MicroPro

MicroPro analyzes metagenomic sequencing data to integrate reads from known and unknown microbial organisms and to associate microbial and viral entities with disease status.

Key Features:

• Dual-Pipeline Architecture: MicroPro consists of two specialized pipelines—MicrobialPip for bacteria and archaea and ViralPip for known and unknown viral entities.
• Inclusion of Unknown Organisms: Incorporates reads from both known and unknown microbial organisms to expand the detectable microbial space.
• Enhanced Disease-Status Prediction: Inclusion of unknown-organism reads enhances predictive accuracy for disease status across multiple datasets.

Scientific Applications:

• Colorectal cancer: Applied to colorectal cancer metagenomic datasets to associate microbial and viral entities with disease status and to identify disease-associated microbial signals.
• Liver cirrhosis: Applied to liver cirrhosis metagenomic datasets and identified significant predictive roles for viral entities.
• Type 2 diabetes: Applied to type 2 diabetes metagenomic datasets where viral predictive roles were less pronounced.
• Prediction improvement across datasets: Considering reads from unknown organisms significantly improved prediction accuracy in three of four studied datasets.
• Novel organism discovery: Enables identification of novel microbial organisms associated with these diseases by incorporating unknown reads.

Methodology:

Integrates all reads from known and unknown microbial organisms using two pipelines (MicrobialPip and ViralPip) and associates viral entities with complex diseases.