Dynamic Meta-Storms

Dynamic Meta-Storms computes species-level taxonomic and phylogenetic distances between shotgun metagenomes to quantify beta-diversity in microbial communities.

Key Features:

• Species-Level Analysis: Performs comparisons using species-level taxonomic and phylogenetic profiles to provide detailed insights into microbial community structure.
• Integration of Phylogeny and Taxonomy: Incorporates both taxonomy and phylogeny and dynamically assigns unclassified species to virtual nodes in the phylogenetic tree using higher-level taxonomic information.
• Efficiency and Scalability: Optimized for high-speed computation with low memory usage, capable of pairwise comparisons of up to 100,000 metagenomes synthesized from 3,688 bacterial species in approximately 6.4 hours on a single computing node.
• Flexible Input Options: Accepts species-level profiles as input, integrates the bacterial species-level phylogeny tree and taxonomy information from MetaPhlAn2 by default, and supports customized trees and taxonomies.
• Pairwise Distance Matrix Output: Generates a pairwise distance matrix that reflects both taxonomic and phylogenetic dissimilarities among metagenomes.

Scientific Applications:

• Microbial ecology studies: Enables quantification and comparison of microbiome beta-diversity across samples.
• Ecological dynamics analysis: Provides a more accurate depiction of microbial diversity and evolutionary relationships to explore community-level dynamics.
• Environmental impact assessment: Identifies effects of environmental factors on microbial community composition via distance-based comparisons.
• Microbial evolution investigations: Supports analyses of evolutionary relationships among species-level profiles within and across metagenomes.

Methodology:

Taxonomic and phylogenetic profiling of species-level profiles; dynamic placement of unclassified species into virtual phylogenetic nodes using higher-level taxonomy; and pairwise distance calculation producing a distance matrix reflecting taxonomic and phylogenetic dissimilarities.