li, Andrew Koh, Xiaowei Zhan

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


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 The example script to reproduce the manuscript is also provided in the above code repository.

Original languageEnglish (US)
Article numberjkab046
JournalG3: Genes, Genomes, Genetics
Issue number4
StatePublished - Apr 2021


  • Joint analysis
  • Metagenomics sequence analysis
  • Microbiome biomarker

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Genetics(clinical)


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