A Multi-Omics Processing Pipeline (MOPP) for Extracting Taxonomic and Functional Insights from Metaribosome Profiling...

Area of Science:

• Microbiology
• Bioinformatics
• Genomics

Background:

• Metaribosome profiling (metaRibo-Seq) measures microbial translation but suffers from inaccurate mapping due to short read lengths.
• This leads to unreliable taxonomic and functional assignments in complex microbial communities.

Purpose of the Study:

• To develop and validate MOPP (Multi-Omics Processing Pipeline), a novel workflow to denoise metaRibo-Seq data.
• To improve the accuracy of taxonomic and functional profiling of microbial communities.

Main Methods:

• MOPP is a modular, reference-based workflow that integrates metagenomic coverage breadth to filter potential genomes.
• It aligns metatranslatomic and metatranscriptomic reads to identified genomes.
• The pipeline generates integrated count tables across genomic, transcriptional, and translational layers.

Main Results:

• MOPP significantly improved detection accuracy compared to standard workflows in a synthetic gut community.
• Coverage breadth filtering at 92% reduced detected genomic units by 99.4% while retaining 87.8% of reads.
• The F1 score increased from 0.02 to 0.61, indicating substantially improved accuracy.

Conclusions:

• MOPP provides a robust and scalable framework for processing metaRibo-Seq data.
• It enables high-throughput, integrated analysis of microbial communities across multiple omics layers.
• The workflow effectively addresses nonspecific mapping issues, paving the way for more reliable microbial functional studies.