Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function...

Area of Science:

• Microbiome research
• Ecological genomics
• Bioinformatics

Background:

• Microbial communities exhibit biome-specific species and gene enrichment patterns.
• These patterns reflect biome-species-function relationships governed by ecological and evolutionary principles.
• A comprehensive understanding of these patterns and their driving factors is lacking.

Purpose of the Study:

• To investigate microbial gene enrichment patterns across diverse biomes.
• To develop an "enrichment sphere" model to elucidate regulatory principles.
• To identify external and internal factors influencing these patterns.

Main Methods:

• Analysis of 1705 microbiome samples from Engineered, Gut, Freshwater, and Soil biomes.
• Construction and application of the "enrichment sphere" model.
• Case studies on copper-resistance genes in Soil and flagellum-related genes in Freshwater.

Main Results:

• Distinct enrichment patterns were observed across the four studied biomes.
• The "enrichment sphere" model successfully elucidated underlying regulatory principles.
• Copper contamination and horizontal gene transfer drive copper-resistance gene enrichment in Soil.
• High fluidity and vertical gene accumulation drive flagellum-related gene enrichment in Freshwater.

Conclusions:

• The "enrichment sphere" model provides a framework for understanding biome-species-function relationships.
• This model has practical applications in biome identification and protein structure prediction.
• The model serves as a foundational resource for microbiome research.