gNOMO

gNOMO performs integrated analysis of metagenomics, metatranscriptomics, and metaproteomics data to characterize host–microbiome interactions and functional profiles in non-model organisms.

Key Features:

• Multi-Omics Integration: Processes and integrates metagenomics, metatranscriptomics, and metaproteomics data to provide a holistic view of host and microbial communities, demonstrated on systems such as Blattella germanica.
• Automated and Reproducible Workflow: Implemented with the Snakemake framework to automate and document analysis steps for reproducibility.
• Tailored Proteogenomic Database Creation: Builds customized proteogenomic databases on-the-fly from metagenomics and metatranscriptomics data to support downstream protein identification.
• Integrated Visualization: Produces integrated visualizations of expression ratios, taxonomic distributions, and functional profiles across omics levels.
• Parallel Host and Microbiome Analysis: Supports concurrent analysis of host and microbial datasets to investigate metabolic interactions within symbiotic systems.
• Optimized Metaproteomics Identification: Enhances metaproteomics identification, taxonomic classification, and functional annotation by leveraging the tailored proteogenomic database.

Scientific Applications:

• Non-model organism microbiome analysis: Characterizes microbiomes and host interactions in organisms lacking well-annotated reference genomes, including Blattella germanica.
• Symbiosis and host–microbiome interactions: Investigates metabolic and functional contributions of host and microbes in symbiotic systems.
• Microbial community dynamics and functional profiling: Integrates multi-omics layers to study taxonomic shifts and functional responses of microbial communities.
• Environmental and applied biotechnology studies: Applies integrated meta-omics to ecological, evolutionary, and applied research in environmental science and biotechnology.

Methodology:

Implemented in Snakemake; integrates metagenomics, metatranscriptomics, and metaproteomics; constructs tailored proteogenomic databases from metagenomic and metatranscriptomic inputs to support metaproteomics identification and performs parallel host–microbiome analyses with integrated functional and taxonomic visualization.