CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets

TL;DR

CViewer is a Java-based tool that integrates shotgun metagenomics with other omics data to explore microbial communities and their interactions with hosts.

Contribution

CViewer introduces a novel Java-based statistical framework for multiomics data integration and analysis with an interactive interface.

Findings

CViewer successfully analyzed a Crohn’s disease dietary intervention study and an obesity gut microbiome dataset.

The tool provides mechanistic insights that align with published literature.

It supports exploratory and hypothesis-driven analysis of complex multiomics datasets.

Abstract

Shotgun metagenomics for microbial community survey recovers enormous amount of information for microbial genomes that include their abundances, taxonomic, and phylogenetic information, as well as their genomic makeup, the latter of which then helps retrieve their function based on annotated gene products, mRNA, protein, and metabolites. Within the context of a specific hypothesis, additional modalities are often included, to give host-microbiome interaction. For example, in human-associated microbiome projects, it has become increasingly common to include host immunology through flow cytometry. Whilst there are plenty of software approaches available, some that utilize marker-based and assembly-based approaches, for downstream statistical analyses, there is still a dearth of statistical tools that help consolidate all such information in a single platform. By virtue of stringent computational requirements, the statistical workflow is often passive with limited visual exploration.

In this study, we have developed a Java-based statistical framework (https://github.com/KociOrges/cviewer) to explore shotgun metagenomics data, which integrates seamlessly with conventional pipelines and offers exploratory as well as hypothesis-driven analyses. The end product is a highly interactive toolkit with a multiple document interface, which makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant patterns. We have designed algorithms based on frequently used numerical ecology and machine learning principles, with value-driven from integrated omics tools which not only find correlations amongst different datasets but also provide discrimination based on case–control relationships.

CViewer was used to analyse two distinct metagenomic datasets with varying complexities. These include a dietary intervention study to understand Crohn’s disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean. Complete analyses of both studies in CViewer then provide very powerful mechanistic insights that corroborate with the published literature and demonstrate its full potential.

Video Abstract

Video Abstract

The online version contains supplementary material available at 10.1186/s40168-024-01834-9.

Figures