A Novel Hierarchical Network-Based Approach to Unveil the Complexity of Functional Microbial Genome

Biological networks serve a crucial role in elucidating intricate biological processes. While interspecies environmental interactions have been extensively studied, the exploration of gene interactions within species, particularly among individual microorganisms, is less developed. The proliferation of microbiome datasets necessitates a more nuanced analysis of microbial genome structures and functions. In this context, we introduce a novel construct, "Solid Motif Structures (SMS)", via a detailed biological network analysis of genomes within the same genus, effectively linking microbial genome structure with its function. Leveraging 162 high-quality genomes of Microcystis , a key freshwater cyanobacterium within microbial ecosystems, we established a comprehensive genome structure network. Employing advanced deep learning techniques, we uncovered 27 critical functional subnetworks and their associated SMS. Incorporating metagenomic data from seven geographically distinct lakes, we conducted a rigorous investigation into Microcystis ' functional stability under varying environmental conditions, unveiling unique functional interaction models for each lake. Our work compiles these insights into an extensive resource repository, providing novel perspectives on the functional dynamics within Microcystis . This research advances biological network analysis, offering an innovative framework for understanding interactions between microbial genome structures and functions within the same genus.