gNOMO2: a comprehensive and modular pipeline for integrated multi-omics analyses of microbiomes

Abstract

BackgroundOver the past few years, the rise of omics technologies has offered an exceptional chance to gain a deeper insight into the structural and functional characteristics of microbial communities. As a result, there is a growing demand for user friendly, reproducible, and versatile bioinformatic tools that can effectively harness multi-omics data to offer a holistic understanding of microbiomes. Previously, we introduced gNOMO, a bioinformatic pipeline specifically tailored to analyze microbiome multi-omics data in an integrative manner. In response to the evolving demands within the microbiome field and the growing necessity for integrated multi-omics data analysis, we have implemented substantial enhancements to the gNOMO pipeline. ResultsHere, we present gNOMO2, a comprehensive and modular pipeline that can seamlessly manage various omics combinations, ranging from two to four distinct omics data types including 16S rRNA gene amplicon sequencing, metagenomics, metatranscriptomics, and metaproteomics. Furthermore, gNOMO2 features a specialized module for processing 16S rRNA gene amplicon sequencing data to create a protein database suitable for metaproteomics investigations. Moreover, it incorporates new differential abundance, integration and visualization approaches, all aimed at providing a more comprehensive toolkit and insightful analysis of microbiomes. The functionality of these new features is showcased through the use of four microbiome multi-omics datasets encompassing various ecosystems and omics combinations. gNOMO2 not only replicated most of the primary findings from these studies but also offered further valuable perspectives. ConclusionsgNOMO2 enables the thorough integration of taxonomic and functional analyses in microbiome multi-omics data, opening up avenues for novel insights in the field of both host associated and free-living microbiome research. gNOMO2 is available freely at https://github.com/muzafferarikan/gNOMO2.